Tuesday, 22 December 2015

Happy holidays

Today I finished my marking from Autumn term. I love teaching but hate marking. I'm sure the students don't enjoy my assignments either. There must be another way....

Still good to have got that done. I also managed to clear my inbox and pack my office ready for our move to the new building week of Jan 4th. So all told I think I'm ready for Christmas.
No emails! A rarely seen gmail screen

The visually attractive green wall on the front of our new building

Kirsty at BES in Edinburgh talking about earthworm - plant communication
Last week Kirsty and I were at the British Ecological Society annual meeting, held in Edinburgh this year. I really enjoyed it, some thought provoking plenary talks and I met some interesting people that I didn't know previously.

The week before we finished the earthworm sampling - generally the weather held although we did spend a little time working inside when it was drizzling.

Working inside in the Diary building kept us warm and dry at times   
But in the sun it was warm enough for   

lunch outside

Miranda and Omar taking soil measurements
Now we just need to identify the earthworms - over to David Jones for that.

Sunday, 6 December 2015

Back in the field

We were back in the field on Friday sampling earthworms for SoilBioHedge. We last sampled in April. We're back sampling to look at any seasonal variation in the earthworm distributions between the hedge and the centre of the fields. But also, now our ley strips have been established we can start to see if they are effecting earthworm distributions.

An arable ley established in pasture (Sub paddock field)
Sorting through the soil using the truck as a work bench

Happiness is a pile of sol and earthworms!
Sampling at this time of year is always a lottery. We were supposed to start on Thursday but the forecast was heavy rain so I cancelled. Needless to say, it didn't rain much, at least in York. Friday was chilly but fine and we got a fair amount of sampling done. Spring sampling involves sitting in sunny fields, winter sampling standing up and working off the truck so we don't get rheumatism! We have Monday and Tuesday pencilled in to finish this tranche. Weather is forecast fine so far - it might even feel slightly warm!

Thursday, 12 November 2015

Chile Day 5

The role of earthworms in agriculture and
the environment
Yesterday I gave my talk. It was due to start at 1200 and we started, according to Chilean tradition as Alexander informed me, at about 1215. There was a good turn out, 50 plus people. I talked and was translated for about 45 minutes and then we had over 30 minutes of questions. I was very impressed by the number of student questions - far more than I usually get in UK seminars. Many thanks are particularly due to Kooichi Vidal who translated as we went along.

Yesterday I also completed the introduction of the paper and Pedro and Jose worked on regressions and tables for the results section.

Today, the main order of business was a field visit with some undergraduates to a contaminated site that people are using phytostabilisation on. Alexander was keen we set an example on timing. The trip was scheduled to leave at 1430. At 1435 we started to go to the bus.....prompt for Chilean time.

Phytoremediation has two main forms - in the first you use plants to extract contaminants from the ground. This is called phytoextraction. It works really well in the lab. and usually doesn't work in the field. The other main methods is phytostabilisation. This just involves getting plants to grow on "nasty" soil to stop the soil blowing away as dust and causing health problems when it is inhaled by people.

The copper smelter in the background
with the degraded "soil" in front
The site we looked at is on the Puchuncavi, down wind of a copper smelter. The soil is developed on old sand dunes. The fumes from the copper smelter acidified the soil and deposited lots of copper and some arsenic. The plants died and the organic matter content of the soil slowly went down.

Gully erosion - the soil is effectively
 sand with few if any roots to hold it
together. Gullies develop when it rains.
The soil now is pretty much sand and subject to lots of erosion.

Alexander's field trials. Along the
 fence are sandy "control" plots - the soil
as is. The plots in front of the people  had
organic matter added allowing plants to
Alexander has run several field trials here. He tried growing plants to take up the copper out of the soil but the copper stayed put. However he was able to add organic matter to the soil which helped plants grow and thus reduce erosion - an example of phytostabilisation.

Some of the pretty yellow flowers
growing on the site.
On the way back alexander spontaneously said that he would buy the students dinner (and the bus driver) so we stopped in Con Con for some Empanada - effectively Cornish pasties, very tasty.

We also made some more progress on the paper and discussed some other things we needed to do before writing it up fully.

Last day tomorrow.

Tuesday, 10 November 2015

Chile Day 3

The best hotel in town
So yesterday Jose drove me to Quillota and my next hotel - the Open Hotel. Contrary to reports it isn't the only hotel in town so "the best hotel in town" label given it by Alexander grows slightly in significance! It is indeed next to the railway line but the Copper trains only go past a few times a day.

At the hotel I was introduced to Alexander, Pedro and Victor. Pedro, like Jose is an ex MSc student now helping Alexander with research, Victor is a current MSc student. We then had lunch. Lunch is the main meal of the day in Chile.

The Quillota Agronomy school campus
After lunch we drove out to the Agronomy school which is on the edge of Quillota just into the country side, very quiet. There are about 500 students in total - undergraduate and MSc.

I was given an office, told where the kettle was and given a tour of the labs. These are pretty good with most of the stuff that I'd expect in a basic UK soils lab.

