Thursday, October 8, 2020

I get tested

Working at a research institute has some occasional benefits. One is the ready availability of materials and expertise for all kinds of lab work and testing.

The overall infection rate in Japan has been very low, and with a very few exceptions, people are still not travelling from abroad at this time (the ones that do face a two-week quarantine).

COVID the PCR edition

OIST has developed clinical PCR testing capability, and in addition to offer it to help the Okinawan prefecture, OIST also uses it internally. If you have travelled outside Okinawa on OIST business you are required to take the PCR test. But you are also strongly encouraged to take the test if you travelled privately, or if you suspect you may have been exposed for some other reason. We've had two cases at OIST so far, but thanks in part to the prompt testing, no spread within the university.

The PCR test kit. You receive it at the guard hut at the entrance, take it to your car or bathroom, do the test, then drop it into a collection box. The whole thing takes five minutes.

The test is simple: no cotton swabs into your nose, but just a bit of spit into a sample tube. You get the kit, collect and seal the sample and record the case number yourself. You get the number by email from an — I believe — automated registration process, and the result is emailed back, so the test result is effectively semi-anonymous. The manager can clearly de-identify a test, but the people running the lab testing have no idea who the samples come rom. 

The sample tube. You spit into the tube through the blue funnel. Remove the funnel, put on the cap and you're done. Easy.

The test is free (of course), but you need to take it three times: the first working day after you return you take the test, then work from home — you're not allowed into OIST. If the test is negative the next morning you can come to work. You then take a second test on the third working day; and a third on the sixth. That's probably more cautious than is really warranted; two tests would already catch all but a very few positive cases.

Interlude: Osaka

We spent our summer vacation back in Osaka. I hadn't been back since last winter, and had a number of things to take care of. But it's also nice to spend some time in a big city again. I really like Okinawa but it can sometimes feel a little cramped.


Itami airport, Osaka. Really, really empty. I seriously wonder just how long it will take for leisure travel — and all the related business — to return to normal levels. Years, likely, and perhaps it will never completely bounce back.

The city definitely felt a bit subdued. It's a bit like during New Year or Golden Week when traffic is light and many offices are closed. Most shops and restaurants are open but customers are few. Definitely a tough time.


Uniqlo in Shinsaibashi.

Ogawa in Osaka, at dusk. Neat colours. You get to see a lot of views like this when you get in the habit of running.

Big Friendly Duck was back to provide a little light relief.


When I returned (two days early due to a typhoon) I of course had to take the test. All three tests came back negative. Pretty quick and simple.

COVID the antibody edition

OIST has also been running an antibody test project. PCR tests look for virus RNA in your blood; that tells you if you are currently infected or not. An antibody test looks for antibodies to the virus and tells you if you have been infected in the past. 

The antibody tests says nothing about whether you are currently infected, or whether you are immune. An immune response only means your immune system has encountered the virus. It doesn't mean that it is actually capable of fighting off an infection.

It's not immediately useful for the tested individual, but it can tell you how many people have been infected in a population at one time or another, and so it tells us a lot about how widely the virus has spread, how easily you get infected and so on. This was a research project, not a clinical test, and participation was completely voluntary.

This time the test was completely anonymous. You picked up a testing kit at random from a box full of kit bags. Each kit had a random ID number, and a QR code that lead to "your" page on the project website. There you got information about the project, instructions on how to take the sample and the final result. At no time could anybody figure out who you were.

The antibody sampling kit. An alcohol swab and a bandaid; a test tube for collecting blood; and an automatic lancet. You remove the safety plug (on the far right) then press the lancet against your finger. It makes a tiny cut that hopefully bleeds enough to give you a good sample. I had to struggle to get enough into the test tube.

The sample is a bit more intrusive than with the PCR test: you had to donate ~1ml blood. The kit included a small finger lancet so it was still easy and painless enough; my only problem — and I heard others complain about the same thing — was to get enough blood into the sample tube before it stopped bleeding. 

