Wednesday, 27 February 2013

Picarros are a Twitter!!

Want to know more about the current carbon dioxide conditions around the City of Cape Town? Well, if you're on twitter, who can get hourly updates of the current concentrations. Very soon these instruments will also be tweeting the approximate emissions coming out of the city and surrounding areas. At the moment, the instruments are tweeting their observed carbon dioxide concentrations, but when we take into account some basic weather data, we'll be able to tell a more interesting story!

Follow @CapeCarbon to get these updates!!!

Cape Carbon Twitter Feed!

Thursday, 21 February 2013

More on Carbon Dioxide Trends

Here's a really nice animation of the global trends in carbon dioxide through time, from the NOAA Earth System Research Laboratory. It helps to bring home just where we are now in terms of prevailing carbon dioxide levels, compared to how things were in the recent to distant past. (Ed Dlugokencky and Pieter Tans, NOAA/ESRL

Tuesday, 19 February 2013

Recipe for Obtaining Carbon Dioxide Emission Estimates - First Ingredient: Measurements

So...what does one need to estimate carbon dioxide emissions for a particular region? Of course there is more than one way, but I'm going to be focussing on the method referred to as "atmospheric inversion". This term is actually a little confusing because those involved with atmospheric or weather modelling also use the word "inversion" to refer to an atmospheric phenomenon, where usually temperature, changes with altitude, and the layer in which this change occurs as the "inversion layer". I'm not talking about that inversion. I'm referring more to its meaning as "back-to-front" or "wrong way round".

Think of the carbon dioxide concentration at a particular point as a credit card balance. It's the sum of all the spending and payments made on that account. If we only knew what the credit card balance was, we wouldn't know how much had been spent at department store A, at the movies, or on petrol, and we wouldn't know how much had been paid back on the credit card. But, if we knew which places had been visited and how long they had been visited for, and what the average spending (or paying) was at each of these places in the past, we could start making a pretty good guess about what each transaction amount was that resulted in the current credit card balance. So we have to "back solve" what the transaction amounts were - hence the word "inversion". OK ... that's a terrible analogy, but it's the best one I could come up with. I'll try to think of a better one and add it in later.

Using this recipe, we know what the carbon dioxide concentration was at a particular point, we know the way the air travelled before it got to that point, and we know something about what's happening on the ground where that air has travelled. So we have carbon dioxide measurements, an atmospheric transport model, and prior information.

The first ingredient, the atmospheric measurements, need to be extremely precise. This is because, as far as the overall make up of the atmosphere is concerned, carbon dioxide is an extremely small proportion. It makes up less than one percent of the total composition of the air we breathe (well most of the time - more about that later!). Small increases in the concentration of carbon dioxide are actually the result of very large carbon dioxide emissions. If we want to make reasonable estimates of the emissions that are taking place, then we need to know, to the parts per billion precision level, what the change in carbon dioxide concentration is over time and between two different points.

There are only a handful of instruments that can measure to the precision required for an atmospheric inversion study. One of these instruments is the Picarro Cavity Ring Down Spectroscopy Analyser (Picarro CRDS analyser Three of these instruments are located around the Cape Town area.
The Picarro's voyage to Robben Island on the Robben Island Museum staff boat. those 4:30am wake ups to get to the harbour in time.
Getting the the Picarro's to their measurement stations was a challenge in itself. On the Picarro website, they refer to the CRDS analyser as a "portable spot measurement tool" and to its "compact portability". Well, I'm not sure if they've ever tried to carry one of these things up the seven flights of stairs leading to the top of the Hangklip lighthouse. Since I started this job, I've had to join a gym - because a woman's gotta get the job done! But I wasn't alone ... I've had to enlist the aid of family and friendly Transnet lighthouse keepers. As anyone doing a PhD will know - you don't do it alone, your whole family does it with you, whether they like it or not. Given the fact that I was able to get the analyser up there at all means it is pretty portable, as far as gas analysing equipment goes.

