Saturday, 7 December 2013

Day 4 of IR beamtime - more sample analysis action

So now we have some data. After 5 hours of analysis this is what you tend to end up with.

A screen shot from the FTIR software showing a series of point analysis.
During our sample preparation we were hoping to get nice round slices cut through granules. As mentioned previously what happened was that the granules crumbled as they cut and we just got material stuck around the edge. We've told the machine to do point analyses around the edge and in the middle screen in the image above you can see the points we analysed. Along the bottom you can just about see some typical spectra from those points. The really sharp eyed will notice the calcite peaks towards the right hand edge. What we need to do now (this will take some time) is process the data to see whether we get any variation in the ratio of amorphous calcium carbonate to crystalline material.

In order to maximise our time, Liane had brought her portable FTIR machine along as well.

Liane's portable FTIR machine in action
In many ways this works in the same way as the Synchrotron FTIR that we're using (it's all FTIR!). We used it to analyse a few samples from Emma Versteegh's project on the isotopic composition of granules. Emma's results suggest some sort of isotope fractionation from the initial secretion of the milky fluid in the calciferous glands to the secretion of the granules into the soil. This is most likely related to crystalisation of the amorphous calcium carbonate and we just needed to confirm that our samples start off amorphous and then crystalise - we have done, job done.

So all told, not a bad session - there is data to analyse that approximates to what we were after in the first place, we have done a few samples for another (related) project in our spare time and we have a good plan for what to do on the next visit in February.

Many thanks to Mark Frogley and Katia Webhe for their help and to Steffi Lutz and Liane Benning for putting up with me.

And the food wasn't as bad as last time either.....

Day 3 of IR beamtime - some success

Plan C sort of worked and Plan D didn't.

Plan C was to try the cryomicrotoming again. The granules still crumbled as we sliced them but we did get a rim of granule material around a hole.

Here you can see the outlines of two granules left on a cryomicrotomed section. Granule material is just left around the rims. We took this image using the FTIR microscope (in visible light) and then told the machine to collect FTIR spectra around the rims. Field of view is about 3 mm.
We are producing maps from these sections (actually a whole host of individual point analyses) to see what we shall see. We need to process the spectra to remove any signal from the glue used in the cryomicrotoming (a pva adhesive) and then look at the ratio of a few peaks to determine the amorphous calcium carbonate content in each spectrum.

A FTIR spectrum of calcite taken off line (i.e. we've done this on a normal machine as a reference material) with an ATR (attenuated reflectance) set up. The 3 big peaks on the right (at about 1400, 870 and 710 cm-1) are characteristic of crystalline calcium carbonate. If the 710 cm-1 peak is missing it's amorphous calcium carbonate.

Plan D was to simply squash a granule on to a slide but it didn't work. You can do IR in a number of ways. For the thin slices produced by microtoming we look at the light going through the sample - a transmission measurement - and that seems to work for our slices. For the crushed granule the sample is to thick for transmission so we look at the IR light reflected from the surface - a reflectance measurement. However, the crushed samples didn't give good spectra in reflectance - they may not have been smooth enough.

When we return in February we're still going to try the slices produced using "normal" methods - embed the granule in resin, polish it down with a Diamond polishing nap to get a thin section. However we will try (another) FTIR measurement technique - ATR (attenuated reflection). In this technique we actually have contact between a diamond lens and the sample. This is how "classical" FTIR works and should be fine giving spectra like the one above.

Meanwhile we were visited on the beamline by Brian Clegg, a science writer, who is doing an article for the Observer. The article will be about Diamond and the science we do here and should appear in January.
Brian Clegg (science writer) and Sarah Bucknall from the Diamond Communications team.

Wednesday, 4 December 2013

Day 1 on Beamline B22 Sample prep nightmares

Another 5.15 am start to get to Diamond for 10 am. This time I'm here for 5 days to try and do some infrared mapping to locate amorphous calcium carbonate in the granules. Liane and Steffi arrived on Monday and have been working to optimise the system for the calcite and also their snow algae. We've hit a few problems. There are problems with the samples we cryomicrotomed last time we were here. The samples are stored at - 80 C but when they are transferred to the sample holders for the beamline water in the atmosphere sticks to the samples and freezes producing ice crystals. This makes the samples no good for analysis.

