Category Archives: PhD Studies

Kyoto winter!

Last winter I chickened out and got out of Kyoto a few times with stops in the USA, Cairo, and Malaysia.  This winter, I am being brave and staying here the whole winter.  It will be my first complete winter in years and years!

All of my apartment windows are opaque, so I don’t see the weather until I open the door to check.  This morning I got a nice surprise and a fun ride to the lab. Yay for snow!


I’ve finished the transcriptions of my raw data.  I have 57 interviews and I’ve transcribed the 42 that were conducted in English.  My research assistant is still working on the Malay and Chinese ones.  The transcription now comes to 493 pages.  I’ll spend the next month or so coding the data and trying to find some patterns.

Goodbye Transcriva!  You were free and you worked great, but I will not miss you!

Screen Shot 2015-04-23 at 4.40.46 PM

The Limits of Institutional Reform

This may become one of the central theories in my PhD work.  Taking it very slow to absorb as much as I can.

Matt Andrews

Being a modern student

Coming back to study at university after a 15 break was bound to be a challenge.  To be honest, I did not know what to expect.  My years of working with WWF were marked with enormous amounts of job satisfaction.  One of the reasons it took so long to come back to start my PhD was that I loved working on marine conservation.  I got to do exactly what I had wanted to do all my life.  But it was also marked by massive levels of stress and week after week with daily schedules packed completely full with meetings, meetings and more meetings.  That only left my free time to complete reports and try to do any real work.  Coming back to school was going to be a luxury to focus on just one thing.  And it has been… kind of.

During my Bachelor and Master degrees I spent hours and hours in the library stacks searching through journals and standing at the photocopier.  I was always better at finding interesting articles than I was at reading them and processing them.  In my 3 years at Kyoto University, I haven’t photocopied a single paper.  Now its all digital.  There are no more card catalogs.

My Kindle is one of my favorite tools.  When I started the PhD, I got a Kindle and hoped to read journal articles on it.  Mostly this was to avoid printing and printing and printing.  Unfortunately, that Kindle was not good at processing PDF files.  It was nearly impossible to read a PDF on that device.  I had a great service that made the conversions for me, but they were clumsy.  Then I lost that kindle.


I broke down and bought another Kindle last year.  This was the 2nd Generation Kindle Paperwhite.  Its has the same kind of functions as my previous one, but it is touchscreen, has a back-lit screen, and is much more versatile.  Amazon has created several features that convert the PDF journal articles to Kindle format and I can simply email papers to the Kindle.  It doesn’t do well for charts and tables but it does a great job with text.

I also read for a bit of pleasure with the Kindle and the amount of material you can find online, for free, is enormous.  With Kindle’s great “Send to Kindle” button my Firefox web browser I can even email webpages to my Kindle to read later.

My other favorite tool is Mendeley.  Mendeley is a free service that helps to keep track of academic papers.  It organizes all my PDFs, gives them keywords, and can integrate with MS Word to create bibliographies.  This makes everything so much easier to manage and access.

Screenshot of my Mendeley online library.

Screenshot of my Mendeley online library.

Lastly, I use Evernote to keep track of my notes on the readings.  I am now linking Evernote to my Kindle so that the passages I highlight when I’m reading get automatically sent to Evernote.  Its amazing.

Great time to be a student.  These tools are stunning.  Information is so much easier to find.  But, I do miss the long hours in the library.

A break from transcription

My PhD has started a new phase.  I am now preparing my data for analysis.  The first step is to transcribe the 39-plus hours of interviews.  I am using a software called Transcriva.  The process is slow and tedious but its nice to make tangible progress.  Several websites mention that it can take 4 to 7 hours to transcribe each hour of interview data.  Mine are taking about 3 hours per hour of interview.  My great field-assistant, Chai Ming, is helping with the Chinese and Malay interviews.

So, I took a break on Sunday and went for my yoga class (taught by my neighbor, Yoko) and then a hike up Kyoto’s second-highest peak, Mt Atago.  Yoko’s boyfriend, Dan, wanted to visit an abandoned cable car station at the top of Mt Atago, near the much-more-famous shrine, also at the top.

Yoga was from 10:30 to 11:30, then I had a nice lunch with Yoko and Dan before we rushed to catch the bus to get to the trail head.  It was a bit of a late start so we packed some extra warm clothes, snacks, and flashlights and head lamps, just in case.  The bus got us to the trail-head just after 2 pm and we started right up the hill at a blistering pace.  It is about a 4 km walk with an approximate 600 m vertical climb.  Both of us have climbed to the shrine before, but not to the cable car station.  We had to be quick and we weren’t sure where the old cable car was so we wanted time to be able to find it.


This is the yoga space. Its a loft above a cafe. We can enjoy the smells of the cafe cooking while trying to focus on the activity!

But…… I had my binoculars and there were birds.  So it went a bit slow at times.  At the very start of the trail there was a bird wave and we saw some pretty common birds but one stood out and I managed to identify it later as a Siberian ruby throat – (update 13 March.  It wasn’t Siberian rubythroat.  It was Red-breasted flycatcher.  Not quite as rare but still very cool)  a lifer for the start of the hike.  Yeah!  We also saw a woodpecker that I may have seen before, but am not sure.

There were lots of climbers coming down and we got overtaken by one guy who was running up (he passed us coming down later on).  As we neared the top it was getting close to 5 pm.  Our return bus was at 6:38, so figured that we needed to turn around near 5.

