Get me the hell off this rock.

Seriously man what a month. There have been more ups and downs for me than Nemesis in Alton towers. Between beamtime experiments, most of which didn’t go too well, the Cheiron School and the passing of my Grandma, I’ve been totally physically and emotionally exhausted. I’ve also not had a free weekend in a month so the past one was a very welcome break.

In the past half a year that I’ve been here the 4000 miles between me and home have never felt as far as last week. At times I just wanted to curl up and sleep but I had to keep going.

The external pressures of work were definitely reaching into my psyche and when colleagues started to say things like “Is that enough for you?”  and, “You know I’ve noticed you don’t take much food.”, I realized it was time for a break to get my head screwed back on. Old habits die hard I guess.

Anyway before shooting on to the weekend I’ll backtrack to Thursday. My experiments with Josie last week did not go so well. I couldn’t take any readings as the DIT just wouldn’t work and being a team of two people we just ended up exhausted without achieving much.

So on Thursday Hikima-san, my colleague on this project, and myself headed to the local Izakaya Shunsai to commiserate our shortcomings. Exchanging an “otsukare sama” and a “kanpai” over a Kirin free and some food was a nice way to wind down and get to know Hikima-san a bit. We had a lovely chat over some food, the mochi bacon was definitely worth a mention. I learned a bit more about Hikima-san’s background and interests, in particular how he found moving to Kansai from Kanto and his fondness of home brewed beer something that is not so common in Japan.

Right so for the weekend I was determined to escape from the mountain. Arnaud was headed for Osaka to take a flight to Spain to attend an international conference so I asked if I could tag along. We were first going to a Mexican restaurant in Shinsaibashi for lunch with a friend of Arnaud’s before mooching about in Namba for a while.

At Shinsaibashi we met Arnaud’s friend, Mai, before ascending one of the nearby buildings for food. Japan never ceases to amaze me for its careful use of space. The building was pretty thin but each floor had it’s own tiny but fully functional restaurant.. They really know how to pack stuff in here.

The place was suitably Mexican with plenty of bright reds, oranges and yellows, tinkling acoustic guitars and interestingly writing all over the walls. Apparently some guy called Gen had been at our table two years previously. The place also seemed to be popular with the non-native contingent of Osaka. I picked Up American, Australian, British and Irish accents during our time there.

The food was nice, tortillas and beans make a nice change from rice, and also something with a bit of spice was very welcome. I was very glad Arnaud had invited me along, I don’t think I would of ever come across this place otherwise and I do love Mexican food.

So well fed and the conversations were rolling. Well sort of. I made an effort to speak as much Japanese as possible but my vocabulary is still frustratingly lacking. I can understand a lot but when it comes to expressing myself I always come up short. Admittedly Mai’s English was excellent but that's not the point really.

I’d voiced this to Arnaud before but what he said is right, I just need to practice more. I guess I make a lot of excuses, I’m too busy, I work with all Koreans, but they are just that. If I really wanted to I could speak better, I just need to practice more and ask more questions. I look stupider sitting there like a lemon than asking how to say something.

After killing about 3 hours in the restaurant, Arnaud was hesitant to leave due to his rather heavy luggage, we spent the rest of the time wandering through Namba and laughing at quirky shop names. I also had my first introduction to “プリクラ” (puri kura) short for purinto kurabu.

This is a phenomenon that whilst originating in the 90’s has managed to persevere in Japan, particularily amongst tweenaged girls. The premise is simple, insert your money and get your pictures taken. However the camera tweaks your looks subtly; emphasizing eyes, skin tone, mouth e.t.c. You can then add objects backgrounds and messages before finally printing the images as stickers. It made a nice souvenir at any rate.

At 6 o’clock we departed, bon chance pour la presentation Arnaud, and I headed to J-hoppers to spend the night. I’m just going to give this place a shameless plug now. It’s a hostel very close to Umeda station that I frequently visit. So much so that the staf recognize me by name and sight.

It really is a nice place. The staff are good fun and very helpful, the rooms and facilities are always clean, the location is great and best of all, it’s cheap. Right so enough advertising I settled myself in with some dinner and started watching the TV. It wasn’t long before I was joined by a couple of Japanese guests who wanted to change the channel. They put on a show called “Ippon Grand Prix.” I really didn’t understand too much but I think it was sort of like ‘whose line is it anyway’. They found it hilarious at any rate.

I moved upstairs eventually, tiring of the fact I couldn’t get any of the jokes and started chatting with a guy from Vancouver called Rob. Another reason I love staying in Hostels is you meet such interesting people. Rob is a freelance animator and had come to Japan, in his own words, because hey he’d never been to Japan, as good a reason as any I guess.