Plan B was to use the samples I prepared in York and Liane prepared in Leeds - these are simply balls of calcite embedded in araldite. We tried microtoming these and the samples just crumbled. It looks like the balls are too fragile to slice into 10 micron thicknesses.

Plan C is to have a final go with basic granules and the cryomicrotome tomorrow but the feeling is that it's a long shot. Plan D is to simply crush the granules and look for amorphous calcium carbonate in the powder - we'll try that tomorrow or possibly Friday depending on how things go tomorrow.

For our next beamtime in February we'll prepare some "classic" thin sections which should definitely work.

Steffi (left) and Liane (right) setting up a sample map.

In the meantime we are running some of Steffi and Liane's snow algae samples that have simply been smeared onto slides.

Liane is now off to bed (11 pm). Steffi and I will stay up until 2 am to put on another sample then we'll reconvene at 9 am tomorrow.

Oh the joys of beamtime

Friday, 29 November 2013

Lights, camera, action

Just finished filming for a BBC 3 documentary on soils. I was there as an "earthworm expert" and talked about the relationship between earthworms and soil bacteria as well as the useful things that earthworms do in the soil.

One fun thing we had was some bacteria culture plates from "normal" soil and earthworm casts. This shows that you get more culturable bacteria in the earthworm casts. It is an interesting question as to whether the numbers of bacteria in soil are increased during passage of the soil through the earthworm intestines or if it is simply that the bacteria were dormant and become active, waking up as it were in the nice cosy environment of the earthworms guts. The plates were kindly prepared by Adrian Harrison in our Biology department.

The white discs in the petri dish represent individual bacterial colonies. The petri dish on the left has colonies from earthworm poo, the one on the right from "normal" soil. You can see that there are more culturable bacteria in the earthworm poo.

Director and camera man with presenter Chris Beardshaw discussing a close up shot of some bacteria cultured from earthworm poo!
Although the plates went down well with the crew what they really appreciated were the bottles of bubbling green stuff. This is the classic telly shot of a lab. In this case we really did have some bubbling green stuff - algal cultures for feeding to Daphnia courtesy of PhD student Annika Agatz.

Green bubbling stuff in a bottle - the stuff of a camera mans dreams! In this case an algal culture for feeding water fleas (Daphnia).

I had a happy two half days filming with the crew which will probably be about 2 minutes in the actual documentary! The documentary will probably be broadcast sometime in the middle of next year - a real treat to look forward to!

Tuesday, 26 November 2013

It's all in the preparation

Last week saw me doing a long day down to the Diamond light source to help with some sample preparation for an experiment next week that I am doing with Liane Benning from Leeds. I had to get up at 5.30 in the morning and was back home by 11 in the evening; I think I'm still recovering.

The experiment next week will involve looking at thin slices through 2 mm diameter balls produced by earthworms.

2mm diameter ball of calcium carbonate secreted by a Lumbricus terrestris earthworm

The balls are made of small crystals of calcium carbon and the individual crystals are sometimes calcite, sometime aragonite, sometimes vaterite and sometimes amorphous calcium carbonate. These are all different forms of calcium carbonate, they vary in the arrangement of the calcium and carbonate molecules and we want to know what these different forms all occur together. The first step towards this aim is to map out the distribution of the different forms.

To do this we're going to do something called FTIR (fourier transform infrared) mapping on Beamline B22 at Diamond and to do that we need thin slices of the granules.

Just as there are many ways to skin a cat there are many ways to slice a granule. Last week "we" tried something called cryomicrotoming. We'd collected some fresh granules and kept them at -80 C so that they were preserved just as we had collected them. Then you simply attach them to a widget and slice them, rather like a salami slicer in the supermarket. It sounds easy but the slices are 5 - 10 micron thick (i.e. about one hundred times thinner than a finger nail) and the blade is in a small container into which liquid nitrogen is being pumped to keep the temperature low (about - 30 C) so it is rather fiddly. So fiddly that really the only person who was successful was the beamline scientist Katia Webhe who was there to give us a hand - many thanks Katia.

Katia Wehbe in action on the cryomicrotome, an admiring Mark Frogley looking on. Both Katia and Mark work on the beamline and help people like me get useful data. They are worth more than their weight in gold.

Inside the cryomicrotome. The white disk, top left is the liquid nitrogen outlet. Over to the right you can see a smaller white disk with a  dark centre - that is our granule, stuck to a widget and below that, the wedge shaped thing is the blade. You move the sample past the blade to cut wafer thin slices. Then you have to somehow catch them and put them on a slide!
So "we" managed to make some slices and I returned home tierd but satisfied. Back in York I'll attempt to make a few more slices in a different way as a back up and then next week it will be another early morning start and we shall see what we shall see on the beamline.

