Monday, 1 September 2014

Mt. Fuji from bottom to top and back for a Festival of Fire

Mount Fuji is Japan's highest mountain at 3776m, a volcano that last erupted in 1707 and which has long been sacred to the Japanese. They have been climbing it for centuries. I suspect it is the most climbed free standing mountain in the world.

I never had a view of Mt Fuji during my 12 day stay in Tokyo and Japan. That was despite climbing it and taking a trip up the Tokyo SkyTree (tallest communication tower in the world at 650m). Despite sweltering hot and humid days towards the end of August in Tokyo, the mountain was hidden by swathes of cloud each time I tried for a view. So, as an introduction, this is Mt Fuji as it could possibly be seen from the SkyTree (100km away) in Spring – at least this is the panaroma photo in the SkyTree:

One of the reasons it is accessible to young and old alike (I saw a 5 year old and 80+ year olds on the upper slopes) is that one can drive about halfway up: to the Fifth Station at 2300m. That removes any real glory in a summit of this impressive cone of solidified lava.

In order to do the mountain justice, one should, in my opinion, follow the old, original route – from the base of the mountain at the town of Fujiyoshida. The torii gate of Kanadorii, which marks the start of the sacred area of Mt Fuji, is roughly 800m above sea level. From here to the peak is just short of a 3km vertical ascent, a worthy climb.

This is the journey my hiking companion, Jules, suggested we take, and this is an account of our climb.

Day 1

Our journey started at the seaside town of Kamakura, and because the train ride had to boomerang via Yokohama it took us over 3 hours to get to Fujiyoshida, roughly the time it would take from central Tokyo. After picking up free, really good hiking information at the train station information centre, we checked into Pension Suwanomori, a lovely Japanese-style guest house at the Yoshida-Guchi trailhead.

The guest house is also very close to the beautiful and elaborate Kitagushi Hongu Fuji Sengen Shrine, the start of the Yoshida-Guchi climbing trail. Here one offers prayers for safe passage to the spirits, although this can also be done at the Memorial Stone to the fallen climbers of Mt Fuji just up the road.

Not a swastika

We then wondered into town, past the Kanadorii, in search of a meal of the traditional udon noodles eaten before the hike.

Day 2 

After a good nights rest and a hearty breakfast, we shouldered our  packs at 8am for the start of our 10 hour hike.

The first stop, after about 1.5 hours through Pine and Betula forests whistling with birds, is Nakanochaya tea house. The woods are meant to be home to Japanese Squirrel, Bears, Boars and Mountain Cats, but all we encountered was a frightened deer.

Still full of energy, with temperatures pleasant thanks to low lying cloud, we pressed on to Umagaeshi (1450m). The name of this station means something like 'horse turn-around' as horses were no longer allowed beyond this point. It was also the last place for free green-tea and water. Close by, an arch guarded by two cheeky stone-monkeys marks the route for every increasing prices for bottled water. Bottled water is about 120 yen from vending machines in town, costs 300 yen at the fifth station, and is 500 yen at the Fuji summit hut. Luckily, Jules was carrying kilograms of water.

We encountered our first hikers about fifteen minutes later at the 1st Station (or Ichi-gome 1530m). A veteran Japanese climber babbled away to us in Japanese, while another carrying the traditional walking stick with bells on to frighten bears took photos of the remnants of the shrine. By this time one has left the gentle incline of the lowlands, and every foot fall carries one skywards. In places the trail runs well below ground level, worn away by the millions of feet that have travelled this route through time. One passes the sites of many old tea-houses, which have become defunct with the road to the Fifth Station. The information signs include photos of a bustling route from a by-gone era.

One of these abandoned stations is the Second Station – Ni-gome – or the Women's Holy Ground. Up until the Edo Era (1832 ad) women were prohibited from climbing past this station and worshipped Mt Fuji from this point.

We emerged from the forests at the edge of the old Fifth Station at lunchtime. The squawk of a parrot led us to a station hut, where yummy Udon noodles were also on the Menu, which were a great supplement to the energy bars and other snack foods that had sustained us so far.