He was actually particularly interested in the art and had been picking out art books from second hand stores. He had a sketchbook to document his travels and kindly let me have a look. I’m always envious of people who can draw, it’s a skill I just don’t have. I guess words are just my means of expression. I had a good natter anyway before finally going to bed for a Good nights sleep.

At least that was the plan. Alas not to be. Unfortunately the guy sharing my room was a bit of a pleb. He strolled in at 4am bladdered, tried to hold a conversation for about 20 minutes before passing out and snoring the hostel down. I kid you not Nori, the manager, told me she could here him on the 2nd floor when she was cleaning, impressive since we were on the 4^th.

Still ever the philosopher, it was a disguised blessing as it gave me the opportunity to have more time exploring. I didn’t have much of a plan but thankfully due to the rain on Saturday a festival in Kyoto I had wanted to see was postponed until Sunday.

Since I was arriving so early, the festival began at 12, I decided to walk to th imperial palace from the station. Whilst it didn’t look so far on the map, never trust Japanese maps, it was actually an hour and a half walk. Still it gave me a fair opportunity to check out downtown Kyoto. It has such a nice vibe, totally different to the world of crazy that is Osaka and it was nice to experience a bit more.

On my way up I dropped by the Higashi Honganji temple. Honganji means primal, original or true vow depending on how you want to translate it, and it is the largest sect of Jodo Shinshu Buddhism in Japan. The complex itself is massive and the front gate, called the Mie-do, is in contention for being one of the largest wooden buildings in the world, it was quite impressive.

The main event began at the gates of the Imperial palace. The Jidai matsuri (festival of the ages) is a huge parade, which commemorates the end of Kyoto’s status as the capital of Japan in the 1800s. It consists of a parade of roughly 2000 people dressed in traditional costumes representing different periods of the cities history. It’s an awe-inspiring sight, especially given that many of the costumes are particularly intricate.

 I arrived to see huge crowds of people lining the streets leading from the palace to the Heian Jingu where the parade concludes. I was supposed to be meeting an acquaintance however she was yet to arrive in Kyoto so I decided to head towards the gates. The parade began dead on 12 o’clock with a group of men dressed as soldiers from the mid Meji period playing various instruments. The parade then takes us back in time from the 1800s back to the 700s when Kyoto was established as the capital.

It was an amazing a different way to get a view of Japanese history.  A bit more engaging than a museum or gallery for sure however as the announcements were all in Japanese I feel I didn't get as much out of it as I could of. Still I did finally get to see Geisha and Maiko, something I still hadn’t achieved since my parents visit.

I didn’t manage to meet my friend as planned, sadly the crowds were a bit intense, but instead met someone new. I noticed a young lady struggling to see over the crowds and let her go in front of me. Whilst I’m not tall back home I do have a good few inches on the average Japanese person and it’s great for situations like this.

We got chatting and I ended up spending the rest of the day with her. She was out in Kyoto for a year studying Japanese language and had been here about six weeks. It was nice to someone who was fresh in the country as I keep finding myself sounding a bit jaded and hearing someone’s fresh enthusiasm really helps bring the amazement back.

I love meeting new people, everyone’s got a story, and I also love a good gab so I was very happy she chose to stick around with me for the whole event. To my delight she was from England and from the North, a double whammy of nostalgia. It was nice to chat with someone from the UK it’d been quite a while.

The hours passed very fluidly, I was lucky to find someone as gabby as myself and with such different motivations and reasons for being in Japan from the norm. It was a fantastic day and as always nice to chat freely with someone my own age. It’s also inspired me once more to study the language a bit harder. I’ll get there in the end, “できるやんか“。しゃしんをみて、たのしんでください。

Mata kondo ne.

Today

Today I lost a spanner,
I also lost my Gran,
So far from home and comfort,
I'll just do what I can.

'Keep calm and carry on.'
Thats the British moto.
"Shouganai" As the Japanese say,
But hell I just don't want to.

Scream and rage and vent,
Thats what I wish I could do,
Or at least talk with the rest of the fam,
I know you're feeling it to.

But that won't honor her memory,
That won't do her Justice.
Dear sweet Thelma you were a wonder,
And by the Jones' will be missed.

The strength you harboured,
Unbelievable,
My drive and commitment,
I got it from you.

Such compassion and heart,
You had that as well.
Upon sad times,
You never did dwell.

Even three years later,
You never faltered,
Even though your life,
Was so drastically altered.

The flame of your courage,
Burns in us all.
Your light will surely guide us,
All over the world.

She put up with us for long enough,
I'm sure she'd agree.
Always the first to quip,
At our quirky family.

