My Geology Note-blog

A chronicle of my PhD journey and other geology writings

Category: Fieldtrip

Trip to BOSCORF!

The prologue: (cue Frankie Howard)

Here follows a “day in the life” sort of piece concerning my trip to Southampton to collect samples for my PhD. The time stamps are when I started writing each section and I am leaving it written as-was for full effect. All photos are shamelessly nicked from Millie Watts’ and the BOSCORF’s twitter feed. For more information on BOSCORF see their website here and follow them on twitter @BOSCORF_NOC and my guide for the day Millie @GeoMillie.  Right, onward!

And so begins my long day there and back to Southampton. Except my day actually began at about half past midnight when I woke up, peered across at my alarm clock, saw the top of the digits over the stack of books on my bedside table, panicked, then checked my phone to confirm that what could have been an eight was actually a zero. Such is the life of the highly strung academic. Putting on a long, rambling YouTube video was enough to send me back to the land of nod until my alarm woke me up at Six. Waiting for my taxi outside the flat, I heard the dawn chorus despite the mist.

I indulge in two things when I go to the railway station, one is taxi cabs (either there, back or both depending on the time of day) and large drinks from the station’s coffee shop (ha, ha, no free advertisement for you here! As they say, other publications are available). And after the newsagent nearly tried to charge me fifteen pounds for my magazine and getting my hot drink, I shuffled off down the platform to find my seat on the train (a Great Western with slam-door carriages, not quite as old school as Northern Rail’s Pacer stock but certainly possessing more charm). Speaking of trains, I recommend to you the currently-on-iplayer episode of Panorama concerning the UK’s current sorry state of train affairs.

The train’s filling up already (because of course it is) but I now have time to reflect upon the day’s tasks, which to the average person sounds a bit off. Trotting off down to Southampton to the National Oceanographic Centre (specifically BOSCORF) to collect some North Atlantic marine core samples for my work. Additional tasks include a shed load (which is an SI unit of measure and don’t let anyone tell you otherwise) of writing to be getting on with. Train journeys, I find, can be ideal writing environments, not least because of the lack of readily available internet (must. resist. checking. for. free. WiFi). All being well I may manage to hash out a good few hundred to a thousand words today. As the sign on a local Chinese Restaurant genuinely says; Win-Win.

Work word count: 414

The train is getting increasingly busy as we pass through the stations onto Cardiff. I am somewhat concerned that what I have written for work thus far is less scientific, academic journal material than it is slightly rambling, single author monograph. We shall see. The fog is even thicker now than it was back in Swansea, probably something to do with the damp farmland around here between Bridgend and Cardiff.

Work word count: 465

On train two of two on the way to Southampton. I had to have one of those awkward “excuse me you’re in my seat” moments with the person next to me because of course I did, it wouldn’t be train travel in Britain without it. For some reason the train is just, sitting, here despite the fact it should have left at half past the hour. It’s probably waiting for another delayed connecting train to come in but dear goodness, if they keep up that trend the entire rail network would end up delayed!
*tannoy announcement*
Turns out the train ahead of us hasn’t cleared the line… for whatever reason. Dear me I deeply dislike being late for things, especially if I do everything in a timely manner and the reason ends up beyond my control. On the plus side for people still boarding the train if they were running late this morning they’re in luck to be sure.

Finally, at 8:39:30 we’re off!

[No further posts were written because the day was so busy when I finally got to Southampton half an hour later than planned.]

Word count: the same
Powerpoint slides for Tuesday: almost updated.

    Very little should be able to dampen my mood right now but by golly, former British Rail is having a good old go at it. The train out from Southampton Central was running late and got to Reading just as the doors on the Swansea train closed. Despite the obvious situation, after 40 agonising seconds the train pulled out without us who needed to get to Wales. Cue a half an hour wait and now a further wait in the train at the station as they wait for a connecting train (how nice of them! Wish the previous train had waited for us… grumble, grumble, ad nauseum). When we’re actually on the move I’ll be in a better mood to wax lyrical about my day. (Also, oh goody, someone near me on the train smells like a brewery… this isn’t going to be a pleasant stint…)


“I’m a trifle miffed” (c) Yahtzee Croshaw

Word count: the same
Powerpoint slides for Tuesday: Completed.

    There is something about trains that provoke productivity. Possibly it’s the knowledge that there is no alternative stimulation or seating arrangement for a good few hours so you jolly well better make the most of it.

