Robots and worms - worm scans rather than CAT scans?

Just at the end of the year I visited Prof. Sacha Mooney at Nottingham University to look at the Hounsfield X-ray tomography facility. In brief X-ray tomography allows you to take images of stuff that isn't see through to visible light. I was interested in whether we could use it to see earthworms in soil.

The facility itself is funded primarily to take photos of the root structure of different genotypes of wheat as part of a project designed to optimise wheat varieties for food production. The whole thing is very impressive.

There is a big greenhouse full of drainpipes in which the wheat is growing. A robot trundles round this greenhouse picking up the drainpipes and taking them to the tomography unit.

You can see the robot behind the plants in drainpipes here.

The robot picks up a drainpipe and brings it towards the tomography unit. You can see the door to the tomography unit beginning to open.

The robot deposits the drainpipe and retreats.

On the other side of the door another robot picks up the drainpipe and puts it in the scanner.

 We also had drainpipes (with soil and earthworms) but we used a smaller scanner to look at them.

A smaller scanner unit that we used to scan our 30 cm high 12 cm diameter drainpipes

It took about 30 minutes scan time then some processing time by senior research fellow and X-ray tomography whizz Craig Sturrock to produce the following film in which you can see the earthworms in pink and the burrows in yellow. So now we can actually see where earthworms are in the soil. Incredible.

The other nice thing about visiting Nottingham is East Midlands Parkway - you get an excellent view of the Ratcliffe-on-Soar cooling towers!

Cooling towers at East Midlands Parkway train station

Welcome to Kirsty High

As of the start of the year Kirsty High joined the lab. to work with myself and Jane Thomas-Oates on our "Whispering in the dark" project. Kirsty has a background in analytical chemistry and archaeology and is perfect for the role,

Kirsty in the plant growth room (we let her out if she behaves!). You can just make out some plants growing in their containers behind Kirsty.

Kirsty has been playing in the lab. sorting out a few techniques and earlier in the week started the first "proper" experiment. Already we have some interesting results - plants growing in soil that has been sterilised don't do as well as plants in "normal" soil. Next week the earthworms will go in as well. We wait with baited breath to see if the earthworms start talking to the plants to encourage them to grow!

Winding up the PhD stagger

Last week I did two PhD vivas. PhD vivas are the rite of passage that PhD students undergo at the end of their PhD. After 3 to 4 years work, researching a particular question they undergo an oral examination to test their knowledge about their research field. Hopefully these are usually enjoyable occasions - an opportunity to talk about what they have been doing for the last 3 or 4 years but my recollection from my own viva (almost exactly 20 years ago today) is that they can be somewhat stressful occasions as well with the candidate wondering precisely what flaw in the thesis each question is designed to expose (in reality the answer is usually none, the examiners are on the candidates side and just give the candidates as many opportunities as possible to demonstrate ownership of the thesis!).

I did 2 vivas last week. On Wednesday I was the external examiner (i.e. the examiner who comes from a different institution) for Gbotemi Adediran at Edinburgh University School for GeoScience (why the capital "S"? Drives me nuts) ably assisted by the internal examiner Saran Sohi. Gbotemi defended his work well and hopefully learnt stuff as well, his supervisors were Bryne Ngwenya (who was a postdoc. at Edinburgh when I was doing my PhD) and Kate Heal with assistance from, amongst others Fred Mosselmans from the Diamond light source. The thesis contained some excellent work, notably the visualisation methods for looking at the co-location of metals and bacteria in phytoremediating plants and tying this in with synchrotron analysis to look at metal speciation.

Then on Friday, I was the internal examiner for Sujung Park, supervised by Alistair Boxall. Dr Iseult Lynch from Birmingham did the honours as external examiner and again, all was well. Sujung has done some really informative research on nanoparticles, highlighting potential issues with standardised methods of assessing their environmental behaviour and toxicity.

Alice Johnston, my PhD student modelling earthworm populations with Richard Sibly at Reading was vivaed a week last Friday as well (by Volker Grimm, the god father of population modelling) and passed with no corrections.

So all told lots of PhD vivas.

This got me thinking about two things.

1. what is the collective name for a bunch of PhD vivas - possibly a graduation of vivas?

2. typically PhD students start in October and then progress at their own speed. Some have funding for 3 years, some for 3.5 years and some for 4. The organised / lucky PhD students finish when their funding ends, others have to plough on a bit tidying up loose ends, though the end of Year 4 is the normal cut-off. In many running races you have a staggered start and as the race progresses the stagger unwinds. In theory, if everyone ran at the same speed my understanding is that they would all cross the line together. For PhDs (despite the 3 vivas above all happening at the same time) there is a tendency for everyone to start together and get somewhat spreadout towards the end so that they all finish at different times. In running people talk about a stagger unwinding. There seems something rather appropriate about the progression and end of a PhD being a gradual process of staggering occurring towards the end!