I bet she took one look at death,
And with a hint of glee,
Told him to get on with it,
I've better places to be.

So I call to all my relatives,
Listen to me well,
Be brave just like Thelma,
One Hell of a gal.

Why am I doing this?

At last the Cheiron School is over. Don't get me wrong it was great fun, met loads of great new people and learned a hell of a lot about X-ray science, but, it was also a massive brain drain, not least because I’ve also been working on the beamline during the nights. Hooray for 4 hours sleep, I’ll be totally out of wack by this Sunday I feel.

But enough of my moaning, I thought I’d spend this post talking a bit more about some of the interesting applications of synchrotron radiation that I’ve learned about over the course of the past week. It really has reminded me what I’m pouring my hours and energy in to.

To bring those who don’t know upto speed, Synchrotrons are giant circular facilities that are constructed to churn out light of high brilliance in the high end o the optical spectrum. What I mean by tha is the light has a ver small wavelength. In general they are in the x-ray region, between 0.8 and 10 nm although they do go higher.

They are produced by the periodic interference of a relativistic electron beam as it passes through large electromagnets, which maintain their curved path around the ring. These magnets can either be large individuals or, more commonly these days, arrays of magnets called undualtors and, yes this really is their name, wigglers.

Whilst synchrotrons used to be firmly in the grasp of high energy physics in recent years their doors have begun to open to all aspects of scientific research, from physical chemistry, materials science, geology and of course very close to my heart, biological and biomedical sciences.

I won’t bore you, or myself to be frank, by running through a list of all the crazy stuff that goes on here but I would like to outline some of the surprising things I’ve heard about. Hopefully after reading you’ll realize the work here is not all just abstract work by grand theorists, some of the applications are very real and close to home.

This is a good thing as these facilities are flipping expensive and horrendously inefficient. In fact the average synchrotron experiment utilizes maybe 1% of the total power output and often even less. This is partly down to the difficulties in alignment since if you want to see small you’ve gotta go big. But that's a story for another time.

So for my first example I’d like to present some work that is helping premature babies to breathe. Whilst being born the contents of a babies lungs have to rapidly switch from a liquid environment to a gaseous one. No one is quite sure how exactly this switch occurs but what we do know is that a lot of the time when babies are born premature, it doesn’t happen.

Now whilst with modern medicine a good proportion of these babies survivee due to assisted ventilation methods, around 30% will develop chronic lung complications in their mid teens. This is an obvious issue and in fact the cause is the assisted ventilation that saves the babies life in the first place, some of the time it will cause the lungs damage that is not fully repaired in the immature infant.

So how can we better understand this process? The answer is X-rays. And when I say X-rays I do actually mean like the radiograms you see get at your local hospital. Sort of. Scientists have found away to utilize the intense brilliance and high coherence of the x-ray sources to take highly detailed snapshots of living tissue.

So how do you do these experiments then? Essentially it is the same as normal radiography, you place the object you want to image in front of the beam and take an exposure. You then measure the change in intensity of the X-rays that come out the other end, due to the different densities of our tissues more or less radiation will be detected.

Of course synchrotron radiation has a very small beam size so you actually have to take multiple thin slices to get a large picture, however due to the much higher peak brilliance (the amount of light photons in a given area) exposure times are much slower.

The other major change is that your detector is a long distance away. By doing this some of the X-rays scattered by the edges of the things they interact with will interfere coherently and increase in intensity. The practical upshot of this is that the resolution at the edges of your image is greatly improved. Whilst thi can happen with normal X-rays it is more pronounced at synchrotrons.

So back to babies. Basically using the techniques described above scientists at spring8 have imaged lungs of premature baby rabbits whilst they breathe. The resolution is such that they can actually see individual alveoli within the lungs. This meant they could quantify the amount of air within the lung at a given time. Incredible.

In doing this they realized something. The rapid filling and emptying of lungs by artificial respirators was causing the lung damage as the lungs never fully filled with air and so water was never fully expelled and the lungs collapsed after each expiration.

They found that by either slowing the rate at which the lungs emptied through a technique know as PEEP (Positive end Respiratory Pressure), or by increasing the length of the first inhalation. the lungs would be fully aerated and would not collapse during expiration. This could really save a lot of lives in the future as it will prevent these fatal lung complications developing in preterm and C-section children.

Example number two of the awesomeness of SR comes this time from a technique known as X-ray fluorescence. This exploits the fact that all elements within the periodic table emit photons (fluorescence) at a given energy following x-ray exposure. Essentially by focusing on a particular energy level you can determine the composition of a material.