Picarro CRDS gas analyser installed at Robben Island
Now if you ever decide to do anything involving air measurements, you better train up on plumbing. Or make friends with a plumber. It seems like a simple thing - suck air in through a tube and sample it at the other end, but there's a lot more too it than that. Most importantly - there can't be any leaks. You don't want to be sampling room air. You also can't just use any old tubing. It has to be a material that will not react with the air and alter the concentration of the air in anyway - what goes in the inlet should be what comes out the outlet. The analysers also don't like get water or particulate matter inside them, so there has to be a special filter in the line which prevents this. And then there are the connectors. These are potentially the weakest points in the plumbing. They come in all shapes and sizes, straight or bent, and with different threads. These have to be suited to the tubing and need to connect to the analyser. The Picarro CRDS analyser has a 1/4 inch Swagelok male connector, and so the plumbing would need to terminate in a 1/4 inch Swagelok female connector. Oh has gender as well.
The more advanced installation including calibration gas, with the VICI rotary valve on the left and its control unit to the right
Just having a inlet tube connected to the analyser is the simplest way to go, but to match up with international standards in measuring atmospheric constituents, it's necessary to check the analyser against a known calibration gas standard on a regular interval, to make sure that it's not drifting off anywhere. That's when the plumbing gets really complicated. An important component in this system is a rotary valve. Basically, it rotates to a new position when told to, and then opens up a different side of the plumbing, and closes the other side off. The first side of the plumbing is the sampling side, and the second part of the plumbing is the calibration gas. Just to make things complicated, the tubing required for the rotary valve is 1/8 inch stainless steal tubing, so there have to be adaptors between 1/4 inch and 1/8 inch.

The Picarro CRDS gas analyser measures approximately once every second, and these measurements are then stored in hourly files. The data gets checked for any anomalies, and then gets converted into an hourly average, which is what finally ends up getting used for the atmospheric inversion.

And that's the more adventurous side of obtaining carbon dioxide emission estimates. It's usually quite fun - but not so much when things don't work out. It's rather disheartening after spending months planning where every little tube and connector is going to go, and then finding out there was a giant flaw in the plan, and needing to go back to the drawing board in the field. But such is the nature of field work and instrumentation.

Thursday, 14 February 2013

Getting into Carbon Science - Part 3

So I guess you're wondering why this is called the Cape Town Carbon Observatory blog, when I've been going on about Kruger the whole time. Well, about a year and a half after completing my Masters, I needed to get a move on with starting my PhD. The questions about when I was starting and what I was going to do were starting to become persistent. I knew that I wanted to do something in carbon science, and was always convinced that it would be centred around the flux tower data, but then a proposal landed up in my inbox that my supervisor was leading, and a large focus of the proposal was on estimating carbon fluxes over a large region, but this time using different technology and science than what I had been working with.

The proposal needed a bit of extra back ground, so I searched up "inverse modelling", and discovered words like "Bayesian" and "Covariance Matrix" which were right up my alley. I discovered that this was the method used to get the estimates published by the IPCC (Intergovernmental Panel on Climate Change Global estimates are derived from hundreds of stations around the world ... but they're not so evening distributed. And so I started my PhD journey.
Map of atmospheric carbon dioxide monitoring stations around the world. From on the 14th of Feb 2013
If you have a look below the equator line, you'll notice that the stations become a little sparse. Particularly the ones on land. So when the IPCC is giving estimates of regional carbon dioxide emissions, and they start talking about Africa, or sub-Saharan Africa, they're basing their estimates on observations that are available at only a handful of stations (and some pretty sophisticated atmospheric transport models). The Cape Point station right on the tip of Africa is probably one of the oldest stations on the continent, whereas the Namibian station is one of the most recent stations.

The goal of the proposed project was to increase the capacity to collect these sorts of measurements in South Africa, and ultimately to be able to increase the density of the network in South Africa. The intention is also not just to become a data provider to the scientific community, but to actively engage with the data, and be able to generate our own regional estimates from the atmospheric measurements.

Since the expertise already existed around the Cape Point Station, and from our group's experience with working with scientific technology, we knew that it would be crazy to try this on our own, we decided to focus in on Cape Town. Scientific measurement equipment rarely comes all neatly packaged in a box, which when opened, automatically deploys itself and works faultlessly for the rest of your days. If only it were so simple. Setting up the monitoring sites and getting the best possible measurements would be a challenge, but fortunately the team at the Cape Point Global Atmospheric Watch station were on hand to assist.
The Cape Point Global Atmospheric Watch Station
We strategically decided to start our first two monitoring sites on the borders of the City of Cape Town, so that we could take advantage of the existing measurements at Cape Point, and the fortuitous location of the Robben Island and Hangklip lighthouses, to get information about the emissions from the City of Cape Town. Why lighthouses? Well, they're pretty tall buildings, they have power (and its important that they always have power or else there would be ships crashing all over the place), and they provide a fairly weather proof environment for the monitoring equipment to live.
A map of the Western Cape region in South Africa, with the yellow markers pointing out the Cape Point measurement station, as well as the new sites at Robben Island and Hangklip. Map generated using Google Earth
The Robben Island lighthouse - an ideal domicile for the measurement equipment
And that's how I find myself heading over to a world heritage site on a fairly frequent basis, for reasons other than historical interest, and dangling from the top of very tall lighthouses with the wind blowing at 80hm/h plus (don't tell the health and safety officer - but don't worry - I'm wearing the appropriate PPE) to fiddle with inlet tubes and weather stations.

