For more information read Cai’s non-technical PhD summary.
March 2015: The Open Source Generation
I’m reading a book at the moment called “Cryptocurrency”. It documents the astronomical rise of the bitcoin technology. Pundits think these new “cryptocurrencies” could revolutionise the way our financial system works. Bitcoin’s software was written by a mysterious character called Satoshi Nakamoto. He gave it away for free to the world; for all to expand and evolve. This software is Open Source1, and I think this term represents a major hallmark of our tech-savvy generation. In my research, I use loads of Open Source software all the time… here’s some of them, with fun facts:
VisualSfM The plug ‘n play 3D modelling application written and maintained by Changchang Wu. Though not necessarily the best scientific tool available to geomorphologists, I used this to explore the world of photogrammetry. Has been at the forefront of some excellent crowd-sourced data projects2.
MicMac The best scientific tool available to geomorphologists. France’s IGN developed this Linux-based software as an alternative to its commercial rival Agisoft. MicMac’s special in that, because of its Open Source status, numerous contributors have developed a huge variety of tools to maximise the accuracy of the feature you’re trying to model – be it a landscape from a plane, or the local skate park with all it’s curves and corners. This is my tool for choice for measuring erosion and accretion along saltmarsh creeks.
Ubuntu, or “Human-ness” in the Bantu languages of Southern Africa, is a free operating system alternative to Windows and Mac. I use this Linux-based system to use the next programme in the list. They have a penguin mascot named Tux.
Meshlab A clean, crisp way to view my point clouds from any angle. This programme is used to visualise and store the output in several ways. Especially valuable for creating “watertight” models needed for 3D printing!
CloudCompare Another marvel to come out of France, this software provides a highly accurate means to detect change between two “before-after” point clouds. Initially developed for use in industrial applications by Daniel Girardeau-Montaut, CC can now be applied to measuring change in ecosystems… like erosion and accretion.
GCD Short for Geomorphic Change Detection, this excellent tool works in a GIS to quickly examine erosion and accretion over landscapes. It was developed by Joe Wheaton in Utah State University in a bid to standardise the way we account of the error involved in each stage of data processing, to separate “true” change from the “noise”. I’ve managed to generate some fantastic visuals showing how deposition and erosion have shifted tidal channels and caused marsh erosion… they also look like pieces of modern art.
QGIS Gary Sherman’s brainchild, The “Q” stands for Quantum. I admit, I’m stuck in ArcGIS at the moment, but Q can do things Arc can’t… And I’ll make the leap for sure one day.
R A scientist’s best friend. Called “R” as to annoy “S” (an excellent commercial statistical programme, whose makers started charging through the roof to use it), a pair of developers in New Zealand decided to undercut them with their open-source alternative.
Three things strike me looking at this list.
- It’s all very international
- Many have spawned in the face of rising costs for software
- The software has often been created by (very talented) individuals. These individuals clearly had a lot of passion and pride in both making and sharing their tools. Each one of these Open Source tools were downloaded from something else very much Open Source… Tim Berners-Lee’s World Wide Web3
Just looking at most of the examples above, there seems to be a movement to resist against established commercial tools, to improve them and share them freely. Are we on our way to the Garden of Eden 2.0? Could this be Paradise, for the data-bloated, software-starved scientist? I think we’re riding a big digital wave… I wonder where it will take us?
1https://www.youtube.com/watch?v=a8fHgx9mE5U
2https://inside.bangor.ac.uk/node/17784
3http://www.ted.com/talks/tim_berners_lee_on_the_next_web#t-118860
January 2015
A while ago, I attended a training event that told me who I am as a person, and how I work. As it turns out, I’m an extroversive-sensing-feeling-perceiving individual. In essence, this mix makes my mind a lightning storm – random flashes of inspiration and intention leave scars wherever they strike. And my desk, I fear, betrays an insight into the mind of this PhD student.
It is a confused tangle of structured ordered neatness and labyrinthine chaotic mess. Surrounding the back and sides of my desk is the office divider, which serves as a blank blue canvas of creativity. I have a motivational quote by Lord Kelvin pinned to it, who reckoned “When you are face to face with a difficulty, you are up against a discovery”. I also have pinned to it a sincere endeavour for order. Labels read “Chapter I: Resilience Theory”, “Chapter IV: Slump Blocks”, “Figures”, etcetera. Beneath these headings is a sad state of affairs. Papers folded open with half-read intentions; Old Faithful Waitrose coffee cup – stained and bruised but still recycled; an empty Chicken and Mushroom Pot Noodle. Then there’s my survey equipment. Neat and ordered columns containing scribbles of data sit in a muddy weather-writer; a camera used for surveying – pictures downloaded but itself lying among empty Mini Cheddar packets and pencil shavings; two knives, which used to serve to spread butter neatly on toast, now lie contorted on my desk serving instead as improvised camera mounts. My monitor display has a folder for everything, like animal pens in a well ordered barn. Still, apps and documents roam free across my desktop landscape.
Other PhD desks seem to be equally as conflicted as mine. Opposite me there’s a well maintained in/out tray… with a small box of earth under the table. I’m sure if he attended the same course I did, our minds would be alike. Reflected in our structured unstructured desks. Might make for an interesting paper actually…
September 2014: Anecdotes
People often go for a stroll to enjoy the majestic scenes of the Glaslyn estuary. On a clear day, you can see the peak of Snowdon standing out proudly; it’s jagged, broken edges in stark contrast to the pure, unbroken blue sky behind. Lower down are the incandescent greens of the deciduous forest that flank the estuary bank. Nestled in its midst, you find Portmeirion and its eclectic spires and domes coloured in a fashion that would make Gaudi proud. Finally, before you lies the massive expanse of the sand flat, broken only by ribbon-like channels that criss-cross its surface. Here swallows dip and dive in the evening summer nights, catching flies stirred up from their mud holes as the tide creeps in. The marsh makes a good viewing platform to enjoy these wonders, and is the place that I call my office.
One thing that always surprises me about fieldwork is people. Birders, ramblers and dog-walkers see me with strange-looking instruments and inquisitively come over to see what I’m doing. The conversations always go as follows:
Me: “Hi!”
Visitor: “Hi! What are you doing?”
Me: “I’m a PhD student at Bangor University, looking at both short- and long-term changes to the marsh here.”
Visitor: “I’ve been coming here for years…” After this sentence, I get an anecdote.
This always surprises me – in two ways. Firstly, I always expect people to ask about my work, yet that first sentence I give is usually enough to abate their curiosity. Secondly, I’m a stranger, yet people still choose to open their hearts and tell their stories. I’ve heard how a land dispute drove a farmer to attempted suicide; the acceptance of a father over his son’s sexual orientation; the pained account of a locally revered author, whose success should not be so graciously celebrated owing to his dark deviances and misconducts; the grievances of a mother who’d lost her only son.
Maybe something about this estuary’s serenity makes people open up, and want to share their stories. I feel honoured every time a stranger chooses to confide in a stranger like me. It is small moments like these that make working in such a beautiful landscape all the more dramatic.
