Blink and you'll miss it

Whoops, it's August and there hasn't been an entry since February. This just reflects high levels of busy-ness and also sometimes feeling that it wouldn't be appropriate to blog about some of the administrative things I was dealing with (which possibly makes things sound more exciting or contentious than they ever are!)

In May I was in Nantes for my first ever SETAC EU conference. The conference kicked off with some traditional dancing and music which was very much like the bagpipes.

Traditional dancing opened SETAC EU in Nantes plus loud pipes

I was there because there was a special session on microplastics in the environment which was relevant to some work we're doing (read about our preparation for the experiment here) which I've learnt is testing the trojan horse or vector hypothesis, i.e. can plastics adsorb pollutants which are then passed on to what ever organism eats the plastic. A whole bunch of York people were there including:

Jo Witton with her poster on pesticide heterogeneity

Mohd Firdaus Mohd Anuar with his poster on nanopesticides

Delegates looking at posters in Nantes

It was my first SETAC EU meeting and I quite enjoyed it, there were a few very entertaining talks but I fear it will be remembered in SETAC folklore for the very long lunch queues (which I forgot to photograph).

In June I was at the Mineralogical Society Environmental Mineralogy Group Research in Progress meeting hosted by Bristol Earth Sciences department and admirably organised by Oliver Moore and colleagues. Lots of good student talks but here the most memorable thing was that the hotel the organisers recommended that I stay in had complementary sherry in the room. I'm not a sherry drinker so I didn't try it but it seemed rather odd to me, and I almost knocked the decanter over!

Free sherry in all rooms at the Berkeley Square hotel, Bristol

July brought two earthworm events at the Leeds univerrsity farm as part of our SoilBioHedge project. On the 19th July we were recording for a BBC York radio programme - Yorkshire Farming - hosted by Gareth Barlow. You can hear our episode here at least for a while. Apparently the worms bit is on after about 40 minutes. I've got an MP3 file of the programme but I don't know how to upload it to this blog site which only does videos. The most bizarre sight was the pink gazaboes that Richard Grayson and Joe Holden were using to keep the sun off their infiltrometers which they use to measure the pore distribution in the soils.

Jonathan Leake and Gareth recording

A pink Frozen gazebo - hi tech field gear

The infiltrometer below the gazebo

Later in July we were back at the University farm sampling earthworms, or at least searching for earthworms. As part of the SoilBioHedge project we're sampling earthworms throughout the year to get temporal trends of earthworm distributions as well as the spatial distributions which are the main aim of the project. Earthworms are about 90% water and in the summer when it is very dry they either aestivate (a bit like hibernation), burrow very deep or (I'm afraid) dry out and die. So, typically you have very few earthworms in the summer. So it was a bit odd, going out to sample in the knowledge that there wouldn't be many earthworms there. To make matters worse, the soil was rather solid, though interestingly more solid in the arable than pasture fields - an important scientific observation related to compaction of arable fields. In the end we were using hammers to break up the arable soil after sampling it with the aid of a pic axe to get through the upper hard layer. We did find some earthworms but not that many.

A slightly pixilated aestivating earthworm. They create a void, line it with mucus and then coil up and wait for moister conditions.

This is one of the pasture fields. You can see it is more overgrown than on previous sampling trips (December 2015)

 The crops strips have grown as well.

Martin digging pits in a crop strip whilst Josh and Miranda sort soil. You can see how the crop strips are well developed compared to in December 2015.

Jamal, Josh, Martin and Miranda sorting through soil next to a crop strip

The full arable fields posed a more entertaining prospect for digging pits....

Jamal, Miranda and Martin deciding where to sample in an arable field. You can see the crops are far better developed than in October last year.

Where as the full grown hedge was less fun....

Jamal digging a pit in the hedge for sampling

Despite the hot weather and baked soil it still managed to rain a bit so there was also sampling in the Diary building (which is where the hammer was used - no squashed earthworms though!).

Sorting through soil in the Diary building during a rain storm

So that brings things almost up to date. I'm off to Nanjing on Monday for another project meeting follwoing winning funding after that meeting in April 2015.

It's not a pantomime, it's a family reunion!

Yes, just like buses, nothing for two months then two entries!

This morning I was reminded of York's panto star Berwick Kaler's regular line "it's not a pantomime, it's a family reunion". I'm here with Liane Benning, who is still kind of at Leeds but also now in Germany. On i18 (microfocus XAS, see previous posts) was Iain Burke from Leeds accompanied by Doug Stewart and a bearded Andy Bray looking at vanadium in steel slags (incidently I'm wondering whether Iain makes all his postdocs grow beards, it seems to be taking a "team look" a little too far).

Doug Stewart, Iain Burke and Andy Bray on i18 - the smiles are undoubtedly due to the quality of the flapjack being consumed

Next door on B18 (bulk XAS, never used this beamline) was Caroline Peacock, also from Leeds, working with Fred Mosselmans on molybdenum in aquatic sediments.

Caroline et al.

And then Paul Hallett (Aberdeen, I'm working with him on RedSoil, a NERC - NSFC funded project on the red soil critical zone in China) is on i13 which is an X-ray tomography beamline though he has gone home with a day to go, presumably because he's driving and it's a long way to Aberdeen.

I sometimes think that there ought to be an official circuit race of Diamond - it would make visits here more exciting if people were competing for the best time around the ring. However, if such a race did exist (and I guess I should stress strongly that it doesn't) then the management seem determined to up the ante - there are now three sets of pipes that block the straight route so that what would have been a simple sprint has now become more of a steeple chase.

Stair 1

Stair 2

And would you believe it, stair 3

There are excellent science reasons for these long pipes, tapping off various wavelengths of electromagnetic radiation for experiments (just don't ask me what they are!) but they have broken up the circuit. It also reminded me of the, possibly apocryphal, story that when Royalty visited Daresbury (Diamond's predecessor), the beam had to be turned off because a pipe that crossed the circuit around the synchrotron had to be cut out for the visit so that the Royals wouldn't have to duck underneath it. Perhaps that's why they've gone for bridges at Diamond!

Adventures at Diamond

Much to my surprise there's been no entry since December. As Head of Department my life has been taken up with budget setting and the like which is not such fun. However, I have escaped for a day or two to do some science back at Diamond.

I'm here with a remarkably relaxed Liane Benning to do some STXM - scanning X-ray microscopy on i08 helped by the beamline scientists Burkhard Kaulich, Tohru Araki and Majid Abyaneh.

A relaxed looking Liane, i08 clearly agrees with her

Avid readers will be familiar with Liane's and my adventures on B22 looking at amorphous calcium carbonate in earthworm secreted carbonate balls. It's much the same here only you get to wear silly clothes when you put a sample on.

Fashion conscious as ever here I am in the room with the STXM

i08 can look at things in far greater detail, i.e. smaller areas, higher resolution, than B22. We hope to identify areas of calcite, areas of amorphous calcium carbonate and then identify differences in the organic molecules present either in or between these areas. This is really a look see - spotting low concentrations of organic molecules on the basis of their C signature against a background of carbonate that containts, the clue is in the name, lots of carbon, is potentially challenging but you have to try these things.

The i08 control screens

So far things look fairly positive. By looking at calcium we've identified areas that appear to be different forms of calcium carbonate, now we are mapping out the carbon to see if there are any differences that match onto these. More later, fingers crossed.

Typical spectrum from one area of carbonate - looks rather amorphous calcium carbonate like

Whereas this spectrum looks far more calcite like

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.

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!

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
re-establish.

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.

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