Saturday, 22 February 2014

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.

Friday, 21 February 2014

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.

Thursday, 20 February 2014

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.

Wednesday, 19 February 2014

A triumph of vegetable variety (at least at lunch)

We had a stand out meal today at lunch time. The Thai green curry vegetarian option started in an unpromising fashion -a beige viscous goo containing obvious yellow lumps and green bits.
The tasty, though sadly not photogenic, green Thai curry

However, as ever appearances were deceptive. The curry contained 11 different vegetables (mange tout, courgette, aubergine, green pepper, red pepper, yellow pepper, sweet corn, butternut squash, spinach, chives, onion) though neither Steffi or I had all 11 (Steffi got lucky with the onion and spinach). Using the vegetable crispness test we were also able to determine that there were at least two generations of vegetable present. The mange tout peas were excellent and crispy however the green beans were soft and, we suspect, recycled from yesterday. So there was an element of getting-rid-of-the-leftovers ness about the curry but none the less it was really good.

Dinner was always going to struggle to live up to lunch but none-the-less it put up a valiant effort. The mushroom risotto was slightly plain but not bad. It was "decorated" with some leeks which was perhaps a mistake however. The leeks looked a bit like they do when I fry them for slightly too long at home. On mature reflection we felt they probably had the taste and texture of burnt grass. Still this shouldn't detract from a highly serviceable risotto.
An "honest" mushroom risotto, set off nicely with some peppers and tomatoes from the salad bar
Workwise we continue to progress. We've now done large scale maps of one really fresh granule and two old ones (somewhere between one and forty two days old) together with detailed areas of each of these. Beatriz arrived from Leeds today and is currently making standards. We'll run these next and then proceed to our last granule - another fresh one. By tomorrow lunch time we should have finished with the granules leaving two and bit days for data processing for me and snow algae work for Liane and Steffi. Only after we've processed the standards will we be really and truly confident that we've caught our elusive prey - the lesser spotted ACC.

Tuesday, 18 February 2014

A pattern is emerging

Once again lunch trumped dinner. We were a bit late getting to lunch and there were slim pickings. However, I had a more than acceptable Thai green curry based soup with lightly boiled vegetables in it. With some chilli seeds and coriander sprinkled on the top this was actually quite tasty.
Thai green curry soup for lunch - actually quite tasty
Unlike yesterday, dinner made a valiant effort to live up to the standard set for lunch. The lamb hotpot was OK but the beans were rather 1970s - I think they'd been boiled for several hours too many. They were watery, tasteless and floppy. Never mind, the chocolate tart for pudding almost made up for them.
Acceptable lamb hotpot with floppy beans
On the research front (it's not all gastronomic adventures) we have produced some more maps. These were completed last night. The one below shows the intensity of wave numbers around 850 cm-1 on the left (calcium carbonate) and around 710 cm-1 on the right (calcite) so the green bits on the right hand image may (but only may) be amorphous calcium carbonate since there is a lower intensity in the calcite peak. We've also produced another higher resolution image (like the one in yesteday's post). Both of these maps took c. 6 hours machine time to produce.

Images of earthworm balls or are they images through someones brain?
Today there has been no beam (always planned like this, not a problem with the beam) so we played a little with the FTIR microscope and a detector called a focal plane array (FPA). I still don't quite understand what this is but it turned out that it wasn't great for my calcite balls (it doesn't get down to low enough wave numbers) so Liane and Steffi did some work on their snow algae. We've now switched to a different detector and are producing some more large scale granule maps like the above to allow us to focus on a couple of areas for detailed synchrotron maps tomorrow.

Beatriz, another of Liane's seemingly infinite number of PhD students, is arriving tomorrow with some chemicals to allow us to make some synthetic calcite and amorphous calcium carbonate. We'll analyse that as well and use the FTIR spectra to confirm the interpretation of the images we've got so far. This should hopefully ease our (healthy scientific) scepticism that we've finally located the amorphous calcium carbonate that we've been chasing for the last two years.

Monday, 17 February 2014

Food peaks at lunch with dinner a disappointment

Lunch comprised walnut dukkah, lentils and grilled aubergine. A dukkah is an Egyptian dish, usually made from hazelnuts but apparently walnuts are an acceptable substitute. Our verdict was a pass. The walnut dukkah was quite interesting - we think it had cardamom and fenugreek in it. Steffi had crunchy bits in hers which we think were whole spices. The walnut dukkah had a sort of brown grainy consistency and the lentils were a dull yellow goo so there are no marks for artistic effect but all told a good effort.