At the fifth station, things change dramatically from several points of view. There is a short transition zone from tropical woodlands to almost bare scree slopes of multi-coloured larva. But it is also where the crowds of people start, and they become the main source of entertainment for the rest of the journey upwards. The trail is clearly demarcated by erosion barriers or rope. Should you not have brought snacks or drinks, these are available at the many huts or sub-huts. Visits to pungent toilets now cost 200 yen.

At the sixth station is a mountain safety hut, where we were issued a pamphlet on the dangers of 'Bullet Climbing'. Those that head straight for the top are more likely to need first aid services, abandon the climb and generally get into trouble. However, the pace of the groups and the bottlenecks on the route mean that one is almost forced to climb at a healthy pace.

We arrived at the Goraikokan topmost mountain hut (3450m) with the last light of the day. These mountain huts pack over 100 people into a very tight space, and you don't really want to spend much time here, especially if you suffer from claustrophobia. One is literally shoulder-to-shoulder with one's neighbour. By comparison, the capsule I'd spent a week in Tokyo was spacious. In our case, we were in the 'attic' with less than 1 meter space between floor and ceiling – we literally had to crawl to our sleeping locations. An evening meal had been included in the price of our stay, and although it was presented t.v. Dinner style, it tasted good to our energy-deprived bodies.

Day 3 

Exhaustion eventually ensured I got to sleep. However, many people have issues sleeping at altitude, and poor Jules had not slept at all by the time people started waking up at 2am. From Goraikokan it is only 1 hour to the summit, but the hut staff had suggested 2 hours may be necessary due to the large number of people. With dawn starting at 4.30 am, we were packed and ready by 2.30am.

Although the last stretch was punishing in the dark, cold, wet and wind, the ascent did only take just over an hour. So we reached the mountain top before 4am – but within minutes the warmth generated by the last leg of the climb had been blown away by the freezing wind and fog. We sought solice in the canteens for some expensive tea and soup, happily paying the inflated price for the warmth more than anything. But by 4:30 it was still pitch black outside with no sign the weather was going to improve. By 5:00am it was light enough to see, suggesting the sun had risen beyond the clouds, and we decided it was best to start our descent.

An hour later and we broke through the clouds for the first signs of a sunrise, and our first views of the five lakes region below us. For the next hour we would stop at the end of each zig of the descending zig-zag trail to distract ourselves from the knee-jarring descent with views of hilltops-islands in lakes of mist. The descent trail is separate from the ascent trail until the Sixth Station, which we reached around 7am.

Since we still had a day to fill before the grand finale of the day, I decided I would return through the forest to Fujiyoshida, in order to try and spot some of the birds we'd only heard singing the day before. As Jules had not slept at all, he opted for the bus from the Fifth Station, and relaxing and refreshing hot-bath.

The grand finale for the day was the Yoshida No Himatsuri – or Fire Festival. This is held at the end of August and marks the end of the climbing season and the start of autumn.

The festival starts around 3.30pm at the Fuji Sengen Shrine, with crowds dressed mostly in white, loose fitting clothing with bells and head sashes. After a ceremony that transfers the spirits of the shrines to the elaborate arks, the procession sets off through the streets of town. For this ceremony, that happened to coincide with a thunder storm, and while the Japanese were well prepared with brollies and raincoats, Jules and I had left ours with our luggage in a locker at the train station, so had to seek shelter in the shrine for an hour or so while the rain wore itself out and had us seriously wondering how they would light the 70 or so three-meter tall pre-prepared bonfires that were the highlight of the evening.

Fortunately, the spirits were suitably appeased and by 5pm the streets were bustling with people examining the wares of the hundreds of street stalls, selling everything from gold-fish and turtles to octopus-on-a-stick. And by the time the last light of the day had died the first of the bonfires was on the go. The ceremony and festivals continue until midnight, and into the next day, but we'd had enough and it was time to head home to family and beds where one didn't feel the breathing of one's neighbour.

All in all, a most memorable expedition.

Notes on preparation. 

I'm normally quite fit, as my work involves lots of hiking and outdoor activity generally. However, 2014 had been proving to be a bit of a laptop year, and in order to get ready for Mt Fuji I regularly hiked to the top of Blue Hill about once a week. Since this was all between 1000 and 1500 meters, I did not have problems with altitude sickness, which afflicts many, and which I have felt before.