See the world with environmental science

Term is well and truly underway, in fact it is racing past at a frightening pace.

Greenery at a former Cr waste site

Just before term started Ian Burke (University of Leeds) and Robert Woods (Bolton Council) kindly gave myself and Laura Bellis, one of our MEnv students, a tour of a former Cr waste site somewhere in the northwest. Laura will be looking at earthworm distributions on the site as part of her MEnv research project. The site has a clean soil cap as part of its remediation and we are interested to see how earthworms have colonised this.

Then last week we took our MEnv students to exotic Huntingdon (it’s on the other side of York!) to the Portakabin site. We had an excellent morning getting a tour of the facility and discussing environmental issues associated with the site. I was particularly impressed by the way they collect fumes associated with the chemical reactions that occur as the foam insulation that they inject into their modules for insulation expands and vent these safely to the atmosphere. Many thanks to the Portakabin team for being so welcoming and helpful.

Walking between rows of Portakabin modules

In the paint shed

The steel framework for our new offices

Meanwhile back at base our new building continues to grow. You can now see the framework for the offices and start to get an idea about the size. Each time I go past I feel guilty about the construction noise that our soon-to-be neighbours in Wentworth college and Biology are having to put up with. We're still all looking forward to moving in next Autumn and are beginning to think about how we should celebrate the event.

Job available listening to earthworms talk to plants

I'm pleased to say that we're now advertising a postdoc position for our "Whispers in the dark" project investigating earthworm-plant interactions. Details of how to apply are here.

PhD vivas and bulging barrels

The Diamond Synchrotron user meeting was very interesting. It was great to hear about the varied science being carried out on the beamlines. Perhaps most concerning was learning about the bulging barrels of who knows what on the Sellafield site. The chances are what ever is inside is radioactive and flamable and there is always the chance that the bulges will eventually burst! Luckily scientists at Bristol like Dr Tom Scott and Diamond are working on techniques to work out what is going on without having to open the barrels. Once we know what is going on we should be able to deal with it, that's the theory at any rate. We also heard about research relating to water and metoerites, generation of magma in subduction systems and whether calcite on Mars could be used as evidence of life.

Delegates milling around the Diamond House entrance hall during the Synchrotron users meeting.

Last Friday I was in Manchester running a PhD viva in the School of Earth, Atmospheric and Environmental Sciences. Nicola Ashton was defending her thesis on soil development on a range of different rock types in Ireland. Nicola has done a tremendous amount of work characterising the inorganic, organic and microbial composition of the soils and defended her thesis well. She passed with minor corrections, well done Nicola.

Nicola and Richard Pattrick (one of her supervisors) celebrating in the bar after the viva

Time travelling made simple

I had grand plans over the summer to blog daily from an excellent conference I was speaking at in Paris this August, entitled "The Geochemistry of the Earth's Surface", a working group of the IAGC (International Association of Geochemistry). For one reason or another my plans didn't come to fruition (certainly not because of the time taken visiting the Rodin Museum, Musee d'Orsay and Musee d'Orangerie) but it was an excellent conference, hosted by Jerome Gaillardet at the Institut de Physique du Globe, where Marie Curie had her lab. The papers from the conference have been published and are available on line for free.

The Arab institute in Paris is near the Institut de Physique du Globe and one of my favourite buildings in Paris. The front of the institute is designed to reflect Islamic art and comprises a series of windows each containing a series of light sensitive shutters which open and close through the day. Magical.

Tomorrow I'm off to another conference I've been asked to speak at - this time at the Diamond light source down near Didcot. It is their annual user meeting and I'll be talking about our use of FTIR (fourier transform infrared spectroscopy) to study earthworm calcite balls. If I'm really good I'll take some photos and write about it. the big news in the area is of course that Didcot A has now been demolished, however Didcot B remains so there are still some of the iconic cooling towers on view.

However, today's main topic is to congratulate Sam Parry, ex Reading PhD student, now at Syngenta, who has had the first paper published from his PhD. The paper looks at calculating how fast minerals dissolve in soils.

As I often write, I still get a thrill when I see a paper with my name on it in the literature. One of the nice things about this one is that although it is published now it has a publication date of 2015! This often happens as scientific publications put out issues early. In reality they do this as it helps the statistics by which journals are judged (perhaps a subject for another blog) but what it means is that I'm already having work published in 2015 which I always think is kind of neat.