Thoughts on British ICT, energy & environment, cloud computing and security from Memset's MD
I am feeling quite pleased with myself this week having taken my passion for environmentalism to the next step, by participating in a field work project! My partner, Izzy, is doing her PhD on the rare, protected freshwater plant Najas flexillis, pictured in its local native habitat to the right. You can read about her exploits at her Web site / blog, Freshwater Conservation. N. flexillis is unusual in that it is believed to be the only exclusively sexually reproducing freshwater plant. It also only appears in a few Scottish lochs, some Irish lakes, Scandanavian fjords and, curiously, Minnesota. N. flexillis is an excellent indicator of biodiversity, which in turn is a good indication of a freshwater body’s ability to withstand change and its overall health. N. flexillis is thought to be in decline due to human factors; mainly utrification (increase in nutrients due to factors like fertiliser run off, industrial input, fish farming and sewage works, which cause algal blooms and prevent light entering the water column inhibiting plant growth and leading to annoxia – ie. stagnation) and invasive species which are not native to the area out-competing the local flora (humans have brought all sorts of bad plants with them from overseas which take over and damage lake biodiversity).
The bulk of Izzy’s actual data collection is surveying some of these locations for N. flexillis and recording the levels of abundance, the conditions it seems to like, and the decline over time. She obtained funding for a trip to Scotland and Northern England from Scotting Natural Heritage, Scottish Environmental Protection Agency, the Botanical SOciety of the British Isles, UCL and Memset. She was keen to use novel approaches rather than the usual throwing a double-headed rake from a boat and seeing what you could dredge up, and that’s where I came in.
The main difference was that Izzy and I went SCUBA diving in Glenastlehi loch on Islay to survey for N. flexillis, with the other half of the field trip team, Ian and Carl, using the boat method. As well as being quite crude, raking the bottom of the loch in hundreds of places does disturb the bottom quite a lot as seen in the picture to the left. This is not actually a problem; plants like the bottom being disturbed, but more importantly you can see how it misses a lot! We saw N. flexillis happily sat right where the rake had been on many occasions.
Anyway, in my capacity as qualified PADI rescue diver I was in charge of dive safety. Also, with the grant money we purchased a diving air compressor which was fun and interesting to learn how to use. Without it we would have had to transport about 25 compressed gas cylinders with us! The compressor was a little petrol Honda engine one and and the compressor system the other. It arrived without its manual so I had to learn “on the job” but quickly figured out which knobs did what. You do have to be careful though; it does have a scrubber but it is important not to get fumes and such in the tanks.
Decoding Lowrance .slg sonar files
My first challenge was to attempt to import bathymetry (depth profile) data from the sonar scanner used on the first day’s recon outing. It was an old Lowrance device which made a .slg file. After much Googling I found some apps that could use the data, Lowrance’s own Sonar Viewer app and 3D field pro. I had to spin up a Windoze VM since they are not Mac/Linux compatible, but that was not hard. The issue was that both required the .slg to be converted to a text file first, and the only way to do that was with a propriatary binary called Slg2Txt.exe. It was such a pain to find that I’ve uploaded it here on hopes of helping some other poor person struggling with Lowrance .slg files!
Unfortunately, even though I managed to partially load the data a big chunk of it was missing, and anyway the XML export capabilities were very limited. We got enough to see that most of the loch was quite shallow other than a 6 metre trench in the middle and resolved to use the dive computers instead. We had been expecting that we’d have to be quite ingenious with our dive profiles so that we could avoid reverse-profile diving or having to surface often, which can become dangerous due to the compressed nitrogen we breathe.
Underwater GPS positioning and cartography
As it turns out, the biggest challenge when doing the survey was that we needed to be able to record our location when we found the plant but GPS does not work underwater. I came up with a solution to this; we attached an eTrex GPS in a waterproof bag to our surface marker buoy and synced its clock with Izzy’s dive watch and set it to record our track. Whenever Izzy found N. flexillis she pressed the button on her dive computer to bookmark the site. Back at base, a lovely little holiday cottage, I was then able to import both the track data from the GPS and the dive log to build a picture of where we found it. As well as location we got the depth of the find too. The action shot to the left shows Izzy recording the location of that stand of N. flexillis.
How to import/export data into a Garmin eTrex GPS on Mac OS X
However, importing and exporting data into the Garmin eTrex GPS was also non-trivial! It uses a serial interface connected into a USB port, and on Mac OSX you need something a little extra. Garmin provides what should be a great suite of software in the form of BaseCamp and POI Loader, but actually neither of these could talk to the device!
The first step to get around this was to download and install Prolific’s PL-2303 Mac OS X Universal Binary Driver, which you can download from here.
Next, although BaseCamp didn’t work, with the above driver Load My Tracks worked just fine! We used this for both importing and exporting waypoints, tracks and routes from the three eTrexs we had with us. To upload waypoints we first exported them from BaseCamp as a .GPX file, then imported that into Load My Tracks. For downloading we just reversed the process.
The added problem was that there are no maps for BaseCamp of Scotland, bizarrely – at least none I could find to download from the Garmin shop. Izzy needed to provide Ian and Carl with a set of waypoints in a grid covering the lake for their surface sampling of water clarity, depth and the rake etc. To do this she first made an outline in Google maps and exported it as a .KML file. You can import those direct into BaseCamp, or convert them into .GPX files via a range of online services. However, they appear as a route when imported which is why we just did the outline that way.
Now that we had the outline of the loch in BaseCamp (in lieu of a map) Izzy made waypoints every 30 metres or so in a grid pattern. On our first try she made a route, which seemed sensible, but BaseCamp was too clever for its own good, recognised that many of the route points were basically in a straight line and stripped out the intermediary waypoints! We needed them since it is impossible to otherwise gauge distance traveled on water.