    In light of making the most of it lets summarise my eventful first visit to the National Oceanographic Centre at Southampton. Approaching from the wharf side past container ships and a cruise ship you don’t fully appreciate the sheer size of NOCS. Laid out spectographically (yes really) with colour coded “nodes” denoting different sections it’s a rabbit warren that I’m glad I didn’t need to navigate by myself. BOSCORF, my destination for the day is separate from the main building and consists of the refrigerated core store with enough space for 5 km of core it is currently overstocked with more than 8 km of core, and a suite of prep and analysis equipment. For most people just the suite of equipment would make them as Charlie was in the Chocolate Factory but for me the best was yet to come in the cores that had been laid out for me.


That’s a lot of cores!

    There is an austere beauty to sediment cores, especially marine sediment cores with their pale fauns, muted greys, deep blacks and sandy browns. A particularly stunning example is BOSCORF’s so called Butterfly Core which contains a clump of mud that had rolled in such a way that layers had formed all different coloured horizons. When it was split and the structure was revealed it looked like a swallowtail butterfly.


The butterfly core in all its beauty

For those who may consider mud to be “mud” these cores from the North Atlantic will change your mind and then some. First off, what a geologist means when they say “mud” is not the same as the mud you find in your back garden when it rains and the soil turns to soup. Mud is a grain size, far smaller than sand grains, usually made of clay minerals and finely ground rock flour. It is so fine grained it can take months to settle to the sea floor and a single centimetre of mud can represent decades of deposition.

    Sub-sampling the cores is a fiddly procedure but satisfying when it works. You only even work on half of a core that is taken. When it is recovered it is split and half becomes an archive section while the other half is the working section that you can sample from. Knowing there’s still a pristine half left is small comfort when you bugger things up so badly your past-self cringes with embracement from the middle of last week. Luckily I had an excellent guide through the process (thanks Millie!) and the mainly fine grained nature of the important bits of the core made it easier to sample.

    You know how if you’re down at the beach and you’re making sand castles, if you get the water to sand mix wrong it doesn’t form a nice solid castle shape after a gentle spade tap but a collapsed blob or a powdery lump? That is the fear as you pull the plastic casing up from the sediment and hope and pray that the sample comes with it and not flop out on the top of the rest of the core. Luckily no such mishaps befell me except for a near miss that was quickly dealt with by a quick thinking Millie and a new piece of cheese wire.

Word count: 512

    At Cardiff. Had it not been for the delays I would be seeing the lights of the Liberty stadium on the outskirts of Swansea-land instead of the inside of Cardiff station. I guess the biggest question is when did I turn into someone who looked forward to bed time? (Granted I’ve been up since 6 and worked at least a 12 hour day so maybe the desire for bed is justified?).

    The rest of the NOCS is basically everything you ever wanted in a nationally funded research facility, more labs with more equipment than you know what to do with, dozens of people all about the place, a canteen with a view of the harbour and a knee high door labelled B. Baggins (yes, they have a hobbit hole in the blue node, and it made me very, very happy). One of the lovely things about big research facilities is the diversity of work being done and the somewhat pleasingly utilitarian architecture. We even noised through the door of one of the newly refurbished teaching labs to see a class learning about geological maps. Truly, I was with my people today! Sometimes being a geologist in a geography department feels like being the classical music reporter to Rolling Stone magazine, there’s a definite connection but the chord progressions are totally different. (Hush, it’s neatly 10 O’clock and I’m tired, I can’t be expected to always come out with witty metaphors).

    I had to wonder whether my enthusiasm was coming off as disingenuous (and I told Millie the same) but I genuinely was getting excited by the things I was seeing and the ideas we were having as I met people over lunch and in BOSCORF. A friend of mine said that when he reached the end of his PhD he found that he had loads of new questions he wanted to investigate if only he could get the opportunity. One key advantage of my work is that I basically recycle other people’s previous samples. Don’t forget that each core section, which is about 1.5 m long at most probably cost on average £1000 to recover on a research cruise so you might as well get the most from them. Contained within BOSCORF is multiple academic careers worth of possible investigations including more than enough tephra deposits for me to be getting on with for now!

    Another big thank you must be extended once again to Millie and the BOSCORF team for hosting me and letting me make use of their samples, some of which are still under limited external use agreements. I needed no persuasion at all to take up the offer of returning to BOSCORF soon but first to analysis the samples I have taken today, that will be enough work to get on with for a little while!

This is losttimelady_PhD signing off at 22:03.


Millie and I (with fellow BOSCORF staff on the screen behind) while we were packing up the cores to go back into the fridge.

The samples and I made it safely back to Swansea and soon they shall be getting zapped in the X-ray machine.
If you read this far, thanks!