Thursday, 10 October 2013

Today Ilkley, tomorrow the world!

or more accurately, yesterday Ilkley, on Sunday North Yorkshire.

Yesterday evening I gave a talk "Metal munching earthworms - Evolution in action" at the Wharfdale Naturalists Society who meet in Ilkley. A great night, good crowd, interesting questions. The highlight of my evening was when a young boy asked me for my autograph!

Then today I've just finished recording a short interview with BBC Radio York's Paul Hudson. it will be broadcast this Sunday at 1200 and will be part of a programme on climate change. We were chatting about the palaeoclimate work we're doing with earthworm poo (see previous blog).
The glamorous location of BBC Radio York

The recoding studio with BBC Radio York's own Paul Hudson

Thursday, 3 October 2013

Earthworms rule

Much excitement today in my very small corner of the virtual world. Apparently our paper on earthworm calcite balls is the most downloaded paper from Geochimica Cosmochimica Acta over the last 90 days.

In the mean time we have had another project start. This is a BESS (Biodiversity and Ecosystem Services) funded project from the NERC (Natural Environment Research Council). Working with Paul Eggleton at the Natural History Museum and Ron Corstanje at Cranfield University we'll be investigating controls on the biodiversity of earthworms in pasture systems to see whether modern agricultural techniques threaten our earthworm biodiversity (and all the good things that they do for soils) or not. David Jones at the Natural History Museum will be leading the earthworm identification end of the project and Jo Witton will be working in York analysing all the soil samples (800 hundred of them).

Jo, practising our method for determining microbial activity in soil samples.

Tuesday, 10 September 2013

British Science Association festival

There's lots of science going on this week at the annual British Science Association festival, held this week in Newcastle.

I was there on Family Sunday with my earthworms, crystal models, lumps of calcite and some microscopes. Apart from having to drive there (given that York and Newcastle are on the East coast line why is it not possible to get to Newcastle for 9 am on a Sunday morning by train?) I had a great day but was hoarse by the end of it and wishing that Emma had stayed around to the end of her contract so she could have been there to help. After all Newcastle is at least as glamorous as the Jet Propulsion Lab. and Pasadena, surely?

Visitor interest in my exhibit "Time travelling to past environments: What can we learn from earthworm poo?"

Lots of interest in the earthworms from three year olds - who tend to point at the earthworms and try and pull the balls off the crystal models - to people of indeterminate age. I think the really good thing about events like these are that people with an interest in science can come along and talk to scientists and hear about stuff that otherwise they wouldn't come across. I talked to lots of people who said they used to do science (say at school or university) but didn't any more and that events like these made them miss it.

Friday, 6 September 2013

Software fun

Having had three days to recover from the Goldschmidt conference it was time to be off again, this time to the Diamond Light Source users meeting down near Didcot at Harwell. Luckily the meeting only lasted one and a half days as my luggage still hadn't arrived from Florence when I left so I was running short of clean clothes!

The user meeting is a far smaller meeting than Goldschmidt and serves a different purpose as it brings together people who use the Diamond light source - physicists, chemists, biologists, material scientists - al sorts of scientists who use the high intensity radiation that Diamond produces to do their stuff. I came along as I will be at Diamond in December using beamline B22 (a.k.a. Miriam which of course stands for Multimode Infrared imaging and microspectroscopy). I haven't used this beamline before, (usually I'm on i18 working with X-rays to find out about element speciation) and the user meeting featured a day and a half course on how to use the software available at the beamline to interpret and display your data once you have got it. It was also a chance to meet up with some of the beamline scientists who will be helping us on the beamline and discuss sample preparation. The workshop was very helpful though I felt we spent to long looking at the different colours you could use to display data and there was a missed opportunity for a sing song when we explored the "Winner takes all" function. I'm sure we'll address this last point during our beamtime in December!

Getting ready to learn more software tricks for displaying FTIR data. Stefanie Lutz, Liane Benning and Andy Bray from Leeds School of Earth and Environmental Science are in the foreground.