Excitingly, as well as finding N. flexillis in huge abundance we also found large amounts of what we think was Nitella conferacea (see above). Interestingly it was quite abundant in areas where N. flexillis was present but sparse with few other plant species around. Although classed as a macrophyte this Nitella is a tiny little plant, only a centimeter high or so. Despite this we found lots of it and I got some great pictures as you can see! 🙂
Diving in a loch was certainly a very different experience. Due to the peat run off it was distinctly brown as you can see in the pictures. Izzy and I had to stay close at all times to avoid losing contact, while also mantaining perfect buoyancy so that we did not kick up the very soft sediment which if we did completely destroyed visibility. We also had the challenge of entanglement with plants. Although individually they were easy to swim through, they rapidly built up and stopped us in our tracks, as you can see to the right.
Normally buoyancy is not a challenge for expert divers, but maintaining depth within a few CM when you are within 2 metres of the surface in a cold water body using multi-layered wet suits is enormously challenging, mainly due to neoprene compression. At shallow depths the relative difference in buoyancy as you descend is very large; descending from the surface to 5 meters down a soft container of air will be compressed by 1.5 atmospheres of pressure, reducing its volume and thus buoyancy by 33%. By contrast, if you are already at 20 meters (3 atmospheres) descending to 25 meters (3.5 atmospheres) only changes the buoyancy by 14%. This is a positive-feedback loop as well, and when wearing 7mm-12mm of neoprene (rubber with bubbles in it) this can be a significant effect.
Navigation was also very challenging. Sunlight was a great help in terms of keeping one’s orientation, but as soon as we got below about 1.5 metres or the Sun went in (it was mostly overcast) that was impractical. The low visibility and stopping frequently to note locations meant we were easily disoriented. My main job underwater was simply navigation, and after the first day where our path was decidedly wonky I realised I had to look at my compass continuously just to stay on track! The plants didn’t always want to help with that either, as you can see. 😉
We also got a real demonstration of the old diving adage that “depth is all about perception”. Izzy and I are used to diving to 10-30+ metres in the crystal clear waters of the Carribean and Red Sea, where sunlight penetrates easily to those depths (albeit with red light filtered out). Because of the peat and general murk sunlight rapidly vanished as we descended below 2.5 metres into the trench in the middle of the loch. It was an extraordinary effect, like the sun being switched off. By 3.5 metres we had to use our torches and by the time we got to the bottom (5.9 metres) we were in utter, pitch black. In all my hundreds of dives I have very rarely been scared, but this was undoubtedly the most frightening SCUBA experience of my time to date! Used to being able to feel like the predator, with the bottom beneath me and being able to see clearly above me and around me (even at night in our usual dive sites when there is lots of light once you allow your eyes to adapt), being unable to see anything beyond the cone about one metre long and wide from my dive torch was very scary. The astonishing thing is that when diving in the aforementioned warmer locations that depth would be considered very shallow – the depth where you’d normally do a safety stop under the boat!
On the final day we switched to a slightly different project. Normally ecologists don’t get in or under the water, and as such not many researchers have attempted to determine the fluidity of the lake beds. This is frequently done on land or around the edges of water bodies using a device called a shear vane (the thing in Izzy’s right hand in the picture – so on the left) which you stick in the ground and twist until the earth shifts, at which point the marker records the force required. Ian had developed a shear vane designed for use underwater in the very fluid sediment one finds there. The main difference was therefore much wider vanes. (FYI, the thing in her other hand is the Garmin eTrex GPS in its waterproof baggie).
Since loch Glensastlhi was actually quite shallow (mostly about 1.4 metres) and we wanted to record additional information, after some experimentation Izzy and I adopted a new technique for this experiment. She remained on the surface with me underneath, her providing nagivation – mainly by reaching down and grabbing my tank to point me back in the right direction now and then (I kept twisting around while turning the vane). When I found a suitable location I would signal her and she pressed the button on the GPS (still in its baggie) to mark a waypoint. Meanwhile, I took three samples of sediment shear stress in a one meter square and recorded the waypoint number (it goes up by one each time), shear force, depth and relative abundance of N. flexillis and other plants (using five categories) on my arm-slate.
This picture shows the shear vane embedded in sediment at about 1.2 metres down (it only goes 10 cm into the lake bottom), and you can see where the marker has moved to after I’ve twisted it until it starts to slip (about 34 on the outer scale). There was a very clear correlation between sediment fluidity and distance from the shore, as one would expect. The surprise is that from my subjective experience, without having seen Ian and Izzy’s analysis, there was little obvious correlation between sediment fluidity and N. flexillis abundance. Generally sediment fluidity is considered to be important to N. flexillis and one of the reasons it gets out-competed by invasive species in many water bodies, but I’m now not convinced. It seemed to be quite happy in a huge range of sediment squishiness.
Unfortunately we had a bit of a scare on this last day and I got to put my rescue diver skills into practice for real, making mistakes in the process, but also learning valuable lessons.
Perhaps most excitingly from this expedition is the knowledge that we have now almost certainly been to places on the surface of the earth that no other human has ever visited! There have never been any other underwater scientific expeditions to that loch and it is extremely unlikely that anyone would want to explore the murky depths for fun, especially given the remote location and how hard it was to transport the very heavy dive gear up and down the hill from the nearest road access to the shore. I am now resolved to get my dry suit and ice diver qualifications to explore more uncharted underwater territory! Izzy and I also both want to try inland blue hole diving; there are some fascinating environments which might provide analogues for extraterrestrial life environments – a first step of our Master Plan to one day (assuming we figure out immortality ;)) venture to Keppler 22b and other Goldilocks planets in Sol’s vicinity.