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.

Whispers in the dark - do earthworms talk to plants

Academics spend a lot of their time trying to obtain the money to do the science that they are interested in. One good source of money in the UK are the UK research councils. For most of my research the Natural Environment Research Council is a possible funder.

However, the research councils aren't flush with cash and funding is highly competitive. At present the success rate of NERC research proposals is 14% or, to flip that around 86% of the ideas submitted to the NERC for science projects aren't funded. There's a debate to be had about how productive it is for UK environmental scientists to spend a lot of time writing proposals that don't get funded but the level of competition does keep us on our toes and the quality of UK environmental science really does punch above its weight, quite possibly as a consequence of this intense competition.

Having written how hard it is to get funding, I'm happy to say that last week I heard that myself and a colleague, Professor Jane Thomas Oates in our chemistry department here at York, have just been awarded a grant by the NERC for our project "Whispers in the dark - do earthworms talk to plants". I really love the title! Contrary to what you might imagine in this project we won't be pressing our ears to the ground and listening intently!; rather we'll be using state of the art chemical mass spectrometry (Jane's specialism) to find out whether earthworms produce chemicals that promote plant growth. It's in their interests to do this since plant growth results in more food for the earthworms - more decaying plant material and more soil micro-organisms feeding on the chemicals secreted by the plant roots. The project starts in October and lasts for 18 months in the first instance - keep listening!

You are the REF

The earth systems and environmental science panel

Every 6 years or so the entire University-based academic community in the UK is assessed to check that we're doing a good job. The assessment is carried out by (in England) the Higher Educaion Funding Council for England (or HEFCE for short), and the equivalent bodies for Wales and Scotland. University's decide on groupings of academics (which often correspond to departments) to be assessed. The assessment is done by a bunch of academics. This process is currently called the Research Excellence Framework (REF), in the past it was called the Research Assessment Exercise.



The Radisson Blu where we are meeting

I sit on the panel of academics tasked with assessing "Earth Systems and Environmental Science". We have to assess "outputs", i.e. research, "impact", i.e. does the research that has been done have an effect on society in some way, and environment, i.e. what the place is like where we do our research. The process comprises reading a lot of documents, grading them and then meeting with other panel members to discuss.

A couple of '60s tower blocks
visible from the hotel

A Chinese pagoda that you can see from the hotel.
It's here due to the closeness of the Chinese district.

We're over half way through the process now and today and tomorrow I'm in exotic Birmingham continuing the work. More than that I'm probably not allowed to say.







Demolition derby

The talk at Daresbury labs. (3 weeks ago now!) went well. A good audience of 100+ with a range of ages. It felt odd being back in Daresbury after I don't know how many years. Given that Diamond celebrated its 10th anniversary this year I probably haven't been to Daresbury for 10 years. The place still looks much the same with the same traffic jams over the rivers on the way there from Warrington station. Sadly there was no time for a nostalgic visit to the Ring O'Bells, a brilliant pub with good guest beers, which made late night shifts on the synchrotron far more bearable.

Audience arriving for my talk at Daresbury labs a few week ago

The following week I was at Nottingham catching up with colleagues and helping out with Soil Biology Professor interviews. Then last week I was at the Natural History Museum in London for a steering group meeting of our NERC BESS project looking at controls on earthworm distributions in grassland sites. The headline news is that "we" (David Jones, NHM) have collected and identified over 13000 earthworms from over 500 soil pits and that we have analysed the soils from the pits as well for all manner of chemical, biological and physical properties. I reckon we have a fantastic and valuable dataset. A very quick look see of the data suggests that Ron Corstanje, our stats maestro from Cranfield will be able to show what impact pasture management techniques have on earthworm populations. I'm resisting the temptation to say what we've found so far but it looks very exciting.

Today I took the opportunity to have a look at the building site that will soon (we trust) turn into a nice new Environment building.

Here is what the site looked like in April this year. Some rather (atypical) slightly worn looking 1960s buildings which I believe provided the cheapest university accommodation at York.

Demolition is now well underway with the aim of a new home for the start of the 2015-6 academic year.

I'll revisit the site later in the year and hopefully we'll all see a new building rising, resplendent from the rubble.

Durham today, Warrington tomorrow

Just back from another catherdralled city, Durham, and the Earth Science department at the University there where I've spent the last two days as "external examiner" for the Environmental Geoscience BSc.

The great Durham cathedral, almost as wonderful as our own York Minster!