On the evening of the first night there was an interesting talk on the Braggs (William and Lawrence) who were pioneers in techniques using X-rays to look at the structure of crystals. They got the Nobel prize for their work, Lawrence remains the youngest recipient of the prize to this day (25 years old). Their Wikipedia entries are well worth a read.

Friday, 30 August 2013

Confessions of a conference attendee

Day 8: 30th August

Up early and off to a ticket office for entry to the Duomo dome, Campanile etc.

There are 465 steps to the top of the dome so important to get there early rather than being stuck behind slow moving tourists. I was there for 8.15 and was about 15th in the queue. To my mind the Duomo dome was more impressive than the pictures in the Uffizi – you can’t beat the solidity of bricks and mortar and there is a joy, for me at any rate, of climbing up winding stairways behind walls, a little like walking through secret passages. Initially the route takes you out to the walk way around the inside of the cupola, just below the level of the massive fresco that covers the inside of the dome. This is slightly vertiginous, the walk way is about 50 cm wide and projects out from the wall but the close up of the fresco is incredible, particularly fun are the depictions of hell and damnation - various people being eaten or prodded by people with pointy horns and tails and a few skeletons prancing about as well. Then it is onwards and upwards. The cupola has a double dome design, one inside the other and the stairs lead you up between the two. Towards the top the stairs are steep and curved and I was reminded of some of the routes up holy mountains I’ve experienced in China. At the top the view of course was fantastic with all of Florence laid out before you.

Then it was back to the conference in time for an excellent talk on B incorporation into  forams (important for climate reconstruction). I also attended a good talk that suggests that oxygen isotope fractionation in soil solution is not significant in temperate climates (sorry, a bit technical but important for the well being of our embryonic earthworm-poo based thermometer). Finally on the way out I bumped into Don Porcelli from Oxford for a quick chat about earthworms and Ben Harte from Edinburgh. Ben Harte organised the Goldschmidt conference in Edinburgh in 1994 in which I was a slide projectionist - do we miss slides and jammed projectors? No we don't.
I bought some lunch in the covered market, popped up the Duomo campanile for another good view of Florence and then went into the  octagonal shaped building next to the Duomo - officially the Battistero di San Giovanni. The unpromising outside (though the doors are rather splendid) gives way to a simply stunning interior - a fantastic Byzantine mosaic covering the dome. This is incredible and far outshines the Uffizi.
The end of conferences are often sad, there are the thoughts of missed opportunities: did you miss the best talks? Should you have gone to more talks? Did you convince people that the science you were doing is fantastic? (possibly is the answer!). There is also a slow drift of people away from the conference, numbers in talks get fewer and fewer as the day goes on. Pity the scientist giving a talk at 5 pm on the last day of a conference.
All told it has been good. Florence is a great city to visit. I attended some good talks. I met up with friends and made new acquaintances.  Now there is a day of travelling to get back home, two days at work then off to Diamond for a two day course on Infrared spectroscopy.

The main mystery remaining is why is Florence also called Firenze? I have difficulty understanding why a city has two different names, perhaps one for best?

Thursday, 29 August 2013

Confessions of a conference attendee

Day 7: 29th August

This evening there is the sound of drums and chanting in the distance. It's all rather reminiscent of an old jungle based movie ("the heat, the flies, those damned drums!") in which the tribes are gathering for war. In reality what I can hear is the locals cheering on their beloved Fiorentina football club.
Today Emma Versteegh and I were running a session on biomineralization and biogeochemical cycling. All told it went well. Running a session is always exciting. The chief concern being whether speakers stick to time or not. At a conference with 20+ parallel sessions each comprising 15 minute talks sticking to time is paramount so that people can scuttle from session to session to try and catch different talks. All our speakers turned up and kept to time. Added to that there was an audience so all told a successful session!
We had talks on earthworm secreted calcium carbonate (obviously the highlight!), a talk on using isotopes to show that a so called "terror bird" from pre-history was probably a cute vegetarian with an over-sized beak and some interesting talks on silica in soils showing how soils are slowly being depleted of the sort of silica that is easily taken up by plants and how this might affect plant yields in the future.

Other than our own sessions highlights were a talk in which my work was cited (thank you Andy Bray) which is always good for the ego and a fun talk in which the C isotope signature of the paper that past editions of scientific journals were printed on was being analysed to investigate climate change. The journals, Nature and Proceedings of the Royal Society, have a very good age constraint and date back to the mid 1800s so are good for looking at fairly recent climate change, or will be in the method works.