The equipment list for climbing Mt Fuji includes the following:

1. Hiking Boots (good idea, although I saw some people did it in trainers)
2. Warm, layered clothing, including fleece and rain jacket and pants.
3. Gloves – both for keeping hands warm at altitude and protecting ones fingers against the sharp lava rocks.
4. Headlamp – especially for the night climb
5. Water – as much as you can comfortably carry, at least 1 litre.
6. Snacks – we carried dried fruit, energy bars,  energy drinks and biscuits all bought locally in Japan at Familymart.
7. Cash – for water, tea and food at mountain huts (or using the toilet!)
8. Compass, Sunglasses and Sunblock were not needed by us – but could be useful.
9. Basic first aid kit (plasters, blister pads, headache tablets).
10. Tissues, toilet paper, toothbrush.

Remember, garbage in, garbage out – you need to carry all rubbish off the mountain – there are no bins.    

Mt Fuji is clearly visible at 100km up on Google Earth. Fujiyoshida, the trail head is the grey area to the north between the lakes. 

Friday, 15 August 2014

Fighting Fire in the Fynbos

Wildfires are spectacular forces of nature, and terrifying if you encounter one live. Living in the Fynbos you are living with fire. Fire is part of the natural cycle of life and the plants are adapted to it. However, we live in changing times – and in the eastern Fynbos fire is becoming more frequent and burning over wider areas. Part of this is due to changes in our weather which are causing increases in Fire Danger Indices (FDI), partly due to increased lightning strikes.

I learnt at Fynbos Forum last week, increased summer rainfall means that the southern and eastern sections are experiencing more summer rain and this means fuel loads are recovering more quickly.  Generally, this is all of great concern to landowners, because fire is a threat to human safety, housing, crops and livestock. Furthermore, landowners are liable for damage from fires that spread from their property to neighboring properties. In the case of those living near pine plantations, this can mean millions upon millions of rands. There is much concern from Fynbos ecologists that as a result the fire cycle in Fynbos is being interrupted because fires are suppressed, and in situations like this Fynbos is then replaced by forest.  We now have a situation where much Fynbos in the lowlands in association with human habitation and agricultural activity is under burnt, while on the other hand the mountain regions are experiencing too frequent fires. Neither extreme is good for Fynbos.

Legally, landowners need to have fire breaks and adequate fire fighting equipment on their properties. However, one hike into the Cape Fold mountains and you will realise that the feasibility of creating and maintaining fire breaks many kilometres long over steep terrain intersected by deep gorges is completely impractical. Likewise, accessing remote areas where fires can result from lightning strikes or even rockfalls is sometimes impossible.

Landowners across South Africa are now being pushed to join Fire Protection Associations, where resources are pooled, and fire control can be done on a bigger scale, thus mitigating the need for each landowner to have fire breaks. However, these associations cost a lot of money to be a part of and many land owners are sceptical of the benefits they bring. For instance, as part of the big fire we experienced in 2012 we received no support from the Southern Cape Fire Protection Association (SCFPA). Subsequently, some landowners in the area did receive compensation for fencing damage.  More recently, they have arranged for insurance premiums to be reduced for members of fire protection agencies. It is clear that these associations are now starting to work harder to justify membership.

We experienced our first tangible benefit of being members of the SCFPA this week when they sponsored a one day basic fire fighting course at Avontuur.  A massive amount of background theory was assembled by Dirk Smit of SCFPA, and presented along with interesting anecdotes by local fire-fighter Wayne Young. Of course, the real entertainment was then setting the veld on fire and letting the trainees get to grips with the mopping up operations.

Here are a few highlight photos:

Fire is a big threat to property, causing huge damage every year around the world

Fight Fire with Fire: creating a backburn is one way to control a fire. 

Hot work: layers of protective clothing couple with extreme heat mean heat exhaustion and fatigue are a major problem when fighting fires.