External examining is an important aspect of the UK academic system. Colleagues from other institutes look at a particular degree programme and highlight the good, the bad and the ugly. This generally involves reviewing exam papers before they are set and then, after the exams, sitting in a room full of boxes of paper, looking at exam answers, course work and marks. All told the degrees and students were excellent.

An anonymous room, somewhere in Durham full of geology and earth science exam scripts

It's not all hard work of course. External examining is a great opportunity to meet colleagues and spread good practice between departments. The department took us to an excellent Italian restaurant, Oro, and put us up at the Seven Stars which was very comfy and welcoming and where the externals were able to discuss the important question of whether it was better to sample the Lagavulin before or after the Laphroaig!

External examiners Douglas Paton (Leeds, Uni), myself, Ian Alsop (Aberdeen Uni) and Iain Stuart (Plymouth Uni) considering the merits of Glen Kinchie, Lagavulin, Highland Park and Laphroaig in the bar of the Seven Stars.

Now I'm back at base and preparing for this evenings lecture on earthworms and climate change in Warrington, feel free to pop in if you're passing!

5000 analyses later

Darwin once said (in his famous earthworm book)

"Even on the same field worms are much more frequent in some places than in others, without any visible difference in the nature of the soil"

We have a project with Ron Corstanje at Cranfield and Paul Eggleton at the Natural History Museum to try and solve the puzzle of why earthworms are where they are.

Last week Jo, myself and Jess finally finished processing our 500 odd soil samples (analysed for pH, soil organic matter, nutrients, bacterial activity etc) and David at the Natural History Museum finished identifying all the earthworms. We are now the proud owners of an incredible data set. For seven farms dotted around the UK we have full soil property information and know what earthworms are present. We have passed the information on to Ron Corstanje at Cranfield our geostatistician to tell us what it all means. Hopefully in five or six months time we'll be able to predict what controls the occurrence and diversity of earthworms in grassland sites in the UK.

However, there's no time to be idle. The summer term at university is always rather odd. With little teaching it always feels like there should be lots of spare time however there is lots of marking to be done. I've also been up to Glasgow to act as external examiner for their environmental chemistry degree and, yesterday was in Leiden, The Netherlands to help examine Hao Qiu's PhD thesis that he completed with Martina Vijver and  Willie  Peijnenburg. It was a long day ( up at 5 for a flight from Leeds Bradford to Schipol and back into Leeds Bradford at about 9.20 in the evening) but a good thesis and an excellent meal afterwards. The European system is interestingly different to that in the UK. In the UK the PhD student is grilled for 1 to 4 hours (or even all day in extreme cases) by a single examiner. It is a real academically challenging rite of passage which I'm sure is valuable though draining. In the Netherlands we had a panel of 7 examiners with 5 to 8 minutes each to question the candidate in front of an audience so it's a completely different experience. Both systems have their merits. I'm not sure about the robes we had to wear during the viva though...

Hao Qiu (and his wife) in front. Far left is Willie Peijnenburg, far right is Kees von |Gestel. I am next to Kees and Martina Vijver is next to me.

Schipol airport concourse

Outside Schipol airport
 

It was good to see all the orange in The Netherlands ready for the World Cup.



Getting ready for the World cup in the Netherlands

World Cup fever is beginning to take root in the Environment department as well. We did the World Cup sweep stake today and I was delighted to draw Brasil (though as I was organising the draw this raised some questions from my colleagues) - roll on the finals.

Deep down and dirty

Caught the BBC soils doc "Deep down and dirty" last night - it's still available to view for 6 days on I player at http://www.bbc.co.uk/programmes/b040y925

Generally it's not bad though, I thought, a little disjointed and of course, over simplified.

The mystifying thing is as ever what happens on the cutting room floor and how a day of filming results in about 2 minutes of air time.

Some science after a week of food reviews

So in brief.

Earthworms produce balls of calcium carbonate which are visually very attractive.

Successive close ups of a calcium carbonate ball excreted by an earthworm, taken using a scanning electron microscope. The ball is about 1 m in diameter

The balls are largely a mineral called calcite, but we have detected small amounts of amorphous calcium carbonate. This is surprising as amorphous calcium carbonate (ACC) is usually unstable.

We've tried to look at what controls the stability of the ACC using bulk analyses but to no avail. The granules are so heterogeneous that we can't see a relationship between granule composition and the amount of ACC that they contain. What we need then is a technique that is spatially explicit. Beamline B22 at the Diamond light source is the answer. This is an infrared beamline and you can use infrared (FTIR) to spot calcite and ACC.

