Trace element paper finally published!

My paper based on the third chapter of my thesis is finally published: 'Environmental and diagenetic records from trace elements in the Mediterranean coral Cladocora caespitosa'. This one looks at the analysis of coral skeleton trace element content to attempt to extract palaeoclimate information.

This was the part of the thesis which caused the most problems: the most time spent in method development, the most time swearing at broken machinery and the most time confused and frustrated by meaningless data – over a year of the PhD all in all.

Turning the chapter into a paper proved just as difficult, we originally submitted the paper in February and I got back to thinking about isotopes (and working at Go Outdoors) for a few months. It took until July for the reviewers to get back to us…they’d been busy, very busy ripping apart the paper – major revisions needed. I received the list of required revisions while on holiday, read it, swore and wrote off the paper as impossible to fix, ignoring it for the next month. Luckily (?) my supervisor was less pessimistic and reckoned it was doable – even if neither of us knew what half the corrections meant. So we begged an extension and got to it. The reviewers’ main issue was the total lack of the statistical analysis (I’m not a stats person at all). The addition of regression analysis, correlation coefficients and frequency analysis turned the study from a thrown together piece of work into something resembling a legitimate scientific study, which was accepted at the start of October. Taking almost 9 months from the initial submission to the final version being available online.

The full paper can be read here (without a subscription until the 8^th of January thanks to Elsevier’s sharing policy), but here’s a summary of the main points:

I fired lasers at coral (Cladocora caespitosa) skeletons: modern ones from Croatia and fossil ones from Greece. The fossil ones date from the last two interglacials: MIS 5e (108-133 thousand years ago) and MIS 7a or 7c (186-195 thousand years ago). This allowed us to measure the trace element content of the coral’s skeleton at a very high resolution (every 200 μm – about a fortnight’s growth) to look at how it changed throughout the year. This is important as trace element uptake by corals is linked to water temperature and therefore could be a good palaeoclimate indicator.

We found that individual modern corals do indeed record seasonal variation of sea surface temperature in both their strontium and magnesium contents. However, every coral analysed demonstrated a different relationship between temperature and trace element content. This is because each growing coral is putting an individual, strong and unpredictable biological control (a vital effect) on the elemental uptake. This means that a universal calibration equation to link trace element content in this species of coral to temperature is impossible to produce. This means that we were unable to calculate growth temperatures for the fossil corals – which is what we were really trying to do.

What we did find which was interesting was that one of the modern corals contained a massive spike in trace element contents which coincided with the 2007 wildfires which engulfed a large area of Croatia. This showed that these corals can be used to inform on any events that cause increased sediment discharge into the coastal zone – such as fires and floods – which could allow fossil samples of these corals to be used to discover whether these events happened more or less frequently during the past interglacials and thereby giving some indication into the past climate.

In other good news this week the final hardbound copy of my thesis is now handed in and I’m due to graduate next month – so I finally get to change everything to say Dr on it.

'It's Dr Royle to you'

I had my viva last week; the culmination of nearly 4 years’ worth of experiments and writing to finally gain my PhD. The thought of being grilled, and potentially torn apart, by two experts in my field (of palaeoclimate and carbonate geochemistry) should have been a terrifying prospect; however I felt strangely unconcerned in the run up.

Procrastination in the week before the viva involved mushroom picking, a three day trad climbing and camping trip to the Peak District and a full day at a climbing wall down in Suffolk – leaving just enough time to read through the thesis twice and stick post-it notes on the important pages!

Taking viva prep. seriously

This probably wasn't the best way to prepare but it did mean I hadn’t been stressing about what was going to happen all week and so was calm come the morning of the viva. Turning up to the department wearing a suit and tie (rather than my usual shorts) felt a bit weird and resulted  in a fair bit of abuse being shouted down corridors – apparently I look like a ‘gorilla in a suit’.