There has also been time to discuss some corrections to a paper looking at the impact of CO2 levels and temperature on granule production rates by earthworms with Emma, look over a draft MSc thesis for a student and mark an MRes thesis. All very productive.


Confessions of a conference attendee

Day 6: 28th August (posted retrospectively)

A mixed day dodging and weaving between sessions, trying to search out that killer talk. The most fun talk I heard today was about earthworm invasions. In Europe we always think of earthworms as happy little creatures keeping our soil healthy. In the northern US the last glaciation wiped out the indigenous earthworm population and European earthworms, that came to the US in the soil used as ballast, associated with European plants and, increasingly as fishing bait, are slowly spreading into the earthworm-free Sugar maple forests. They are having a significant effect on the ecology of the forests reducing the thickness of the layer of leaf litter on the soil surface and changing soil properties. It's a great natural experiment to see the effect of earthworms and Kyungsoo Yoo from the University of Minnesota gave an excellent talk on this.

I also spent some time looking at the outside of the Duomo cathedral. I'm always amazed at the amount of time and energy people put into building these things in the past. The plan is to return on Friday to have a look inside and also, early in the morning, pop up the tower for a view over Florence.

In the afternoon Emma Versteegh and I had a poster detailing our novel palaeothermometer showing how we can use the oxygen isotopes in earthworm-secreted calcium carbonate to interpret past climates. We got quite a lot of interest and chatted about how we can take the study forwards.

This evening there was a concert courtesy of the conference - string quartet, spinet and an alto for some songs. The concert was OK but the soprano used far to much vibrato for the early music (Vivaldi, Pergolesi etc.) that she was singing and the musicians came across as journeymen professionals rather than being excited by the music. There was much clapping (too much?) at the end so perhaps this critic was in a minority.

Confessions of a conference attendee

Day 5: 27th August (posted retrospectively)

Truth be told I found yesterday rather dull. Today I had a better plan. I got up bright and early and queued outside the Uffizi gallery to buy a ticket. The Uffizi gallery is listed as a “Must see” in all the guidebooks, having a whole load of pictures collected by the Medici’s including various Botticellis. The ticket office opens at 8.15 and I got there at about 7.40, there were only 15 or so people ahead of me. I could have gone in straight away but I bought a ticket for 12.30 then headed off to the conference. I had my eye on two sessions - one on soils (known as "the critical zone" at geochemistry conferences to try and sex them up) and another on the formation of calcium carbonate. I heard some good talks by which I mean talks that make you think about your own data, think of new experiments or see ways in which you could do experiments differently. In my case there were some good thoughts about how soil particles stick together and also how to try and spot proteins in calcium carbonate. Then it was off to the Uffizi.
The Uffizi was excellent. There were some stunning paintings by various Italian masters. Many were originally hung in churches / formed the backs of altars. It made me wonder what the churches felt like - a bit like the Greeks (justifiably) wanting the Elgin marbles back perhaps. There was one painting that had been in a nunnery and apparently the nuns got a copy of the painting and a full upgrade of the nunnery plumbing in exchange for the original. Seems like a fair deal. The other interesting thing to note was that the original Botticellis looked far better than the posters you can buy. I guess this is vaguely reassuring!

Confessions of a conference attendee

Day 4: 26th August (posted retrospectively)
First day of the conference proper and everyone is very keen. The talks start at 9 a.m. and are well attended. There’s a minor problem in that the rooms where the talks are given are rather dark and stuffy (unless the air conditioning is on threatening to drown out the speaker!). The rooms have movable partition walls and whilst that’s understandable in terms of giving the venue a flexible space it does mean that it is quite noisy.

Each day as well as the talks there are poster sessions and I duly stuck up a poster I’d brought along for a small White Rose (Universities of Sheffield, Leeds and York) project on earthworm secreted calcium carbonate. Poster sessions are wonderful places to observe human behaviour.  It is somewhat akin to being in a bazaar with hawkers positioned at their posters keen to pull customers in and customers often avoiding eye contact so as to be able to pass a poster without getting stuck there for 30 minutes whilst someone talks to you about it.