My office
A soils lab. I'm pretty jealous of the space
for soil sieving - I'm hoping we get
something similar in our new building

After the lab. tour I was bombarded with data that Victor, Pedro and Jose have gathered and was told that the idea of the funding was that we wrote a scientific paper. In essence there is an earthworm test you can do to see if soil is unpleasant or not. You get a container fill one side with your test soil, the other half with a "nice" soil. Then you put earthworms in the middle of the container and see which soil they go into. If the test soil is unpleasant they avoid it and all go into the "nice" soil.

The experiment that Victor has done is to investigate whether this test could be used to assess Chilean soils for metal contamination - there's a lot of copper mining going on and it can contaminate the soils. The challenge is that other stuff can make soil unpleasant for earthworms and so working out why an earthworm doesn't like a soil isn't always straight forward. Anyway we pondered that and then it was time to go home. Alexander drove me into Quillota to see the sights - took about 5 minutes - then we had a bit of a drive to a restaurant that turned out to be closed and got a puncture so we had to change a wheel. After that we kind of gave up on food and Alexander dropped me at the hotel.

Jose, Alexander, Pedro, Victor and myself 
tucking into a pastel di chocio washed 
down with custard apple juice
Today we made some progress on looking at the data. Despite a lot of uncertainty the  avoidance test does actually spot the contaminated and clean soils quite well. So we now have a plan for a paper as well. At lunchtime we went back to the restaurant that was closed yesterday (no punctures this time) and had a "pastel di chocio" which is like a pie filled with mince, egg, olive, bits of chicken etc. and topped with mashed corn. Apparently this is traditional Chilean cuisine, it was OK. I also had a custard apple fruit juice. Again this was OK but I don't think that I'll repeat the experience.

This evening Alexander tried to take me to a Peruvian restaurant but again it was closed - I can see a pattern emerging! Tomorrow I give a talk to the MSc students. It will be translated into Spanish as I go along. I'm sure it will be a big hit!

A custard apple

Sunday, 8 November 2015

Chile Day 1

Ola! from Chile,

for a change, I have travelled over two days which have been strike free, all very pleasant.

I am here in Chile on the invitation of Dr Alexander Neaman, I've never been to Chile and it's always nice to be asked so here I am. I flew out via Madrid yesterday and arrived this morning. I was met at the airport by Jose Verdejo - he is a very cheerful and friendly sort. I fear the photo doesn't do him justice!

Jose dropped me at the hotel in Vina del Mar and will pick me up tomorrow to take me on to Quillota where Alexander and his team are based in the School of Agronomy, Catholic University of Valparaiso. A bizarre (at least from a UK perspective) thing is the way the trip is funded by the Chilean funding authority. I have to pay the hotel costs but rather than claiming the money back from Fondecyt, the Chilean research funder, I'm given a per diem to spend. Given that £1 is currently worth about 1000 Chilean Pesos this makes things look rather grand - it reminds me of when we did Turkish field work back when I was a postgrad. and we all ended up, near enough Lira millionaires.

This afternoon I walked to the station and went to Valparaiso, the local big city. On the way there I saw pelicans. Valparaiso itself is built on hills so has lots of funicular lifts to get you up and down the slopes which is quite fun. There were some good murals on the walls in one part of the town but other than that, perhaps Valparaiso guards its charm carefully!
Pelicans  - the rock colours show what pelicans do!

Concepcion ascensor - the first of the funiculars and originally powered by steam.

The view across town

The first of several murals in the Concepcion districut

I thought these painted steps were fun as well

I'm pleased to see the hotel has both tsunami and earthquake safety advice - don't use the lifts in either case, if there's an earthquake stay away from the windows, if there's a tsunami get as high as you can. Jose picks me up tomorrow at 11. Before then it's an early night to catch up on some sleep but also I need to finish writing a talk for Alexander's MSc students. As long as the barrel organ player on the plaza below my window stops playing before I want to go to sleep all should be fine.

A quick catchup on various things

I'm horrified to see that I haven't blogged since July. I kept on meaning to but I've clearly been too busy.  Since July I've become head of department and it has all been a bit of a whirlwind. None the less there has been time for a few bits and  bobs of fun.

Kirsty and I were busy in September at Yornight, again telling anyone who would listen how wonderful earthworms are.

Then in October I got invited to a European Chemicals Agency workshop in Helsinki that was all to do with risk assessment. I'm still not entirely sure why I was invited but I'm very found of Helsinki and haven't been since that viva in 2013 so went along and chatted to various old friends from the UK and the Netherlands.
Here we are in a debating chamber discussing risk assessment
I love the view across Helsinki harbour to the islands

and here's Helsinki's cathedral

 The railway station at Helsinki is fine as railways go but I love the outside - these two stone figures holding the lights always remind me of The Pillars of the Kings from the Lord of the Rings

Then in October we were out at Leeds University farm looking at the SoilBioHedge project - it's come along a lot since we were sampling in April. Now in the arable fields the ley strips are well established, hopefully providing superhighways for earthworms to crawl through from the hedges into the arable soil.