Saturday, 9 February 2013

Getting into Carbon Science - Part 2

Working on the flux towers was just the beginning. These flux towers exist under a larger international project called CarboAfrica, which links back to CarboEurope, Fluxnet and Ozflux. These are large international collaborations which link various flux tower projects into a coordinated effort ( There are flux towers measuring every manner of ecosystem, particularly those in the Northern Hemisphere. Through these programs, research projects are coordinated, funding opportunities are leveraged, and data are shared. For anyone involved in carbon science, these communities are essential, because they provide support, share resources, and peer review.

CarboAfrica was my first taste of international science. I was lucky enough to attend two of the conferences held in Africa to present the results we were finding in Kruger. The first in Accra, Ghana, and the second in Pointe Noire, Congo. Both were eye-opening experiences for me, and I made some new friends from all over the world who were kind enough to pass along some of their knowledge and experiences on to me, from the do's and don'ts of the flux tower instrumentation to modelling tips for gap-filling data.

So, what should you know when traveling around Ghana and Congo? Well, Ghana is English speaking, so if you can manage in English, you'll do pretty well. The people there are exceptionally friendly, but terrible drivers. Watching people drive in Ghana makes you realise the importance of proper intersections and road rules. The roads in Ghana are not that great (although they were busy with a major highway project while I was there, which is probably going to be amazing when it's done and change the way people travel there). My boss was along for the Ghana trip, and he wanted to have a look at what savannas were like in Ghana, so we took a bus trip up north towards Kumasi, and so we got to see a lot of Ghanaian driving.

My experiences in the wilds has mainly been around Kruger and similar areas. Here, the largest tree you're going to find is a Baobab,  but that's mainly in the northern parts of the park. Most of the time, the largest tree is going to be a Marula (about 10 -14 m tall),or possibly an Apple-leaf (15 m) or an African flg tree (20 m) if you're in the riparian zone. All pretty impressive, or so I thought. 

Sausage tree (Kigelia africana) not far from the Lower Sabie rest camp in the Kruger National Park, about 12 m tall.
Image of a Ghanian forest ( where trees can grow in excess of 60 m in height.
A more or less scaled drawing of the difference between a 10m tall tree and 60m tall tree

 Although Ghana has experienced a lot of deforestation, the remaining forest trees are incredibly huge.  I didn't get to see one of them up close and personal, but just seeing them out of the bus window, I felt completely dwarfed by the majesty of these trees. Those trees store a lot of carbon. Very roughly, from literature on rainforest tree species, the trunk diameter of a tree that is 60 m tall is going to be about 2 m. Now, there exists a very strong relationship between the mass of a tree and its diameter (this is called allometry). Using a very generalised equation for rain forest species, a tree which is 60 m tall is then going to weigh about 83 000 kg or 83 tons. Now 1 kg of dried tree material has approximately 0.45 kg of carbon. That means that a 60 m tall tree holds 37 350 kg of carbon. Now how much Carbon dioxide does that relate to? Using a similar logic as used here, one ton of carbon in carbon dioxide gaseous form means that you need 2.67 tons of carbon dioxide (since the two oxygen molecules are a lot heavier than the one carbon). Therefore the 38 tons of carbon on this 60 m tall tree would have come from 100 tons of carbon dioxide. In gaseous form, at about 25 degrees Celsius, the volume of one ton of carbon dioxide is 556 200 litres. That means the volume of 100 tons of carbon dioxide is 55 620 000 litres. The volume of an Olympic sized swimming pool is about 2 500 000 litres, and therefore, it would have taken more than 22 Olympic sized swimming pools full of pure carbon dioxide to make one of these trees. That's a lot. When one of these giants goes down, it means that a lot of carbon is going to make its way back into the atmosphere, by one means or another. By the way, if you ever come across an Olympic sized swimming pool fill with carbon dioxide, and you somehow know this (since it will look like a regular old air-filled Olympic sized swimming pool), don't climb in because you will die.

So that was my breakthrough during the Carbo Africa conferences, which were both held in countries with rain forests -  without these forests, this world is going to be an entirely different place to live in. Probably not one that can accommodate humans.

Other things to know about Ghana is that it's really hot, don't leave that sunscreen behind, and it's incredibly humid, particularly in Accra. It's so humid, you could cut the air with a knife.You can bite into the air. Fortunately the local beer is really good. It was a huge relief after a long day to settle at one of the many fine establishments, and have a nice cold beer. The other great thing about Ghana are friend plantains and chili beans. They're delicious.