First you have to polish your granules to get a nice flat surface.

Polished slice through a calcium carbonate granule and a close up

 

 

We can then do infrared spectroscopy (actually Fourier transform infrared spectroscopy or FTIR) to map out chemically or structurally different regions distributed across the grain. These are identified by how the areas interact with infrared light. Different wavelengths of the light are absorbed or reflected. We focussed on two regions that are both present in calcite but only one of which is present in ACC. We can map out the relative intensity of the different regions in our sample.

 

This map shows the relative intensity of a peak characteristic of all calcium carbonate

This map shows the relative intensity of a peak characteristic of calcite BUT NOT ACC

 



From the above two images we'd argue that there is calcite in the top right of the image and ACC in the bottom right. To check this we can look at the ratio of the two maps.

 Here we can see that the ratio of the ACC to calcite peak is high in the bottom left and low top right

 



 



That is all very well but it relies on our judgement which at times is questionable (see previous post on the polka!). So next we do some statistics to show that we're not just seeing things. The first thing we did is called cluster analysis. This groups bunches of similar spectra together.

Cluster analysis shows that there is a group of similar spectra bottom left and top right (different coloured zones)

 

 

That is all well and good but we'd like to know if these distinct zones correspond to ACC and calcite. So we have done something called component regression. We use some standard spectra - one for ACC, one for calcite - and see whether these spectra match the ones in our maps.

 



 A component regression map using an ACC standard. The spectra at the bottom of our map are similar to the ACC standard

 

And for good measure a component regression map using a calcite standard showing that our spectra are more calcite-like at the top

So it looks to us that we have located the ACC and calcite in our slices. What we need to do now is to map these elementally to see if there is an elemental control on the ACC stability, i.e. is the ACC stabilised because of an unusually high (or low) content of a particular element, Mg is a potential candidate. We'd also like to see if the different zones of the calcium carbonate have a different organic compound signal. We may be able to do this with our FTIR data but there are potentially problems with contamination as we use an organic-containing resin to make the thin slices of the granules that we map.

Incidentally we want to know why the ACC is stable to learn about crystallisation processes, there is lots of interest out there in what controls the way that calcium carbonate crystallises. This can have relevance to the control of industrial scale and the production of pigments for example.

So all told this has been an extremely successful period of beam time. Many thanks to the beamline scientists Mark Frogley, Katia Wehbe and Gianfelippe Cinque for all their help and support. Thanks also to the very many scientists making Diamond work and also to the non-science staff and in particular the cooks, mass catering isn't easy!

The final furlong

Lunch was some sort of pasta bake. It shows how tired I am after a week on the beamline that I can't remember what it was. The plus side to this means that it can't have been too bad, on the down side it wasn't memorable. Looking at the picture I think it was a spinach type thing. Looks beige and green to me.

What looks like a pasta bake with cheese on top and spinach

Dinner is more recent so I haven't forgotten it yet. It was fish pie. It actually tasted quite pleasant but seemed to be more a rehash of the spinach from lunch with copious quantities of peas and a few bits of fish thrown in for good measure. The beans, I am afraid to say, were not good; I didn't eat them.

Fish pie?

Looks good so far (even the beans LOOK OK)

But what's this under the crust? Lots and lots of peas. Where's the fish?

 

Last night I forgot to report the evening discussion. Following the data processing break through I thought we ought to dance around the beamline and suggested a polka. Sadly no one took me up on the offer. Steffi thought I was talking about pole cats and Liane wondered why I wanted to put a cat on a pole! Just so there is no doubt.....

Two happy beamline scientists dancing a polka after processing their data successfully

A somewhat shy postgraduate student wondering if it is safe to come out from hiding

A Leeds geochemistry professor sitting in lofty isolation.

 

 

You can tell we've been here a week. If anyone is interested I'll summarise the science we've achieved (which has been great) in the next post.

 

 

Is beige the most common food colour?

For lunch I had a roast vegetable tagine with cous cous and I'm delighted to say that it was tasty with a pleasant zing to it.

Roast vegetable tagine with cous cous and flat bread

I am already regretting not making the most of the "Fryday" theme in the restaurant - it bought back happy memories of Aberdeen in the late 1990s.