Again, the test was negative. Probably a good thing. We now know that even a mild infection can cause lasting and perhaps life-long damage to your heart and lungs especially. But an asymptomatic infection with a strong immune response Could have meant a much lower chance of catching it again later on. 

I haven't heard about the overall results yet, but with such an isolated group of people on a fairly remote part of the world I would be surprised if there are more than a handful of positive results at the most.

Saturday, August 29, 2020

Long, long summer

A long, long summer and a long, long year. After a very well-contained first wave of infections, COVID started spreading rapidly in Japan again, and especially here on Okinawa. 

A small part of the blame might be put on the American bases; they imported the out of control situation from the USA, and some employees apparently decided that quarantine recommendations didn't apply to them, not when they could join large outdoor parties on their national day. But that outbreak was contained pretty well.

No, the main culprit — of this as of so many other Japanese problems — is the LDP-led government. The economy is tanking, here as everywhere, and after several earlier public relations fiascos (such as spending a fortune on badly designed masks people didn't want) and dogged corruption charges they decided Something Must Be Done. Something with public appeal; something that puts money in the pocket of their corporate donors; something that distracts people from misuse of public funds.

And in a pandemic, when the key thing is to avoid crowds, avoid unnecessary travel and staying at home, what could possibly be a better stimulus idea than a "Go To Travel" summer vacation travel campaign? Yes, they are simultaneously telling people to stay at home and giving a 30% discount on resort hotel bookings.

So of course people travel. And they bring the virus along with them. Especially to Okinawa, the premier summer holiday destination. But also the poorest part of the country, with the fewest ICU beds and a shortage of qualified medical personnel. We are now the hardest hit area in the country by population.

Fortunately, the government has been as inept at creating the campaign as they are with anything else. The whole thing has been a confused mess with contradictory information and no guidance for the businesses. As Tokyo infection rates soared, they added a last-minute restriction excluding Tokyo residents, with no plan of who would pay the inevitable cancellations, or any idea if such an exclusion would even be legal.

And as the infection numbers continued swelling, people sensibly started to rethink their vacation plans. Stores on Okinawa are almost as empty again as they were during the first wave of infections, and the number of rental cars on the road — a good indication of tourist numbers — have declined a lot again after the initial burst in June and early July.

Now the infection numbers are finally dropping slightly again, both on Okinawa and on the mainland. Turns out that people in general have the sense to take precautions and avoid undue risk, whether the government wants them to or not. 


Speaking of which, the government is in turmoil again, as Abe has decided to quit. This is only about a year before he has to leave the post and call a new election, and less than a year before his last pet project, the Olympics, may (or may not) finally be held in Tokyo. 

I wish I could say the reason is political; that he was ousted in some party power struggle, or that his several corruption scandals finally caught up with him. Indeed, some Japanese seem to believe he is quitting before he can get fired. But the reason seems to be both more prosaic and more sad. He has been visibly ill lately, and the announcement came just days after a follow-up medical appointment. 

Abe has a chronic intestinal disorder; that's what ended his first round as prime minister years ago, and a lot of people speculate that this has taken a turn for the worse. This is very possible. But he is not actually leaving just yet; instead he will stay put until his party can elect a successor. He is well enough to continue to work for the time being in other words, but too ill to stay on until the end of his term in a year.

This could of course — as some speculate — simply be a pretext to leave; he has become the longest sitting prime minister, he has no real hope of accomplishing anything else of substance (the Olympics probably don't stand a chance), and leaving may take the wind out of the ongoing corruption cases dogging him. But this could also be the final political acts of a man who received some very bad medical news and is putting his affairs in order while still able to do so.

If the reason is medical there's no reason to be happy. I may dislike his politics, the corruption scandals and his lack of leadership, but I wouldn't wish a life-threatening disease on him for that either. I hope he pulls through, gets better again, and can enjoy a long healthy life out of the stress of the public eye.