Monday, 13 July 2015

Food at Diamond improves?

It's 0715 on our final morning. The beam goes off at 0900 and a new set of victims / scientists arrive for their beamtime. Over the last two days we've taken lots of element maps and measured the form of calciumj and strontium in four earthworm species - Amynthus and Pontescolex as initially planned and, thanks to John and Stephen's hero run to Cardiff, Eisenia fetida, Lumbricus rubellus and Lumbricus terrestris. So two Azorean earthworms then a compost worm and two good old fashioned worms from  UK soils. We've checked out the calcium and strontium in the skin (epidermis), liver like tissues (chloragog) and the calciferous gland (Amynthus doesn't have one, E. fetida's is rather different from that of Pontescolex, L. rubellus and L. terrestris). We've got some lovely images and there is possibly a story emerging about how calcium is stored in earthworm tissues but I think that will need to be digested a bit before something emerges.
A calcium map of a L. rubellus calciferous gland - you can even see the structure in the gland - the vertical stripes. The image reminds us of a fish.

The food has been instructive! Last visit I drew the conclusion that most food served in the staff canteen was beige and not great. I may be forced to reassess. Because of the open day on Saturday food on Friday and Saturday was served in the accommodation block, Ridgeway house. These guys are set up for breakfasts but have a small kitchen. I'm sure that they did their best but lunches and dinners were less than inspiring.

Standard lunch and dinner choices at Ridgeway house - the ubiquitous baked potato, beans, sausages and soft veg.

On Sunday the staff canteen was open and it shone in comparison to Ridgeway house. So perhaps I take all those food reviews back!
Stephen, John, Dave and Pete (clockwise from left) enjoying dinner on Monday evening.

All told we've got quite a lot done, working in shifts. Five people seems to have been a good number to run things, get enough sleep and have time to get to Cardiff and back for more specimens.

John and Dave on the beamline.

Pete either catching up on some sleep or deeply pondering our data.

Stephen organising files.

Saturday, 11 July 2015

Beamtime fun at Diamond

I don't think I've been on this beamline since 2012 and the famous "which chocolate bar floats the best" experiment. On that visit we were looking at the calcium carbonate secreted by earthworms and it's pretty much the same system we're looking at on this visit, but in more exotic earthworms.

The reason we're at Diamond again is (or was) to investigate how earthworms deal with carbon dioxide. Specifically we're looking at earthworms from the Azores that live on the sides of mountains with high levels of carbon dioxide flowing through the soil that they live in. Normally these high levels would be sufficient to suffocate the earthworms but not in this case. There are two types of earthworm that we're looking at, Pontoscolex and Amynthus. Pontoscolex has a calciferous gland and so perhaps locks up the carbon dioxide by precipitating it as calcium carbonate whereas Amynthus doesn't have a calciferous gland. There is an enzyme, carbonic anhydrase, that moves carbonate around and contains zinc. Luis de Cunha, a postdoc. from Cardiff, has shown that zinc is concentrated in the skin of Amynthus, so we thought that perhaps that is where the carbonic anhydrase is as well and maybe Amynthus copes with the carbon dioxide by precipitating calcium carbonate in its skin. Two days in and we can say that this isn't the case which isn't particularly exciting but there you go.

The way this beamline works - i18, microfocus spectroscopy - is that first you section your sample which is a skill in itself, done on this occasion by John Morgan in Cardiff.
Thin section, about 6 cm x 3 cm. The faint white patches are slices through earthworms.

You then place these in the beamline and zap the section with X-rays to produce an XRF plot - this shows you the distribution of the elements you're interested in, e.g. calcium for us.

The top screen shows a close-up optical microscope image of our sample. The lower screen shows the XRF map. You can see a bright white diagonal line that indicates high calcium. From the optical image we can see this is associated with the earthworms chloragog - a liver like organ.

Once you have the map you can identify individual points that look like they have an interesting concentration of the element and do something called XANES (or EXAFS depending on precisely what you want to know). XANES is a fingerprinting technique - different forms of the element have different patterns and this allows you to work out what form your element is in.
Here, the lower screen shows a wiggle - this is a XANES spectrum, characteristic of the form that the calcium is present in the chloragog. By comparing with standards we can see that it looks like the calcium is present as a calcium phosphate. 

The controls look rather intimidating but as long as everything works there are relatively few buttons to press and we have had excellent instruction from the beamline scientist Tina Geraki.
Tina Geraki on the beamline.

i18 control screens
So we've shown that our hypothesis was incorrect - there isn't calcium carbonate concentrated in the Amnythus earthworm skin. We now have two more days beamtime so John Morgan and Stephen Short have high tailed it back to Cardiff to get some more samples so we can do a fuller comparison of calcium in calciferous glands.

Today has been a little odd as there is an Open day across the entire Harwell campus. True to the promises they made there were dinosaurs and volcanoes. Everyone seems to have had fun.
A dinosaur overlooks members of the public. Scientists use the synchrotron to investigate chemical traces in fossils.

and a model volcano - not sure what that was all about