XRM 2016 conference day 3: “Hay Jude” parody songs

“Day 3 in the XRM-house, the delegates are in Lecture room 1, singing.”

That is a thing that actually happened. In celebration of 3 of the founding members of the XRM conference who are also X-ray microscopy pioneers, Professors Schmal, Kirz and Burge, a lyric-swap of The Beatles No. 1 sing-a-long song was sung. Who say’s science conferences are dry affairs? (Granted, I think some people were a bit bemused and/or embarrassed by it but my time as a young worker has helped me embrace silliness such as that when I used to be among the embarrassed group).

Today was a half day but no less packed. Session one saw talks on studying art using microprobes; chemical mapping of low concentration elements in the tests of foraminiferas; and a talk on scanning theory and reconstruction that I would probably appreciated more had I had the right background in X-ray physics.

The second set of talks I attended discussed improvements to 4D tomography reconstruction (where the 4th dimension in this case is time). Once again freeware is on offer to try out the techniques back in the lab and I have been assured by the presenter that although the maths is complex (he showed us all the equations) it’s easier to use.

Today I presented my poster which is always heartening but quite tiring too. I like chatting over my work in that sort of situation because it gives me ideas that I wouldn’t have thought of before. It’s a bit of a problem in one sense though, I end up coming back with even more ideas that either would add directly to my work or would be really exciting to do.

In my free afternoon I mooched about, firstly, around a bookshop (they seem to call to me like a dog whistle). I always find that different cities have different types of things in their charity shops. Oxford, I predicted, would have a good selection of academic related texts (not necessarily textbooks, just notable works relevant to the field). To my delight I am now the proud owner of a very good condition copy of Flatland by Edwin A. Abbott. Another future blog post may be a review of said book. Books are one of the few things I have a genuine weakness for buying. Luckily charity shop books are always at a discount which is great for people who have to weight up buying food vs. books.

My second stop was the Oxford Natural History museum which I really enjoyed. I know I’ll have to go back again when I’m less brain dead from X-ray science as I didn’t do my usual amount of reading of signs. It’s a very beautiful building both inside and out, especially the stone pillars inside that are all made of different rocks from the British Isles complete with chiselled labels. Once again, photos will be forthcoming.

My only complaint is the frequent use of wet preserved specimens next to fossils in displays to show modern similar species. I’ve got better with spirit collections over the years (a biology classroom with a resident half-eviscerated rabbit in formaldehyde will do that) but most of them were invertebrates today and things like slugs and leaches make my skin crawl. The dinosaur skeletons are terrific and I really liked the “you can touch” style displays of rocks, fossils and even a stuffed black bear.

Notebook page count for today: 18

Time for bed, said Zebedee.

Day 2 at XRM 2016: Taiwan vs. Hamburg

Another packed day has been and gone at XRM 2016, so packed in fact I’m surprised that talks that happened only this morning weren’t actually from yesterday’s programme.

Update: I now know what ptychography is! But don’t ask me to explain it because I don’t understand it well enough to properly articulate it.

Today’s talk highlights included:
– imaging phase separation in Li Batteries
– 4D imaging of various stripes, 3D plus spectra and 3D plus time series, with the latter examples being Li Battery explosive failure and watching a match burn from inside it.
– Imaging and analysing the compound eyes of bees (including some seriously cool image segmentation methods) which I found particularly good.
– Lots of open source software

…….and the battle for the 2020 location of XRM, Taiwan vs Hamburg. Imagine the Olympic bidding only without the corruption and the presentations are more interesting. One of the fun things about the bid talks, and a lot of the other talks for that matter, has been finding out just how many X-ray and Synchrotron facilities are out there in the wide world. Voting closes later in the week so we’ll know then where the conference will be held in 4 years time. (In two years the conference will be in Saskatoon, Saskatchewan, Canada. And yes I did have to look up the spelling of ‘Saskatchewan’).

Today I did a lot more chatting to people. People who know me back in Swansea probably wonder if I ever shut up but I’m usually quite shy around new people so it helped that it was other people who instigated the conversations. In particular I ran into people who I’d met at the ToScA conference last year in Manchester. It’s always great to catch up and exchange lab stories.

People will often say that conferences are the best place to start collaborations. I never really understood how that actually happened but after the last 2 days I’ve realised that you don’t need to persuade a scientist to collaborate. It comes up so effortlessly; whether it’s an offer of an exchange of samples, machine time, software code or even just a lab visit. It really is heartening that although we can often feel like individual islands of research just a tiny bit of activation energy is enough to bring people together.