Scottish haute cuisine on offer at the Diamond restaurant

At dinner I found myself pondering the question, is most food beige? That would certainly be my conclusion based on this week's food. And if it isn't beige it is red! Regardless, the leek and blue cheese fricassee with rice tasted good - definitely leeky, better than the over fried leeks earlier in the week - but it was an uninspiring beige colour. I'd rather have flavour than colour any day but both would be good.

Another beige Diamond dinner

Steffi and Liane at dinner - despite the faces we did enjoy the food!

On the science front, today has been a day of intense data processing. I started at 0830 and now it is 2250 and I've just finished. I have contour maps for the wave numbers that we're interested in for all my samples, the ratio of the wave number ranges, cluster analysis maps and component regression maps. The wave number contour maps highlight where we get a key carbonate peak that is present in all calcium carbonate and a peak that is not present in amorphous calcium carbonate (ACC). The ratio map shows the ratio of these. Our contention is that ACC is present where the calcite peak is absent. These maps depend on our judgement. To move away from that I did some statistical analysis as well. I used something called cluster analysis which essentially groups similar things together. By and large the cluster analysis suggests that the areas we think are ACC are more similar to each other than to the areas that we think are calcite. It doesn't confirm that the areas are ACC but it does indicate that they are distinct from the other areas. Good. PCA analysis seemed to indicate the same thing (but is more complicated so I have stuck to cluster analysis). To try and confirm that the areas are ACC I have also done some component regression. This involves having spectra of pure end member ACC and calcite and getting the computer to determine how much of each spectra is present in our contour maps. In theory the areas that we think are ACC should have a large amount of the standard ACC spectrum in them. At the moment these are giving mixed results and I think I might have the analysis wrong! Checking things is tomorrow morning's job. Then in the afternoon I want to see if I can spot any organics in the granules as well - the resin used to make the thin sections we've analysed may or may not stop us from doing this.

Food that tastes of what it is made of

After yesterday's culinary heights, today turned out to be a bit more tricky. For lunch I had a chickpea and red lentil strudel on butter bean puree. This sounds quite exotic but, like much of the food we've eaten this week it was beige. Certainly the food here seems to lack visual impact. In terms of flavour the strudel and puree did indeed taste of what they were made of. This was OK initially but I soon found that you can have too much butter bean puree. I think this would have been improved with some chilli infused olive oil or something of the sort.

The strudel and puree. The excuse for the sticky toffee pudding and sauce was the 4.30 start and consequent missing of breakfast as I slept from 7 to 11 (see below)

Dinner was gnocci gratin. This turned out to be underlain by a tomato-based sauce with onions and peppers. The gnocci were fairly inoffensive and could have been forgiven much if they had been accompanied by a good sauce. Alas, they weren't. The tomato sauce was the generic Diamond tomato sauce and not great in my opinion; on top of that the slices of onion were rather on the large side. I tried to pep things up with a slice of pork pie loaf which tasted fine. In addition it stimulated much discussion regarding the preference amongst European member states for cold vs hot pies and savoury vs. sweet. I remain sure that the UK can't be the only civilised country to eat cold meat pies, what about pate en croute in France for example? Perhaps it is only Germany (Liane and Steffi) and Spain (Beatriz) that don't  have a pork pie equivalent?

The gnocci gratin

On the work front it has been a mixed day. After Beatriz arrived she busied herself in the labs making some amorphous calcium carbonate (quickly washed with isopropanol to wash away the water and therefore stabilise the ACC), some ACC stabilised by incorporation of magnesium and some calcite.


.

Beatriz in the lab. making standards



We had hoped to use these standards to confirm our identification of ACC in the FTIR maps of our granules. Unfortunately the ACC managed to crystalise a bit and investigation showed that the Mg stabilised ACC showed peak shifts that meant we couldn't use them as standards. The calcite standard also had shifted peaks compared to our samples, we're not sure why, possibly something to do with the synthesis. The long and short of it is that we can 't use the standards. Shame, good try.

Last night we set up a map that we estimated would finish at 4.30 this morning. Liane and I left the beamline at about 11.30 in the evening and arrived back at 4.30. Unfortunately for reasons we don't fully understand the map didn't finish until 7ish despite our calculations and those of the computer. This means we could have stayed in bed until 6.30 (which in synchrotron terms is almost civilised). So that was quite annoying, however the map was good and we were then able to measure the standards (sadly unusable) and a final detailed granule map. This finished around about lunch time and we then switched to Steffi's snow algae.

I have spent the rest of the day processing data and will try and get some more processing done now.