Caught in a fire: hopefully the carbon monoxide kills you first, as death by fire is the most painful way to die

Young or old, black or white - you all get together when it comes to fighting fires

Firefighters: all that stand between you and the flames

Wayne Young: remembering the on-average five fire-fighting helicopter pilots that die each year

Friday, 25 July 2014

Helping Fynbos

Last month we had our first intern from the Living Lands, Ted – from Holland. Living Lands is a collaborative partnership based on the eastern sections of the Baviaanskloof, working with the community and really interested in ecosystem services. Ted was looking for a restoration type project for a third year university assignment. Perfect – we had just the job.

In 2009 the first black wattle clearing operations were undertaken around the Hartbeesrivier community, where we live. The wattle infesting the streams of Blue Hill was cleared in 2011. Follow up operations have been ongoing ever since to varying degrees. However, certain areas are looking pretty bad in terms of erosion. So we wanted to know how the vegetation was doing, in terms of biomass and the types of vegetation (functional groups).

We really wanted to know whether or not clearing the alien vegetation had made the erosion worse. So this was Ted's task – systematically take samples in cleared, uncleared and natural vegetation. After a month of bashing through spiny cliffortia, phragmites, mud puddles and crumbling canyons, we were able to run some models.

Turns out even now several years later, and despite natural vegetation having burnt two years ago, the cleared area was lower in biomass and in terms of natural functional groups. And while erosion was really complicated in terms of contributing factors, areas with high livestock use were clearly worse.

So – what do we do about it? Well, it was clear the land needed some help with the regeneration process. Also – after the big fire of 2012 proteas were resprouting everywhere, including in the roads and tracks – not ideal. So we've started digging up those plants doomed to be squashed by 4x4 tyres and replanting them in the areas clearly struggling to recover. Win Win Win. 

Well, we hope - it will be some time before we know if the transplanted plants have taken. So this is a documentation of the pilot project. 

Road Warrior - Wendy Foden digs up a young Protea nerifolia in the track. Skeletal remains of the parent plants can be seen behind her.

Beata (Starbucks Supervisor and volunteer) guards the rescued plants

An example of the areas cleared of wattle with replanted proteas here and there. Note lack of vegetation recovery around the stumps. 

Alexa-Storm, helping the Earth recover with love and care

A pretty shot of the winter moon setting over Hartbeesrivier
Protea nerifolia - maybe the plants we've planted will look like this one day

Making it through my MOOC: the Data Science specialization through the Johns Hopkins University

Although I completed my PhD in 2010 and have been taking data through my postdoctoral research project on the birds of the Fynbos, its been over 20 years since I did stats 101 at University. Although I've muddled through partly through a focus on a few statistical techniques, it was brought home to me that I needed to do something about my patchy statistical knowledge when I had a paper rejected from the world's lowest ranked ornithological journal, partly because of a basic statistical error.

Up until this year I didn't even know what a MOOC was – it stands for Massive Online Open Course; basically, learn anything online, and for free. Some of the big platforms for hosting these include Coursera, edX and Udacity and you read a comprehensive review of these big 3 here:

So how did it all start for me? My university sent out a postgrad-development-program email including links to some Coursera classes, where I spotted the Foundations in Statistical Inference course offered via Duke University. So in February I enrolled in my first MOOC. The course consisted of weekly lectures that could be downloaded or viewed online as videos, as well as course notes, a link to a free basic stats book, weekly practical tutorials using the R programming language, weekly quizzes, a mid term exam, a course stats project, and a final exam.

The course was put together by Mine Çetinkaya-Rundel; material was clear, lucid and the best of all the online courses I was to subsequently take. The course does what is says on the box – and leads you by the hand from understanding Means and Standard-deviations all the way to an introduction on Multiple Regression. Since there are thousands of people signed up to any MOOC, support is provided not provided though interactions with the teacher but through the online discussion forums, with students helping each other. Yip – cheating is practically legitimized (ok, answers to quizz questions are not posted, but steps on how to get them often are; ok – not cheating, but serious collaboration).