Walnut dukkah on a bed of lentils and grilled aubergine

Dinner time brought roast vegetable frittata with garlic bread and tomato sauce to the table. This was a far more colourful affair than the dukkah and looked good on the plate but sadly it was strangely devoid of taste. The tomato sauce had a synthetic flavour to it and the frittata had some strange grey bits in it, possibly the remnants of mushrooms.

The promising looking roast vegetable frittata

Half way through - note the grey bits with a spongy texture

Work wise we appear to be doing OK. We've done a map of a slice through a granule and processed the data - it's a lot easier doing it here on the software rather than via remote access. Here's a screen shot showing the intensity of two wave numbers, c. 850 cm-1 on the left and c. 710 cm-1 on the right. Calcite has peaks at both wave numbers whilst amorphous calcium carbonate (ACC) lacks the 710 cm-1. So these maps suggest that, for the granule we looked at there is amorphous material bottom left and top right. To be honest this seems too good to be true so I'm treating this with a pinch of salt for now.
Intensity of the c. 850 cm-1 wave numberon the left (main calcium carbonate peak) and c. 710 cm-1 on the right (present in calcite but not ACC)

What we're doing now is taking a coarser resolution map of the entire granule to see if there are any other likely spots for ACC identification.

Sunday, 16 February 2014

Water, water, where?

Off to Diamond on the train. Because of all the rain there is a lot of flooding down south. Diamond itself is built close to the Ridgeway and isn't threatened by the flooding as far as I am aware but getting there may prove more problematic.
To get to Diamond using public transport you take the train to Didcot parkway. You can approach Didcot from the east, via Reading or the north via Oxford. Both directions have problems with flooding of the Thames so travel may be interesting. The train companies tell me that since on Sundays there is a reduced service anyway they are hoping that the usual Sunday service will run anyway despite the flooding. We shall see.

Water, water everywhere.... Both the lines from Reading and from Oxford to Didcot are affected by the recent flooding of the Thames.

As it turns out (for once) the rail companies seemed to be correct. A trouble-free journey to Diamond.

Conscious that the comments on Brian Clegg's Observer piece in the Observer state that Diamond has the best restaurant of all of Europe's synchrotrons (a scary thought at times) I thought I should document the food this week. Photos will be forthcoming as well though tonight my camera is recharging.

So tonight I ate an acceptable mushroom and spinach curry followed by a chocolate brownie with cream. Sundays are often a low point in the culinary week at Diamond in my experience so hopefully this augurs well for the rest of the visit. Mind you, the minute steak baguette on offer looked well dodgy!

Tuesday, 4 February 2014

New Year quizzes, Grauniad and FTIR preparation

It's been a busy January with a fair amount of teaching to do. In addition the REF work has now started in earnest. The REF is the (about) once every 6 years assessment of UK academic effort in Universities. The quality of research in all disciplines is assessed. I am part of the effort assessing "Earth System and Environmental Science". Currently I'm reading (and grading) 8 academic journal papers a day. This will go on for some time - I have more than 400 to read - and then we also have to assess things like the impact that academic research is having in society. We have a meeting this Thursday to compare scores so far.

So not much time for research at present. However I am gearing up for another trip to Diamond 16th to 23rd Feb. So far there has been no time to analyse the data we obtained on the last trip but the plan is to spend some time on data analysis this time round. Additionally I have located the right software in York (thank you Paul Elliot in Green Chemistry) which I can use whilst not at Diamond.

Jo Witton has started analysing the 800 odd soil samples gathered by David Jones et al. late last year as part of our project on earthworm distributions in pastures and Hongling is busy determining whether some earthworms have moved the carbon present in soil from one form to another. Hongling's big field experiment is still on going. We've given up hope of seeing a difference between the with- and without earthworm treatments, we think perhaps the earthworms are no longer there! So next week we're going to do the earthworm equivalent of turning the volume up to 11, i.e. we're going to add more earthworms and see if that makes a difference.

There's been some good press coverage lately of the earthworm calcite work in the Guardian - despite a few factual errors - and I was delighted that the research was the answer to a question in the York Link 2013 quiz. Q: Scientists at the University of York revealed how they could find out about the planet's climate in the past. But what rather unusual substance helped them achieve this?"

The answer of course (as always) is earthworm poo!