So that's all about Ghana. Pointe Noire was a whole other experience. When traveling in the Congo, it's a good idea to learn some French. I had luckily done a bit of French while in high school, so I managed to struggle along as I murdered the French language. If you only speak English, it's going to be a bit unpleasant. I did a lot less exploring while I was at Pointe Noire, mainly because I was traveling on my own. so I don't have as many stories to tell. One thing I did remark on was how passionate my French colleagues were about their work in Congo and other countries like Gabon. Originating from institutes in France, many of them had spent years of their lives away from home, working on their sites and with the local people. I found their dedication to their work to be commendable because I'm not sure I could live apart from friends and family for that long, and so far away, adapting to a culture so different from my own.

Wednesday, 6 February 2013

Getting into Carbon Science

Obtaining estimates of Carbon emissions through the method of inverse modelling was not something I had in mind for myself five years ago. I got into the CSIR with a background in mathematical statistics and ecology. I had just finished a three year lecturing position, which I did while completing my Masters in stats, at a nearby university (attempting to teach statistics to first year biology students – fun), and couldn’t wait to start my career in pure research. Best of all, the group I was joining was a systems ecology group, and so I was going to get to do work in both of my areas of interest.

I started off with processing and modelling data from our Skukuza eddy-covariance flux tower. The data collected here provides information on carbon dioxide and water fluxes at a landscape level. This helps us to better understand processes like primary productivity and ecosystem respiration, as well as evapotranspiration. At the same time meteorological variables like air temperature, relative humidity, wind speed and direction, and net radiation are measured, as well as soil variables, like moisture and temperature. This helps us to understand what the drivers are, and also to predict what will happen with ecosystem productivity and respiration under different climate change scenarios.

Skukuza Flux Tower – Kruger National Park
See for more information on eddy covariance methodology 
I was minding my own business one day in the office, doing fun and exciting things in R, when my boss called me up and asked me if I was interested in instrumentation and getting things to work. Looking back now, this was a turning point in my life. If I knew then what I know now, I’m not so sure I would have answered yes. He handed me an old broken PP Systems carbon dioxide gas analyser, specifically for measuring soil fluxes, which looked to me like it had been built back in the day of the first black and white TV, and basically told me to get it to work. At university, when you’re studying statistics or ecology, nowhere are you taught any electronics courses. That’s the sad reality of it. So I was deeply overwhelmed, but fortunately got given the name of a very nice man who was at the manufacturing unit, and was a whizz with a soldering iron, and he helped me to figure out what the problem was. Really – he figured out what the problem was and I watched. That was my first experience of getting down and dirty with measuring carbon dioxide. The next thing I found myself attending a summer school for flux measurements held at The University of Colorado Mountain Research Station. I should have known it wasn’t just so that I could have fun in Colorado.

It wasn’t too long before I was asked to write a program for a datalogger to collect information from a soil moisture probe. This basically entails having to understand how the instrument works, and what instruction to give it to work, and how to interpret the output of the instrument, which is usually voltage, and turn it into a measurement. I’m always amazed every time I wire an instrument up to a datalogger, and it starts giving out actual measurements. It leaves one with a real sensation of satisfaction when the data all looks good. On the other hand, when you wire up an instrument exactly the way the instructions tell you to (or you think you have), and it gives out garbage, that’s an entirely different sensation. Frustration, anger, resentment, disappointment, despair, hopelessness …

This may look like a mess of wires to you, but each of those has its place and needs to correspond exactly to the program written to collected the data
 Before I knew it, I was writing a program to get an entire flux tower and all its meteorological instruments to operate. And not long after that, I was finding myself in the field, attending to the every whim and desire of the instruments. We have two flux towers in the Kruger National Park. When things are working, life is great and the world is a happy place. But sometimes you can arrive on site, and be inundated by every manner of problem that can befall an instrument. Everything from elephants pushing a tree over onto the solar panel, ants squatting in the instrumentation box and causing all sorts of shorts, or in fact gecko’s taking up house – or scratch that – an entire ecosystem existing in the instrumentation box. You’ll also be surprised how much damage the African sun can do to instrument cables. Many of the instruments that we use are shipped in from America or Europe, and having to deal with the kind of UV we have down south here doesn’t always come into the equation. Don’t factor out the wind and rain either. And then there’s human error, which is the kind which causes me the most frustration and sleepless nights. I’m particularly good at making those, and I’m always gobsmacked by how spectacularly wrong things can go when just a tiny little detail is over looked.

Repositioning of the foliage by the local elephant hooligans
 Let me tell you … working with instrumentation is not for the faint of heart.