More practically, if you are good, this can be used in forensic like the example I’m about to show here. This case dates back to 1998 at a festival in Wakayama, Japan. During it many people grew critically ill and four eventually died. At the time no one knew the cause however after post mortem analysis it was found that they had been poisoned by an Arsenic trioxide laced curry.

The problem lay in the source of the poisoning. It was discovered however, through XRF, that all of the people who had died contained unusual amounts of certain trace elements at a given ratio. By analyzing various samples from the crime seen they manage to discover containers with these elements at the same distinctive ratio.

It was too distinct to be a coincidence and this evidence has been used in the prosecution of the culprits, which even now ongoing due to the circumstantial nature of some of the earlier evidence. This kind of analysis can only be carried out at a synchrotron due to the intense brightness of the X-rays allowing the weak signals from such trace elements to be significantly detected.

Well I hope you have enjoyed that brief insight into some of the more unusual science that goes on here at Spring8. As a final present I’ll leave you with an image from my first attempts at electron microscopy. This is a microtubule, one of the protein structures involved in maintaining the internal organization of cells, at 70,000 times magnification.

So what really amazes or inspires you from your chosen path in life? What keeps you doing the things you do?

Mata ne minna,

Two hikes to Two steps

So I finish the Cheiron school on Wednesday and following this I’ve got a couple of slots of beamtime, so yeah busy. Thankfully last weekend was a three-day one so I managed to have a good few days of chilling.

Day 1 and hike one was a trip to Ruriji temple with Sam and some of the retired folks that have been helping us to learn Japanese on Wednesdays. Wasn’t sure what to expect from this one but I was promised a monkey park so I was already keen. Also Ueda-san, the main organizer, is a wonderful person. Her English speaking isn’t so great but her understanding is very good and she is always so energetic.

 

We started at around 10:30 and as we were leaving from the mountain it meant we could lie in for a change. We hitched a ride down to the start of the course in the neighboring town of Sayo. It wasn’t to far although for some reason we seemed to take the longest route around the mountain possible.

We arrived at about 11:30 but could not start as we needed to wait for the rest of our group. Sadly they’d been involved in a minor car accident just outside Kakogawa and so would be a bit late, no-one had been hurt though “よかった“　

At the start of the hiking course there was a museum dedicated to insects so we went inside to kill a bit of time. This was no big surprise to me really since judging by the creepy crawlies I’ve seen where I’m living Japan is pretty full of bugs of all shapes and sizes.

It was only very small so it didn’t really take so long to look around, and given that all the displays were in Japanese it didn’t take too long. Thankfully Sam and myself were not the only none Japanese speakers. Some of the other members of our Wednesday Japanese class had also come along. Along with Sam there was Klara, a PhD student at spring8 who is from the Czech republic, a student from Bangladesh studying at the nearby university and a couple from China (Anily and Wang I think but that could well be wrong).

It was nice to talk to some new people as always. I’ve got such a gob on me. Myself and the guy from China seemed to have a good knowledge on bugs and were more than happy to share our knowledge, though I got the distinct impression no one else really cared. He also knew a fair bit about traditional Chinese medicines. There were some pretty incredible remedies for scorpion stings that involved using spiders to draw out the venom, mad.

After stoping for lunch we were invited to join a show put on by the owners of the museum for some of the kids in attendance. They told a short story about a grasshopper or something and then sang a famous kids song called “Mushi no koe” (insects voices). I think I shocked a few people by knowing the words, thank you online Japanese lessons.

After that we did a quiz, made much more difficult by the fact we couldn’t understand the questions. I think myself Sam and Klara did alright none the less, with a fair bit of help from Ueda-san.

After that we finally began the ‘hike’. In fact we just walked about 600m from the car park to a nearby temple and back again. Well most of the people were well into the 60’s and 70’s I think so not too surprising. The son of the temple’s head monk also joined us.

We were informed by him that the stairs leading up to the top of the shrine where known as the insect stairs as there where 64. To explain six in Japanese is rokku, but it can also be read mui. 4 is yon, but it can also be read shi. Therefore 64 is mui-shi and mushi is the Japanese word for insect. Gotta love the foreign language puns.

We then returned home, though not before stopping at another shrine, there is always another shrine, on the way back. This place had a very large Sakura tree in its courtyard though sadly it was the wrong type of year. Also there was a plant that bears soap nuts (Sapindus). I’d not come across them before but you really can get quite an incredible lather from them. I’d be interested to do some mass spec on them to figure out the active ingredient.

Saturday saw myself, Arnaud, Sam and Stratos joining some of our teacher friends and a few others to go trek along an abandoned rail track. I was really looking forward to this outing. It had been a while since I’d last met up with the “せんせいたち“ and they are always fun.