In February I started my first Johns Hopkins Data Science specialization courses: the foundation courses being the Data Scientist's Toolbox, and R programming. You won't get anywhere on this course without embracing the R language (and if you have to analyse data at any level, you probably should do this anyway). The Data Scientist's Toolbox is a good overview to the rest of the course, and includes a good motivational first video. Its a very easy 'tick' in the serious of 9 courses. I believe it is presented by Jeff Leek, who has a clear lecture delivery style, is well prepared, and imparts a lot of information very quickly. For the later classes I had to pause videos frequently in order to back up over key concepts, but that is the joy of being able to do these things at your own pace (it is all doable if you are disciplined or motivated).

I've been getting by for the last decade with SPSS for my statistics. However, this is expensive licensed software and it was clear with conversations with clever colleagues that there were multiple benefits in learning R programming - not the least being that it is free. However, R is like learning a real language, and takes time to get to grips with syntax and idiosyncrasies. Six months into all of this, and I still struggle with some aspects of its use for things I could do very quickly and easily with Microsoft Excel. With Excel at least what you do is presented straight away in front of you in terms of data manipulation and reshaping, while in R its all hidden away in data.frames, and little mistakes can severely f***up results. However, my mind has also been blown open by the possibility of all the things that can be done, from charting, to exploring and acquiring data, to running extremely complicated data analysis models.

Enter R programming – presented by Roger Peng. He is great, and he is the only one of the three lecturers to video himself as part of his lecture presentation, which kind of makes it all a little more personal – which is actually really important considering the whole series could be presented by some archane Artificial Intelligence robot. The videos are a little less polished, and I often found myself distracted trying to read the book titles on his book shelf, or found myself amusing myself following the movement of coffee cups and personal items between video lectures.

Then I did something a little crazy during April/May once the Duke course was finished. I took four of the courses simultaneously – Getting and Cleaning Data (by Jeff, excellent); Exploratory Data Analysis (Roger Peng, good – a bit unclear at the end); Reproducible Research (Roger Peng, fundamental lessons here – very important); and Statistical Inference. Basically, the MOOCs became a full time occupation because each one takes about 8 hours a week, and some of the projects can take days if you get stuck, especially if you are learning R along the way. And don't kid yourself – you really need AT LEAST the recommended hours to get through each course proficiently.

Ok – now – back to that last course, Statistical Inference. Having just done the Duke Mooc I was pretty sure the Johns Hopkins version wouldn't be an issue – it was only a typical Data Science 4 week course. However, it is without a doubt the worst of the series and about the most terrible lecture style I have ever encountered in my life. Feedback on the discussion boards was scathing, and included an attempt to start a petition to refund those Coursera students who had paid the fee for Signature Track – i.e. those that wanted official recognition for their course participation. My course score for the Duke Mooc was 85% - and as I'd been on holiday for 2 weeks of it I had missed a quizz and the project proposal submission deadlines, which all counted for points. But despite completing everything for the John Hopkins regression course I scored only 72% - in other words my basic understanding of statistical inference at the end of the second course was actually worse!!!! By comparison, I scored 100% in Reproducible Research and Getting and Cleaning Data. The Statistical Inference course notes were also a disaster – I can only hope for those taking newer versions of course that things have improved. The presenter - Professor Brian Caffo - may be some later day genius in his field, but that does not translate to good teaching style by any means. I also had to suffer through Regression Models, where I am sure it was only some a-priori knowledge on these subjects that got me through.

At the moment I am in the last weeks of the Practical Machine Learning module, which has been a real eye-opener, and TG its Jeff Leek. I have one more course to go – Developing Data Products, and then apart from a Capstone project for those doing the paid version of the course, I'll have nailed it. So far – its been worth it, mostly because I am far more confident in using R – which like any language, only gets better the more you use it. And unlike stats 101 twenty years ago, all paper and equations, I can honestly say that stats is fun now. I never thought it possible that I could say that – but really, the way one can quickly visualize complicated data sets, explore data and interpret data – its almost like telling (or writing) a story – only with numbers and charts on a laptop. And the utility of it all – well, the sky is the limit (literally; get good with these skills and you could work for NASA).

So – Thanks to Coursera and John Hopkins University – this education revolution will change the world. Get on board before national governments start to see free and fair education as a threat to national job security and start to regulate who can participate. That, or global demand brings down the servers – in fact I wrote this entire post while waiting for the Coursera website to come back online from a temporary time out.