Confessions of a conference attendee

Day 3: 25th August (posted retrospectively)

A good long sleep has set me up well to spend the day exploring Florence. My guidebook lists 3 walking tours so I decided to do “Walking tour 1” which should take me around Florence. The walk appeared to involve following a bus route, at least initially making me think that “walking tour” was somewhat inaccurate and that the guide book was probably aimed at the majority of people, who, according to a recent newspaper article, never venture more than 500 m from their car. The walk took in the old city wall, the old city gate of Porta Romana, then up hill to Piazalle Galileo before a slow descent back into central Florence via a lovely church San Miniato al Monte – apparently a good example of Romanesque architecture and on a site that has had a church since the time of Charlemagne - and Piazzale Michelangelo with its stunning views across Florence. Then it was time for conference registration and the general initial mingling of delegates / bumping into colleagues and friends.

Confessions of a conference attendee

Day 2: 24th August (posted retrospectively!)

The day started nice and early with the bang of the corridor door at 6 am. The joys of airport hotels. Still it was a good alarm clock. All went well with my travel up to arrival in Rome (though annoyingly in Paris – I flew Air France via Paris – I saw there was a flight to Florence leaving at the same time as my flight to Rome, can’t think why it didn’t come up when I was looking for flights unless it was already fully booked, full to bursting with happy geochemists off conferencing). After arrival in Rome airport it was always going to be tight getting to the Florence train – I’d left myself 2 hours – and unfortunately it was too tight. The trains from the airport to my station in Rome were every 30 minutes, not every 15 minute as I’d read and what is more my train was 20 minutes late. In consequence I missed the Florence train by 5 minutes. Still it wasn’t like the 2 km sprint I once had to do in a Mexican airport to catch a connection and the matter was soon resolved by the purchase of a ticket for the next train. To prove that all clouds have a silver lining, I now had time to get something to eat in Rome.

I’m now on the train to Florence, due to arrive 2217. The hotel is near the station. Nonetheless it has been a long day and I’m looking forward to a lie in tomorrow before exploring Florence and then registering at the conference later in the day.

Friday, 23 August 2013

Confessions of a conference attendee

Day 1: 23rd August

I left York at 6 pm en route to the 2013 Goldschmidt International Geochemistry conference in Florence via London Heathrow tomorrow morning and flight to Rome, changing in Paris and a train ride to Florence. I should always remember that I am lucky to have a job with these opportunities to travel. The flights and train rides are an excellent opportunity to catch up on reading and reviewing papers and proposals if nothing else.
What should be an excellent blogging opportunity has been rendered slightly less exciting as my wife has the camera in Edinburgh. Therefore I’ll add photos retrospectively.
The lack of a camera is particularly disappointing tonight as I am staying in the architectural splendour of the Heathrow Central Travel Lodge “Welcome to the best Travel Lodge” said the receptionist, though at least she had a smile on her face. I shall compare the architecture with great interest to that on offer in Florence tomorrow!

Friday, 12 July 2013

Landfills and housing

Just back from a really great site visit to the Sandford Farm Remediation site near Woodley, Reading.

The site was a landfill tip from the 1960s to 1990s and has since been disused. At the end of its life the tip was capped with clay and top soil it was just left as scrub.
This gives a view of what the site was like before development started

The site is now being developed for housing. There are two issues for consideration - gas emissions from biodegradation going on in the land fill and subsidence as the material in the landfill degrades and compacts. Neither is good for housing so the site has to be made safe.

The first thing that is done is the top soil is removed and stored - it is used to form a raised mound around the site, shielding near by residents from the noise and view of the site. The clay cap is also removed and stored for re-use.

Top soil removal

The soil stays on site and is used to create barriers to reduce sound and visual pollution from the site.
Once the top soil has been removed you are left with the clay cap that is also removed

Next the rubbish has to be excavated from the landfill for removal of biodegradable material that could result in gas emissions.

Material that is relative fine grained, or is predominantly soil can be hand sorted on a conveyor belt.
The rest of the material is dumped for processing, really coarse material is separated into wood (for re-use off site), rubble (for re-use as fill on site) and plastics / tyres (for disposal off site).

Otherwise the material is sorted with machinery, initially removing coarse material.

Air blades blow off the low density plastics into a cage for collection and off site disposal. 
The remaining material is put through a soil washing plant.

This works just like a gravel quarry and produces materials of different grades.

The really fine material is dewatered using a filter press.

The water is treated at an on site water treatment site and then reused.

The various stock piles of material are reblended to an engineering grade material and the excavated landfill refilled. It has had the biodegradable material (wood) removed so there is no longer a gas hazard and the refill is designed to an engineering specification so there is no subsidence risk.