Thursday, May 14, 2020

The Pinebook Pro

I'm bored.

I'm working at home because of the Corona virus; we've spent our weekends and the entire Golden Week vacation at home because of Corona; my emails, Line and other communication all involve Corona; NHK news and morning shows is nothing but Corona stories; newspapers, Reddit, podcasts, even Steam forums are filled with posts about - well, you know what. My life has turned into the All Corona All The Time Multimedia Extravaganza.

This is an ongoing disaster, it's disrupting all our lives, and we absolutely must protect those who would otherwise die from the disease. But I'm also fed up with the constant media bombardment about something I can do nothing about.

Okinawa has had no new cases for two weeks now, and we're finally preparing to get back to work again from Monday next week. It's probably only temporary of course; the infection rate is bound to bounce back, especially as we are moving into the main tourist season. Oh, and just to spice things up a little bit, the first typhoon of the season is expected to hit us on Monday morning. Not a strong one, but still - we got a million problems, why not add a typhoon?

I'm bored. Let's talk about something else.

Such as things I get in the mail.

A package! for me — I wonder what it could be? Oooh, it's a computer! "Pinebook Pro". It certainly looks very slick.

Around the time we moved to Okinawa three years ago I got myself a HP Spectre 360 for a lightweight, high-performance laptop. It was light, fast and beautiful. It was expensive — and as fragile as a Faberge egg.

About a year ago we spilled water on the dining table — not on the laptop, just the table. Some of the water trickled its way under the computer, where the bottom fan sucked it inside and promptly killed the machine. Repairing it would have cost as much as buying a new computer.

That expensive mistake soured me on the whole idea of a laptop for a long while. I've relied on my desktop and my smartphone. But I missed having a portable computer, and when I saw this thing I had to try it out.

The Pinebook Pro

The Pinebook Pro in all it's glory. It looks and feels just as good in real life as it seems in this image. Thin and light, fanless, good screen, good keyboard, metal shell.

In short, the Pinebook Pro is a slim fanless — completely quiet! — 13" laptop with a metal chassis and a 1080p screen; 4GB ram, 64GB eMMC storage, and slots for an SSD and SD-cards; USB A and C ports, a web camera, a headphone jack all the rest you expect from a decent modern laptop. The USB-C port can charge the machine and run an external display.

It uses an ARM processor, it's built to run Linux — and it costs all of $200.

Pine64 produces and sells single-board ARM computers, embedded systems and things like that for end users and hobbyists. But they also do fun projects such as the Pinebook Pro, the Pinephone and Pinetime (a DIY programmable smartwatch — I really need one of these!)

The outside case is metal, and feels like a much more premium device. The screen is decently clear and bright, with no corner fall-off or glare. The keyboard is clackety but feels fine and is absolutely good enough for extended use. It's not at the level of that HP laptop or a Mac, but it feels much higher quality than the $200 price tag would imply.

The CPU is a Rockchip RK3399 ARM SOC. ARM CPUs don't have to be slow — look at the Fujitsu A64FX — but this is a mobile CPU meant to sit in a smartphone. It's a "BIG-little" design, with two faster power-hungry cores, and four slow but very efficient cores. Background tasks can run on the small, slow cores, using very little power, while the big cores will run your foreground work fast.

It comes with 64GB eMMC (flash) storage built in. 64GB isn't a lot and MMC isn't very fast but you're not going to do anything really data-intensive with this laptop. A full Linux desktop installation takes about 4-6GB so almost all of the space is available for your data.

The SD-Card slot lets you boot from an SD card as well as add external storage. You can add a real SSD though an optional M.2 adapter, though it needs to be thin and low-power, and it will drain the battery noticeably faster.

The low power draw and the USB-C port has an unexpected benefit: I can charge it with my USB-C phone charger. When I write this or surf the web the phone charger can just about manage to trickle-charge the device. If I play games or compile software it can't quite keep up. Still, it means I can bring just a single, small charger for both laptop and phone.