Pages of notes made today: 27

I’ve also been taking lots of pictures of the displays within the Institute including crochet hyperbolic planes, porcelain topographic sculptures and a modular origami bee hive with model bees. So there’s another blog topic for after the conference!

Tomorrow is a half day so I’ll be visiting some of Oxford’s sights and trying to bag a few more colleges to add to my list.

Analysis technique of the day: STXM (sticks-’em), scanning transmission X-ray microscopy
Best acronym of the day: MANTiS software (with a mantis shrimp as it’s logo), Multivariate ANalysis Tool for Spectromicroscopy




Ouch! My brain! XRM 2016 Day 1

If how well a conference is going were to be judged by the number of pages I’ve filled in the first day only XRM 2016 is doing rather well (18 pages!)

Got out of bed very much feeling like an undergrad in halls again, not least because I’m staying in a room in Keble College and had breakfast in their Great Hall (I think petite pans are the signature breakfast roll of academic institutions from one end of the country to the other). Bright sunshine and pretty architecture certainly make for a pleasant walk even when you know you’re going to be inside all day.

As a geologist and not an X-ray scientist by trade I feared that coming to a conference billed as “X-ray Microscopy” (of which X-ray tomography is only a tiny part of XRM) might leave me in over my head.

Well, yes and no.

Talks today ranged from overviews of several research facilities and new scanning components to direct applications. Talks on applications included an summary of an on going study hunting for why Alzheimer’s Disease develops and how; using sandpaper to enhance imaging (no really); and my personal favourite, a talk on what the structure of dinosaur teeth can tell us about their diet and evolutionary path (answer: a lot!)

But the title of this is “Ouch! My brain!” and for good reason. The science of X-ray microscopy, which seems to me to be three parts physics to one part algebra to two parts geometry, did go over my head at times so to dilute my shame here are the definitions of some words or vocabulary I had to look up later:

Microphages: In there more common recent usage, a microphage is a white blood cell in a vertebrate immune system.
Dark field X-ray: X-ray signals produced by scattering caused by porous structure within a material. These signals are dependant on the orientation of the sample in the case of materials showing anisotropy.
Spherical harmonics: mathematical functions applied to coordinates on a sphere surface. Handy for when you’re dealing with points on the surface of the Earth (which is more or less spherical in an oblate spheroid kind of a way).
Coloured X-rays: Bands of particular X-ray energies similar to how different colours of light are confined to certain wavelengths. Useful for detective chemical composition of a sample.
Ptychography: err… something about diffraction patterns and… yeah I’ve got no Earthly clue. Questions for someone tomorrow.

Despite attending the conference alone I did a surprisingly large amount of chatting to folks today, mainly because I set myself the goal that if I saw anything that a colleague might be interested in or relate to their work I should make enquiries.

I may submit something to the conference blog before the week’s out but for now, further updates will be here (including pictures hopefully when I work out how to get them off my phone).

Roll on Day 2… but right now I need sleep!

Grasmere Cave and Bracelet Bay

Today I’d like to share a couple of recent little trips I took and the geology I saw:

Firstly, before I started work I went out walking with family around Grasmere. Not only were we enjoying a nice walk we knew we’d be passing an old quarry, now more man-made cave, that is in the hills between Grasmere and Rydal Water.

A fun fact about the cave is that a) it’s been used for concerts. (Good Acoustics?!)

b) It could fit the entire population of Ambleside within it.

Below are some typically arty photos of the cave.


P1010510 P1010508 P1010515

Before the weather recently broke in Swansea I went on a little field excursion to Bracelet Bay which is by Mumbles Head on Swansea Bay.

I took some photos (no surprise, see below) and made some poor quality notes in the back of my diary. So I followed good practice in keeping notes but didn’t record them in the right sort of place. So to preserve them for prosperity and to illustrate how a geologist might keep a notebook (I make no promises that my notebook technique is exemplary! In fact, I know it’s not, don’t follow my example!). Anyway, here goes:

Bracelet Bay 27/9/14 10:55

Around the back of the café by the stone benches.

After receiving a tip off from a dept. geologist I’ve gone in search of fossils!

– Fine grained, grey rocks.
– 2 scales of bedding ~40 cm & ~10-15 cm
– Jointed twice in the vertical ~E-W and NNE-SSW
– Highly fossiliferous
– Minor veining – calcite
– Fossils are matrix supported.

Wackestone (?) limestone
Some more dense – packstone

– Shells both concave and convex upwards (death assemblage?)
– Possible bivalves – vary from <1 cm up to 5 cm.

Photos taken.

P1010528 P1010530 P1010532 P1010534 P1010528 P1010529

I’ll admit the photos are more interesting than the above.