In the words of Rob Schneider (Adam Sandler's sidekick) - “You can do it!”

Thursday, 10 July 2014

Citizen Science in South Africa: iSpot and ADU's Virtual Museums

Over the last couple of years there has been a recognition that the general public can play a very important role in science, and wildlife monitoring in particular. Anyone from the librarian's daughter to the postman can now also be a 'citizen scientist'. In South Africa, probably the most rigorous in terms of raw data collection is the South(ern) African Bird Atlas Project (SABAP2) where birdwatchers upload lists of birds to a central database. Due to the local focus on going 'wide and deep', as well as encouraging repeat surveys, this is an outstanding database. In some initial analysis I did on bird distribution of the fynbos, it proved way better than the global ebirds project, and even Birdlife International range maps. There is no ornithologist working on South Africa's birds that does not refer to this major database. Join the atlas efforts at

Citizen science projects cover a range of activities, from really specialized skill sets, like bird-ringing, to submitting photographs to online archives. The age of digital photography has been around for a while, and now almost everyone has a camera – ranging from built in cameras on mobile phones to fancy D-SLR cameras with massive lenses. Recording nature has never been easier. However, there is also now competition among citizen science programs to recruit people willing to record their observations. There are 2 major photo archive platforms in South Africa: iSpot and the Animal Demography Unit's Virtual Museum.

iSpot was launched in South Africa in 2011 and has an online community that boasts many expert members that has grown very rapidly through the institutional support of SANBI and a vast amount of time dedicated to the task by Dr Tony Rebelo. Tony's focus was initially to use the tool for documenting the plants of southern Africa and he has succeeded remarkably well – aiming to have 95% of South Africa's plant life documented by 2015. He describes iSpot first and foremost as a learning tool (i.e. you can upload photos and let others identify them). However, you can also contact them to obtain spatial and other information.

iSpot was developed through the Open University and they have brought incredible developmental power to play to create a slick interactive tool – iSpot allows multiple commenting streams which creates conversation and users are a tight knit community. The South African iSpot community can be found at (don't get confused with the UK site). Through a single portal it is easy to upload photos to a range of groups (Amphibians and Reptiles, Birds, Fungi and Lichens, Fish, Invertebrates, Mammals, Plants, Other Organisms). Members collect points through interactions (agreeing with ids). Apart from plants, birds and insects feature prominently in group interactions (see

The Cape Town University's Animal Demography Unit (ADU) Virtual Museum has been around for a few years more, but created their virtual museums from scratch. Despite constant financial constraints, the team led by Prof Les Underhill has done a remarkable job. Registered users number only a quarter of those of iSpot. A key difference is that identification is confirmed by an expert – as opposed to iSpot where the users agree or disagree on an identification. I prefer to do this than get involved with dialogue, but each to their own. I also prefer the mapping feature with the ADU's VM. There are several Virtual Museums (but only one data upload interface at – you then choose which museum your photo belongs in). Apart from trees, they don't do plants, but have more focus on the animal kingdom – including weavers (PHOWN) and Starfish (EchinoMAP). There flagship group is the MammalMap (, but their LepiMap (Butterflies and Moths) formed a major contribution to the recent “Conservation Assessment of Butterflies of South Africa, Lesotho and Swaziland”, part of their proven track record of doing something with the data submitted.

So which platform to use for documenting your wildlife in the most helpful manner? While both platforms would beg user loyalty, a simple answer is: Plants on iSpot and Animals on ADU Virtual Museums. In fact, iSpot has been courteous enough to link to the MammalMap and SABAP2 under their survey pages – so there is a tacit recognition of the broad domain of each of these.

Participating in citizen science programs is a really useful and rewarding exercise. Its a great way to do something useful with your photos collecting real or digital dust, and for recording your legacy – the information exists for as long as we can produce electricity to run servers, and in any scientific publications that result. By uploading photos with dates and locations you are contributing to a database that allows one to see where and when animals were documented at various locations, a valuable conservation and management tool – but their value will only be realised through sufficient participation – so register for both now!

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