Open Source

This is built for Linux and BSD - neither Windows nor OSX will run. As of this spring, the default distribution is Manjaro with the KDE desktop. Manjaro has been a very positive experience for me (and worth a post of its own, I think). KDE is a very polished, full-featured desktop. I haven't used it in years and I'm not comfortable with it for various reasons, but it's easy to replace it with a lighter, less intrusive desktop such as XFCE or even i3 if you like.

There are a number of other distributions available for the Pinebook already. You can easily test any of them by copying one of them to an SD card and boot it on the laptop. I've tried 3-4 different ones already; so far Manjaro — with XFCE or KDE — has been the most polished experience.

The openness extends to the hardware. The Wiki page has instructions on disassemble it and extensive documentation on the internals, up to and including the exact measurements of the case parts in case you want to mod or replace anything.

In Use

With 4GB memory, a mobile ARM processor and MMC storage, this is not a fast laptop. There are things you can't do or won't do with it. But it can do a lot — and at $200 I can literally get ten of these for that HP laptop I managed to ruin. I could break one of these every six months and still come out ahead.

The Pinebook Pro on the beach. I'd hate to take an expensive machine to a place like this, but with the Pinebook I don't worry at all.

I wanted to do a performance test, so as a quick, dumb comparison I picked building and running POV-Ray, a fun, scriptable raytracing program that's open-source.

I downloaded the latest release (, then ran two different tests: compile the POV-Ray source, and run its built-in benchmark test. All were built with GCC 9.3, using the default configuration for POV-Ray ("-O3 -ffast-math -march=native"). I didn't touch the power settings on any system, or tune things in any way.

The compilation is a decent real-world test of a common computing task, and is mostly memory and I/O-bound. The POV-Ray benchmark itself, where it raytraces an image off-screen, is fairly simple numerical data processing. I did briefly consider running some BLAS benchmarks as well, but I don't really see the point. If you need BLAS you need a bigger computer.

I ran these two tests on the Pinebook Pro using the two big cores. For comparison I did the same with my desktop sporting a six year old i7-5820K CPU; and with the four year old Lenovo X260 laptop I use at work.

The Pinebook and the 5820K both have 6 cores, but only two of the Pinebook cores are fast. The X260 has two cores in total (multithreading doesn't count), so I ran all the benchmarks using only two cores.

Compilation (left) and benchmark (right) of the POV-Ray ray-tracer on my six year old i75820K CPU, the four year old Lenovo X260 laptop and the Pinebook Pro. All run using two processor cores.

The Pinebook is about 4× slower than the others for compilation. It's about 2.6× slower than the laptop and 3× slower than the desktop for the POV-Ray benchmark.

This is really not too shabby at all. It's quite good, in fact. The Pinebook is 4 times slower compiling the POW-Ray source, but that's mostly due to the relatively slow MMC storage. An SSD would probably speed this up quite a bit.

For the POV-Ray benchmark — lots of simple math and branches — it's 2.6× slower than the X260 laptop and 3× slower than the desktop. For a slim, fan-less low-power machine like this I'm quite pleased, especially at the $200 price. Just the i7-5820K CPU itself still sells for more than the entire Pinebook Pro today.

As an aside, I'm also surprised how good the X260 laptop is. I expected it to fare worse than it did against the desktop. Now, the desktop has another four cores that will speed up the second test almost three times, but per-core there isn't much difference between them. Welcome to the end of Dennard Scaling. (1)

What You Can't Do

Steam and many games won't work. Closed source software in general is usually built for X86 processors and won't run on ARM computers. The current virus-laden elephant in this particular room is Zoom. I, and many with myself, use Zoom on a daily basis while working from home, but there is no Zoom client available for Linux on ARM.

Some open source games and applications will also be difficult or impossible to run — they may need more memory, a faster CPU or a more powerful GPU than this laptop can deliver. Gimp will run fine but you'll struggle to edit larger images. I wouldn't try to run Blender, Pytorch or Eclipse on it.