Thanks to Arnaud the time of the hike had been pushed back an hour meaning we could sleep an extra hour. Cheers Arnaud. The train journey was quite a long one, we had several changes along the way. It wasn’t so bad and I met my first of many new faces at Aioi, a Jet from Perth. Nice guy though he immediately started talking coding with Sam and Arnaud. “ぜんぜんわからへん。“

We arrived at Namaze station with a little bit of time to spare, for a change, and it wasn’t long till the whole gang was assembled. There were many people I’d not met before from all over the world, Australia, America, Singapore, Peru and even Oxford. There were a few familiar faces to including Gerard a quality bloke from New Zealand and Kelly, event organizer extraordinaire.

We got moving fairly quickly, actually we were moved on by the station staff I think such a large congregation of foreigners in one place was making them anxious.  Off we trotted with Sam and Kelly chirping away in French in front of me and Tomoko and Yuki nattering away in Japanese behind me I’d never felt more like an ignorant Englishman. Most of the people I meet speak at least two languages, I struggle with one most of the time.

The route itself had a big sign outside it informing us we should not hike here. Of course there were many Japanese families wandering along the tracks so I doubt it was too rigorously enforced. The views were pretty impressive. The old rail tracks actually lead through Mukogawa river valley and I think the recent typhoons have done wonders for clearing out the water. I haven’t seen rivers that clear since I was in Vancouver.

The other cool thing about following old rail tracks? Old rail tunnels of course. There were plenty on the 2 hour walk and we regularly had to get our torches out (no that isn’t a euphemism). It really was an excellent hike route, just something a bit different to the normal mountains, and of course the company made it all the better. Oh and also the opportunity to drool over some amazing crag, I so need to go back when I know a bit more about trad I think.

We finished up at some izakaya close to the train station to grab drinks and what not. Apparently there 名物 (specialty) was wild boar but I wasn’t too peckish. Since there were around 20 people or more I didn’t get chance to chat with everyone but everyone seemed pretty cool.

The range of backgrounds of people on the jet program is really quite astounding. Two people that really stuck out where a neurobiologist from Singapore and an Austrian whose dad had been part of the team who developed golden rice. Hmm I think I may have a biology bias in my memory there.

After a grand day out I headed back to Himeji with Arnaud, Gerard, Sam and Stratos. We wanted to find somewhere to watch the rugby, since Gerard is from New Zealand and Sam is from France it was a matter of national pride. The place we settled in was Hosanna a “British” pub.

Hmm Japan you may have gotten it a bit wrong here. Where to start? Well besides the fact it was spotless and had waiters in Texan ties. Also the German music and pizza on the menu were a little off to. They did at least do “チプース“ (chips) although they were actually wedges with a garlic and herb seasoning. Meh close enough.

So onto Sunday then since I’m sure you don’t need to know about the rugby. First things first I had to wait in for my bike to be delivered. It was expensive getting it repaired but I am very happy with it. On a personal note I did manage to sort out the delivery time by myself even though the driver spoke no English, small victories I guess.

Anyway on the agenda was a reggae concert with the lovely Miss Kelly. Apparently it was co organized by the Japanese foreign embassy to promote Jamaican culture to the locals. I love reggae, so it was a no brainer ,but it would be interesting for other reasons. Reggae is loud, brash and very forward, everything Japan isn’t. I was actually curious to see what the crowd was like.

As it was a 3pm matinee I guess I shouldn’t have been too shocked that the audience consisted of mostly old couples. All the same the music was fantastic. The first half was a Jamaican music medley going through a brief history of music on the island, including some fantastic djembe playing. The second half focused on more modern music and gave the artists a chance to promote some of their own work.

 

I had a fab time jiggling along but the whole event was a bit stilted. The crowd weren’t particularly into, it seemed a lot were there as a curiosity not because they were interested in the music. That's fine and all but not what I was expecting. I guess it’s difficult when you don’t understand what the band are saying, I think some of the subtleties of ‘welcome to Jamrock’ were lost on the audience.

It was as good excuse as any to get off my rock none the less and it was all very nostalgic. I think ‘no woman no cry’ actually brought a tear to my eye making me think of all my roodies back home, (you know who you are.)

It was nice to break away from ‘Japanese culture’ for a bit anyway. I’ll be honest I’ve just come out of the honeymoon period right now. A lot of myths about Japan have been dispelled, nothing feels particularly new and exciting and small things are getting on my nerves. Don’t get me wrong I do love this place, I enjoy my job and like the people (mostly) but I am missing home.  Seriously if anyone could mail me a loaf I’d love you forever.

Hona mata.