Levelling off a refilled landfill site.

At the end of the process the site is all ready for building houses. The majority of the old landfilled material has been reused as engineered back fill and the plastic waste that can't be used occupies far less space than before. And no green belt land has been used to produce some urgently needed new family homes. All excellent stuff.

Thursday, 27 June 2013

The Stephanie Powers or Katie Price of Science?

After my major triumph of not being evicted in the first round of "I'm a scientist - get me out of here!" I have now been evicted. Nonetheless, I view it as a major triumph not being evicted first. Looking at the "I'm a celebrity - get me out of here" Wikipedia entry (yes there is one!) I see this puts me in the same company as Stephanie Powers, Limahl, Sheryl Gascoigne, Nigel Benn and Katie Price (second time around) amongst others. August company.

Stephanie Powers (with Robert Wagner) in Hart to Hart, a long time ago

Meanwhile back in the real world, grass is growing in our soil columns (or at least in the ones where we want plants to be present) and Hongling has put in the earthworms. The challenge of course is knowing that the earthworms are still in there!

A column with grass

One of our grass free columns with (honestly) an earthworm burrow in the centre
The grey rings in the centre of the columns are where we put the smaller bit of kit for measuring gas flux - you can see photos of it in earlier blogs. By having two rings we can get gas flux from the soil with and without vegetation (from our columns with grass). The thing coming out of the middle of the soil is a rhizon sampler for sampling soil solution. Next up (next Monday) is to do our first batch of gas collection since the grass started growing and we introduced the earthworms. Hopefully we'll see some differences.

Tuesday, 25 June 2013

I'm a scientist - get me out of here

I’m currently taking part in “I’m a scientist – get me out of here”. Luckily there are no bush-tucker trial equivalents where you have to eat as many chemicals as possible to get points for the camp! It’s a scheme funded by, amongst others, the Science and Technology Facilities Council to help with science engagement. School pupils post in questions on the web that you have to answer. There are also live web-chat sessions. I’m competing against 4 other scientists (all PhD students as it happens) and trying to avoid being evicted by the votes of the school pupils. The first votes are in and much to my delight I haven’t been evicted! This is probably the pinnacle of my scientific career.

Hard at work answering questions from School pupils in real time

A random selection of questions for you to consider (imagine these questions coming in every 5 seconds and trying to answer them all quickly):
How do electrons flow through a graphine sheet? 
Hey im lewis and when im older i want to be a car sales man does this involve science?
What is the relationship of gravity to the other basic forces of the universe?
Where do bananas come from?
How do snails have babies?
Why does your tongue heal quicky?
If you put a mirror a really long way away in the universe will you see dinosaurs?

Tuesday, 11 June 2013

Busy bees

Things seem to be rather busy at the moment. Two weeks ago (seems like yesterday) I made my first trip to Finland. I spent a brief day and a half in Helsinki acting as the "Opponent" for the PhD defence of (now) Dr Salla Venalainen at the University of Helsinki, Faculty of Agriculture and Forestry. Salla had written an excellent thesis about how mine waste pilings from a mine in northern Finland could be used to stop phosphorus pollution in streams and remediation shooting range soil that is contaminated with lead due to all the bullets that miss the target (this is a common problem, it's not that the Finnish are particularly bad shots!). Helsinki was lovely and sunny with some great architecture, I can recommend it.

Helsinki harbour, the large white building is the cathedral

I've also been up in Glasgow acting as external examiner for the Environmental Chemistry BSc. Once again I've been very impressed by the practical skills that the students develop on the course, really good hands on experience.

This isn't a current Glasgow chemistry student but Joseph Black. He was (according to Wikipedia) an 18th century physician and chemist who discovered, amongst other things carbon dioxide. Perhaps without him global warming wouldn't exist? The chemistry department building in Glasgow (and coincidentally in Edinburgh) is named after Joseph Black.

There is also preparation for "I'm a scientist - get me out of here!" which luckily doesn't involve eating grubs but instead doing live web chats with school pupils about science. That kicks off next week - wish me luck.

Then there are grant deadlines coming up (for anyone reading this not familiar with the academic system, to do research you have to fund it and to do this you have to persuade some one to give you the money, a grant) - and a conference "Minerals for life" next week in Edinburgh all about how we are dependent on minerals for 21st century living. Should be good.

A view of Edinburgh, a lovely city surrounded by extinct volcanoes.