Today (May 2020) there are still a few rough edges. The power management is a little flaky, so it doesn't reliably go to sleep, and it uses a semi-low power state when sleeping that will drain your battery in a couple of days. But the laptop boots fast enough that I'm OK with shutting it down when I'm not using it.

The keyboard firmware needs some tweaking — the meta ("Windows") key doesn't work with all key combinations — and the trackpad firmware really needs another round of fine tuning to make it a little more responsive.There is a user-created keyboard firmware available but I'm not bothered enough by the issues that I want to take the risk of updating it.

What can you do, then?

Really, almost anything.

Manjaro is built on top of Arch (again, worth a post of its own) which makes a huge amount of open source software available for the Pinebook Pro. If you are able to build it on the laptop at all, you can probably get it through the repositories. Just about any normal desktop or workstation application — compilers, editors, browsers, office apps, computing tools and so on — are at your fingertips. It would be easy to create this entire post, from editing images and creating the graph, to writing and posting it online (and I partly did).

The Pinebook Pro in its natural setting: a hip seaside cafe with shabby-chic furniture and a good selection of third-wave coffee beans. 

Steam is not available, but a lot of open source games are, and even some closed-source games based on Java or Mono — Minecraft and Stardew Valley included — can apparently be made to run with a bit of judicious tweaking.

For computing, my particular niche in this world, Python and most of its enormous pile of packages work just fine. If you need something Matlab-like, you can get Octave (a Matlab clone), or move to Python or Julia for a more modern, up to date experience. I don't recommend using a tiny ARM laptop for numerical computing, but the fact is that you can.

And really, this may be slow by today's standards, but this would have been a decently fast CPU just ten to twelve years ago, and people did manage to perform serious numerical computing long before that.

A lot of modern productivity tools run in the browser today. Microsoft Teams, Gmail and so on will all work fine on the machine (Teams will take a fair bit of the limited memory, mind you). Youtube videos play OK. I'm sure you can use Facebook, Twitter, Instagram Slack and the rest.

Still missing for me is a way to run Zoom. It's our default video conferencing tool at work, I use it a lot to talk with our users, and there is no Zoom client available for download. It's possible I could get it to work though the Chromium browser but I haven't tried that yet. Of course, I can use Zoom on my phone so the problem is not insurmountable.

I would love a Pinebook version of the Steam remote client. That would let me play any game I own on it. It wouldn't be impossible - Valve has released a version for the Raspberry Pi after all.

Could I use the Pinebook Pro as my only computer? Yes, sort of, if I could also use my phone. But it works great as a secondary machine. I'd be happy to bring it for travel — once we can travel again — without fear of losing or breaking it.

And it exudes a sense of fun that I haven't felt with computers in a long time. Never mind being useful, I just enjoy using this.

1) I ran this test on a node on our HPC cluster as well. It may surprise you to know that a state-of-the art HPC node is no faster than my old desktop per-core. In fact, the cluster nodes have a lower clock frequency so they're slightly slower. 

But clusters aren't built to have very fast cores; they're built to have lots of them. I can use up to six cores on my desktop to speed things up, but on our cluster you can use up to 128 cores in a single node, and tens of thousands if you can scale across nodes. That's where the speed comes from.

Sunday, April 26, 2020

Corona, The Work From Home Multimedia Experience

I've now worked from home for three weeks. During this period Japan and Okinawa predictably went from "I'm sure somebody is taking care of it" to "Oh wait, this is actually really bad!".

We're on semi-voluntary lockdown and telework until the end of May at this point. It's not that Okinawa has so very many cases yet, but it's increasing far too rapidly for the rather limited hospital resources to cope if it continues. And Okinawa is home to some of the oldest people in the world, who would be very vulnerable if they got infected.

An empty shopping mall in Osaka, from last time I visited. We were going back to Osaka again over Golden Week. That idea has been well and truly scuppered.