When we were nearly at the top a group of three young men were coming down and Dan (who speaks better Japanese than me but still not a lot) stopped to ask them if they knew where to find the cable car.  Their English was not great but they indicated that they were looking for the same thing but they didn’t seem to be able to tell us.  We gave up and went up to the top of the shrine and made ourselves a quick cup of tea and headed back down…. at 5:15 pm.  We needed to hurry.

These guys were friendly but couldn't tell us where the ruin was.

These guys were friendly but couldn’t tell us where the ruin was.

As we went back down the trail we noticed something on the ground.  An arrow pointing to a small side trail.  And above it, written with cedar leaves was the word – RUIN!  Dan spotted the word.  I completely missed it.  The guys had left us a message.

The sign! Clever guys!

The sign! Clever guys! Can you see “ruin” just above the arrow?

Despite the lateness (and some pain I was having in my hip from yoga and the climb) we rushed down the side trail to see if we could find it.  Dan was faster and ran ahead…. and there it was!  The abandoned building!  What a find!

We spent a few minutes looking around.  Dan wondered if we should go straight down the old cable car route but we decided it was best to take the trail.  We rushed back to the trail.  Now 5:30ish.  We had an hour to get down and catch the bus.  By then my hip was hurting.  Dan was faster than me but we scurried down the trail.  At 6:15 it was dark and the head lamps came out.  We continued to scurry.  Dan phoned Yoko and found out that there was another bus at 7:00 but it would only get us to the nearest town and not all the way into Kyoto.  We would need to find another transport back in – either bus or train.

The trail down... it got much, much darker!

The trail down… it got much, much darker!

At 6:30 we hit pavement at the bottom of the valley and the road.  Dan jogged back up the little hill to the bus stop.  My hip was burning and I tried to go as fast as I could.  When I reached the bus stop, Dan was there and we had missed the bus by 5 minutes.  Boo!  So we waited for the 7 pm bus.  And reveled in the rush of having gone up and down so fast and the wonder that the guys had left us that cool message.

And then out of the darkness the 3 guys came up the hill!  They had gone down the cable car route!  We were so happy to meet them.  We showed them pictures of their trail sign and the building.  They were all law students at Osaka City University and one Spring Break.  We all caught the same bus and had a nice chat on the way.

We met up with the guys who helped us find the ruin! Thanks guys! (photo: Dan Marsh)

We met up with the guys who helped us find the ruin! Thanks guys! (photo: Dan Marsh)

Dan and I went back to get our bikes and stopped for some yakitori and a couple of beers.  I didn’t get any transcriptions done on that Sunday but it was memorable and fun.  I doubled up on the transcriptions on Monday.

Final field trip

My PhD research is a year behind schedule.  The process of getting my research permit and subsequent visa was supposed to take 4-6 months.  It eventually took 14 months and left me with a very short period to complete my field data collection.

I have now finished two data collection trips to Malaysia and am now back in Kyoto processing the data and getting ready to analyze, write, and publish.

Over the course of the two trips I conducted 59 interviews, interviewed 75 respondents, taking 34 hours and 14 minutes.  Interviews were conducted in Kuala Lumpur, Putrajaya, Kota Kinabalu, Kudat and Semporna.  I interviewed government officers, consultants, NGO representatives, and fishermen.  During the second trip, I had the help of a great research assistant, Lau Chai Ming, who assisted with translations and scheduling of appointments.

Chai Ming - My research assistant for the second trip.  Was really lucky to find such a great assistant.

Chai Ming – My research assistant for the second trip. Was really lucky to find such a great assistant.

We hung out around fishing jetties in Kudat and Semporna and met with fish traders and fishing boat owners. Trawlers are common in Kudat.  They drag a net behind them along the bottom of the sea and scoop up anything that is living along the bottom.  Its a pretty destructive form of fishing.

This slideshow requires JavaScript.

We also got to visit Pulau Banggi and see the great work of the Banggi Youth Club.  The Youth Club conducts awareness activities with local communities and works closely with WWF.

Some members of Banggi Youth Club.

Some members of Banggi Youth Club.


In Semporna we observed the Mabul tuna landing.  Fishermen use small boats to spend 2 to 3 days at sea and pull up tuna with just a line and a hook. Without any other equipment they can land tunas that weigh up to 70 kg.  The ones we watched them land were in the 20 to 30 kg size.

We were even lucky enough to get invited onto a purse seine boat during a trip out in Semporna.  Unfortunately, there was a full moon the week we were in Semporna so the purse seiners were not able to fish very much.  They spent most of the week at the jetty doing repairs and mending nets.  On our last night we got invited out.  Here’s a short video of one of the exciting parts – little fish jumping in green light.


This slideshow requires JavaScript.

Side projects nearly complete

On Friday I have to give a progress presentation for my PhD.  I could give the presentation in one slide, but I won’t.  That slide would say: “Bit off too much. Research permit took 18 months.  Not much progress.”  So, what have been doing since May last year, when I last seriously thought about my PhD?

I have completed several consultancies including a major edit of Malaysia’s State of the Coral Triangle Report, completed a final report for Malaysia’s USAID Coral Triangle Support Partnership Programme, proof-read a book about ecological connectivity, published 5 articles in Action Asia magazine (with Eric Madeja), traveled to USA, France, Japan, Malaysia, Indonesia, Timor Leste, Papua New Guinea, Solomon Islands and one day in Australia.  And, this week, finally, submitted the last of the major products for the Coral Triangle book.

And now I need to get to writing a progress report.  And then…. a PhD.  And then…..