I guess it's all better than being bored but I'm hoping things quieten down next month.

Tuesday, 21 May 2013

I can't believe you'd kill me for a field of empty holes.

So, a trivia question first - from which film is the above a quote. And possibly more importantly why on earth did it stick in my mind from an otherwise rather unmemorable movie?

Anyway, we don't have a field of empty holes (can a hole be empty?) but a field of intact soil columns. Far more valuable than holes.

Today we set up our in situ gas monitoring kit and measured green house gas fluxes from (and into) our soils prior to adding grass and then earthworms. We need this initial measurements to see how varied the gas emissions are across our soil columns and to have a base line with which to compare emissions once our plants and earthworms are doing their stuff.

Hongling and Sylvia setting up the N2O (lower big box) and CH4 (upper, smaller box) samplers.
Connecting the tubes - the yellow box just in shot is an IRGA and measures CO2 flux. It contains a pump and, thanks to the tubing that Sylvia and Hongling are connecting draws the gases coming out of the soil through itself (to measure CO2) and the N2O and CH4 monitors.
So now measurements are in progress - you can see the measuring chamber of the IRGA sat in a column just in front of Sylvia's right foot.

  Here is a close up of the IRGA. Below the metal cap you can see the black bellows and below that a white chamber. When it is time to measure the gas emissions the white chamber moves down onto a grey collar (you can see one in the next column at the front of the picture) and the gas starts to accumulate in the chamber. The gas is pumped through the IRGA and other analysers and we measure rate of gas accumulation in the chamber, i.e. flux.

We also measure soil moisture content with a Theta probe (the grey cylinder) and temperature (the white cylinder) as these will impact on the rate of greenhouse gas emissions from the soil and vary over time.
Finally, here is a screen shot of our real time N2O gas flux measurements (the top line, the lower line is real time isotopic analysis of the N allowing us to determine the source of the N2O - nitrification or denitrification). Each peak corresponds to a separate measurement and the different peak heights show us that the soils in our columns are releasing N2O at different rates.

Wednesday, 15 May 2013

Last week I took my penguin to the zoo......

A joke I was fond of as a child goes like this. A man found a penguin in the street and took it to the police station. "I've found this penguin, what should I do with it?" the man asked. "I'd take him to the zoo Sir" was the reply from the policeman and off the man went. The next day the policeman happened to see the same man in the local park with a penguin. "Hello", he said, "I though you were taking that penguin to the zoo". "I did", replied the man " and he enjoyed it so much that today I thought I'd take him to the park.".

I liked it anyway.

Anyhow, whilst we haven't taken our soil cores to the zoo we have taken them to Leeds School of Earth and Environment. We did this because the easiest way of getting rid of any bugs and beasts in our soil prior to adding earthworms and monitoring gas emissions was to freeze the soil. We needed the equivalent of about 10 domestic freezers worth of space and Leeds had this space free - they have more freezers than an electrical store!

One of the many freezers in Leeds School of Earth and Environment, temporarily full of soil

We left the cores in the freezers for a fortnight and have now returned them to York where Hongling is busy burying them again back where they came from.

Hongling putting the defrosted, fauna-free columns back in the soil. Note the white mesh on the bottom (held in place by a ring of car inner tube) to prevent beasts getting in or out of the bottom of the column.

Next week we'll monitor gas emissions from the soil to see what the emissions are like before the experiment begins and then we'll sow some grass, let it grow and then finally add the earthworms and start to find out how earthworms influence green house gas emissions from soils.

Thursday, 11 April 2013

Burying pipes and digging them up again

Welcome to Dr Hongling Qin from the Chinese Academy of Science, Institute of Subtropical Agriculture who has joined us for a year to work on earthworms and greenhouse gas emissions. Hongling has wasted no time getting an experiment set up. We have buried 60 drainpipes to obtain intact soil cores and are now digging them out. We'll then get rid of the macrofauna in the columns, return the columns to the soil and add different earthworm species. The plan is to monitor greenhouse gas emissions from columns with and without vegetation and with and without earthworms to see how much green house gas earthworms give off from the soil. The literature is equivocal about earthworms role in greenhouse gas emissions and we hope our work will address this gap.

Sylvia Toet and James Stockdale providing much appreciated assistance hammering the pipes into the ground.

Hongling demonstrates the "comedy" hammer

What do you do after burying pipes? Dig them out of course! Next we have to remove any resident beasties.