I save almost 3 hours every day from my commute. We still get up at the same time as before, so now I can go on a long morning run everyday. It feels great!

On the other hand, I no longer have car-time for my podcasts, so I'm running with earphones instead. It would be fine if my earphones — got for free with my phone — didn't kind of suck. I've got a pair of bone-conduction headphones on the way.

Sunset beach in Chatan, last year. This year the whole place is closed.

Surprise: I'm more productive at home.
It's quiet; I have fewer meetings, interruptions and random requests; a standing desk and a nice, big second screen helps a lot.

But also, we've long had access to Microsofts online collaboration tools, including Teams. This situation has forced us to actually start using them, and relying on them for collaboration and information sharing. We're now getting up to speed and they really help improve our workflow a lot

Teams is really surprisingly good. And — major surprise! — they even have an app for Linux. Sure, it's mostly the website wrapped into an Electron app, but everything works fine, including phone and video calls. Microsoft has a  tendency to have two or three confusingly similar tools for everything; a document describing when to use what would be helpful.

Cafe 21 in Shinsaibashi, Osaka. We're teleworking but we're not allowed to work from just anywhere. It's work from home or not at all, basically; channeling your inner hipster from a neighbourhood cafe is a no-go.

Anyway, we're all getting fairly used to meet over Zoom, talk about issues in Teams channels and chats, track tasks in Planner and so on. There's even a modestly active social channel for the IT department; we'll see how that one evolves.

I'm pretty sure we will continue to use these tools after this is all over. It's a lot more efficient to raise minor issues over chat than through email, and it's very convenient to meet without having to traipse across half the campus.

I drink coffee without my co-workers. But I do drink much better coffee, now that I have access to our own kitchen with a proper grinder, beans and so on. 

I'm productive, but I'm also bored. I do miss meeting other people at work, walking around campus, running in the beautiful hilly area over lunch and having coffee breaks with a view.

Two kinds of home-made gyoza, with fried goya and shiso leaves. 

On the other hand, I have time to cook! I'm made most of our dinners and half of the lunches over the past three weeks and I've enjoyed every second of it. As we stay at home and cook by ourselves we're eating way healthier than we used to. I've lost a bit of weight and I feel a lot better overall.

As a side effect we're spending a lot less money. The car sits idle most days, and we're not eating out, going to cafes or anything like that. Good for us; a disaster for the economy. So we do try to spend a bit of that money, on takeout, coffee beans and so on from shops we like.

It's never not time to bake cinnamon rolls! And now I have enough time in the evenings to do so whenever I like.

Restrictions are voluntary,
but people and businesses mostly do understand the situation and at least sort-of follow the recommendations. Except Pachinko parlors. The Osaka mayor tried to shame them into closing by naming them, but a few still stay open, with a flood of gamblers looking for a place to play. If you ever needed proof gambling is an addiction here you go.

Oh, and the Japanese Olympic committee president, Yoshiro Mori, has stated that there will not be a second delay of the Olympic games due to the pandemic, because "The prime minister has determined that one year is sufficient."  I'm happy somebody is keeping their crystal ball well polished...

The fishing pier in Suma, in western Kobe. It was damaged in a typhoon two years ago, and never re-opened. It would be a shame if they let it rot; it's a fun place to visit even if you're not into fishing. For now it's a nice illustration of loneliness.

Saturday, April 4, 2020

More Corona

It's been a month and more, and here on Okinawa we're still doing well. Japan was one of the earliest countries to get infected, but until recently they've managed to curtail the spread. We've mostly had isolated clusters of outbreaks around the country, but no real uncontrolled spreading. The reason has been a lot of voluntary closures of events, people taking "social distancing" measures, and testing of people around confirmed patients.

People are still pretty chill about this on Okinawa. Nobody is panic-buying toilet-paper for instance, so there's plenty to go around for everybody. More and more residents are using masks now - it used to be only tourists - but most seem to wear it just to make other people feel safer.

Here on Okinawa we had three cases right at the start, all connected to a visiting cruise ship. We didn't have a single case for over a month after that. Two weeks ago we started getting new cases; it gradually rose to 12, with all but two infected abroad or on the mainland. There has been little spread on the island, but just today another six cases appeared, three with unknown source. So now we have it spreading on the main island as well.

The local economy is fairly dependent on tourism and the loss of travellers has hit that sector very hard. Many hotels have special deals for Okinawa residents, so a couple of weeks ago we spent a weekend in Yomitan near Cape Maeda. We supported local business and got a relaxing weekend getaway.

Japan in general has been lucky so far — Japan at large has been doing something right, or our hospitals would be overrun with patients by now. But now the infection rate is increasing rapidly in Tokyo and Osaka. The political response has been anemic; there's a sense that the government has been slow to react, and more interested in protecting its own image and the economy than trying to keep on top of the disease.

The weather was sunny and warm. We took a walk along the beach, and the sea was warm enough to swim in already. Here a washed-up coconut on the beach that's become shelter for a group of hermit crabs.

They announced yesterday that every household will be given two cloth face masks. This sounds ridiculous on its face (sorry); cloth masks don't really help much at all, and the whole thing sounds like an pointless empty gesture. However, more than a few people think this is the precursor to declaring a state of emergency with self-quarantines, and the cloth masks would be a key element of that.

A Common Rose Swallowtail butterfly.

The Japanese central government doesn't have much constitutional power (they have bad historical experience with powerful governments) so, for instance, they simply can't force people to stay at home or businesses to close. Even a state of emergency enacts only limited powers, and mostly to the prefectures, not to the central government.

But they could require people to wear a mask when entering public areas. As every household has two of them, nobody would have an excuse not to wear one. And as a household only has two, that would directly limit the number of people that could be out and about at any one time. Even though you could substitute another mask, it would establish a general pattern of not going out unless you have a valid, specific reason to do so. Don't underestimate the psychological effect.

If they combine it with semi-voluntary closures of non-essential businesses, this will effectively create a similar lock-down state as we see in other countries without having the legal resources to enforce it directly.

Fishing harbour in Maeda. This sure beats winter in Osaka.

Okinawa still has only a few cases, so I would not be surprised if the local government greatly restricts travel to the islands if or when the state of emergency is declared. As all cases so far have been around Naha and one of the US bases, I would also not be surprised if travel between the islands is suspended or curtailed as well.

My workplace OIST is still operating, but with heavy restrictions. People are increasingly working from home, or are preparing to do so. If you have any cold symptoms at all you need to stay home for 14 days. Most in-person meetings and teaching has been suspended, no visitors are allowed on campus, and we are discouraged from gathering in groups. We are not allowed to travel for any but the most dire reason, and if you do you must self-quarantine for two weeks.

And as of this week, if we meet with anybody travelling from the mainland we need to self-quarantine at home for two weeks. This impacts me directly, as Ritsuko has been in Osaka for the past week or so (for good reasons) and will return tomorrow. I will need to work from home for the next two weeks.

Going outside and getting exercise is usually allowed, and always a good idea. Do it alone and stay outside, and you'll be safe. This is from my usual lunchtime run around OIST.

We have been preparing for this of course; I can do all my current work online, and some colleagues already work from home part time. Working from home for a few weeks won't impact my job directly. Hopefully OIST will still be open in two weeks time.

"There's a swallows nest; please watch your head". Life goes on.

Thursday, February 27, 2020


It's Ritsuko's birthday, and this year we were going to celebrate with a concert and birthday dinner in Osaka this weekend.

Except the recent corona virus outbreak decided otherwise; the concert — like most public events in Japan — has been postponed or cancelled to avoid the possibility of spreading the infection. Tokyo Marathon already cancelled the general event for most participants (only the 200-something professionals will run) and there's talk about the possibility that the Tokyo Olympics might have to be cancelled or be held without spectators as well.

Nakanoshima at night. I haven't had a chance to upload (or take) pictures so far this time, so all pictures are from around New Year.

And today the government announced the closure of all primary and secondary schools at least until the new school year starts in April. They lose "only" two weeks, but that includes final exams for some schools and graduation ceremonies; and working parents are caught in a bind having to find day care in a hurry. Preschools and kindergartens are not yet closed but it seems more than likely if the number of cases continue to rise.

With only 171 domestic cases so far, and concentrated in only a few prefectures, more than a few people feel the measures seem a little premature, arbitrary and poorly planned. The conspiracy-minded might notice how a number of simmering government scandals have been pushed off the public consciousness; more likely it's about trying to get ahead of the developing situation. It's better to be criticized for overreacting if it comes to nothing, than for not having done enough if it does blow up.

Utsubo park, almost deserted. Except that this picture was taken around New Year — before the corona virus became more than a curiosity in Japan — fairly early in the morning, and there were plenty of people around if you just chose a different angle for the shot.

Concert or not, we arrived in Osaka earlier today and we intend to enjoy our extended big-city weekend. It's not as if we're in any greater risk of getting sick here than on Okinawa anyhow — Okinawa has three cases so far, while Osaka has one (all connected to tourism). With about 1.4 million people on Okinawa and almost 9 million in Osaka the risk is very low either way.

We do take common-sense measures such as washing our hands frequently (a great way to avoid all kinds of diseases), and avoiding hospitals (another great way to avoid infections).

We don't wear masks. Those paper masks can help prevent spreading it to others if you're already infected and coughing or sneezing, but they do absolutely nothing to prevent you from getting it. Even if they didn't leave big gaps, the paper is much too porous to stop bacteria, never mind a virus like this. It's like using a soccer net to prevent mosquito bites. What they can do is stop big droplets of liquid from spreading when you cough.

To put it this way: I work at a research university, where microbiology and genetics is the largest field of research. We have hundreds of people there who work professionally with bacteria or viruses on a day-to-day basis. Many of them have kids in the day-care center. And not a single one of them wear a paper mask at work. They know just how pointless it is.

What are those masks good for then? My exhaustive research (20 minutes searching the web) says they're mostly used for hygienic reasons, not to stop disease. If you're a dentist or a surgeon, you don't want to drop saliva, nasal mucus, skin flakes or stray hair onto your patient. Same thing when you work with food preparation or any other job where good hygiene is important.

JR station and Daimaru department store in Umeda.

We still have plenty to do here in Osaka. We have dinner reservations on Saturday, we already visited of our favorite places in Kobe on our way here, and I have some errands of my own to run. Ritsuko didn't get the birthday concert she expected, but my brother and his family sent her an impromptu song number instead :-) She loved it.

Saturday, February 15, 2020

Valentine's Day

The tradition for Valentine's day in Japan is that women gift men; then the men reciprocate a month later on "White day". That's twice the business opportunity for retailers I guess.

This year Ritsuko decided we're eating more than enough chocolate already (she's right). I don't really drink any longer so beer or whisky is out. Instead she got me this:

Three speciality coffees from a local roaster in Naha. Emerald Mountain from Colombia; Ethiopian Alaka — I've been into Ethiopian coffees lately; and Costa Rica Honey.

Emerald Mountain is a high grade coffee from Colombia and apparently limited to the Japanese market under an exclusivity agreement. Ethiopian coffees tend to be light and fruity or chocolatery with a lot of floral tones; we'll see what this one is like. Costa Rica "Honey" apparently refers to a processing method where the beans are dried with the fruit only partially removed. This will be interesting to try!

All three come from Churamame coffee in Naha. It's a good, very reasonably priced coffee roaster and shop; we often buy our coffee there.

Ah, coffee! This is Emerald Mountain (not that you could tell). Light bitterness, with balanced flavour and spicy tones. Very agreeable. I'd say it's a great morning coffee if it didn't cost so much...