Sitting down in the viva room was when The Fear finally hit, seeing the examiners with their copies of my thesis covered in notes, questions and corrections – the shear number of red ‘major edit’ post-it notes on the external’s copy filled me with dread, ‘Shit, it’s major corrections, I'm going to end up like Andy and never graduate’.

So much red

However, I needn't have worried, as many had already told me (although I hadn't believed) the viva was actually quite an enjoyable experience. Having the opportunity to discuss my work and ideas with two people who (at least seemed) actually interested in what I had been doing and what I had to say about my science was quite novel. Most of the corrections were oversights on my part with how I'd presented the data and the thesis should be a lot better for them once completed, with (thankfully) no real issues with the science itself – so no more time in the lab (for the PhD anyway)!

Three and a half hours later and it was all over, PhD passed with minor corrections, champagne in the coffee room and an evening celebrating properly in The Fat Cat.

Prepared for any outcome

The viva ‘experience’ was everything that handing in (see The Great Anti-climax) wasn't, bringing closure to the PhD in a proper, final way. It seemed to both validate and celebrate all the hard work that went into the last few years, so that the final version of the thesis should be a document I can really be proud of.

If I could offer any useful advice to anyone faced with their viva it would just be to not worry too much, if you've got to this stage, as long as you know what you've written (or what you meant to write) it'll probably be fine - or they've already failed you whatever you say in there - so just enjoy it!

The Great Anti-Climax

I've been meaning to write this post for a while now.

It’s now been about 6 weeks since I handed my thesis (The coral Cladocora caespitosa as a high resolution palaeoclimate archive) in after three and a half years working solidly on it at UEA. All the work, years of my life, stress and swearing that went into it all fit into about 45,000 words – which doesn't seem like a lot when you realise it’s only 35 words per day of the PhD.

There was no grand finale, no fireworks, no celebrations, the copies of the thesis were printed off, bound and handed in with no more than a ‘Well done, that must be a relief.’ from the office staff. After so long working on it actually finishing and handing in was a great anti-climax, and I actually felt a little bit sad that it was over rather than any kind of relief. It was almost some sort of Stockholm syndrome, I’d developed some sort of dependence on working on the thesis at the same time as hating the damn thing.

Now the thesis is done and the funding is all gone I'm now back in a part time, minimum wage job (retail assistant at Go Outdoors, Norwich) like the last three and a half years never happened. It is nice to have a break from science but I do feel that if I stay there too long my brain is going to shrivel up and die from complete lack of use, it seems as though I've already gotten stupider in the last 6 weeks (having managed to miss a few shifts, lose things and, most of all, write a car off).

It’s now a case of waiting for my viva (thesis defence) in a month’s time, hoping that they don't completely rip the thesis apart and I only get minor corrections to do so I can start looking for a ‘real’ job. I still have lab work to do for a clumped isotope paper that needs finishing off but I can’t get on the mass spec. for a couple of months yet as there’s a queue of people desperately trying to finish off their own PhD’s. And I’m still waiting on the proofs for my stable isotope paper and the reviewer comments on my trace element paper (both on the coral Cladocora caespitosa). So all in all it’s just been a period of quiet waiting; not really the great celebration I always thought would be waiting at the end of the thesis, but maybe it’ll get better after the viva. Maybe…

This post might sound pretty negative but I don’t regret coming to Norwich and doing a PhD at all. It’s been a great (although frustrating at times) experience, these have probably been the happiest few years of my life so far. I've met many great people (including the amazing Charlotte who got me through a lot of the shittier bits of the write up), had some great experiences – mostly with the UEA Fell and Mountaineering Club, and discovered (hopefully lifelong) passions for running and climbing, while doing all of the science.

It's not been all bad

My First Lecture

So the other day I gave my first undergraduate lecture, An Introduction to Fossils, as part of the second year Skills for Earth Scientist’s module. I was asked to do it over Christmas as the Professor in charge of the module is a full-on physical sedimentologist, with a total disdain for anything living that might wiggle around and mess up her nice strata with its bioturbation and burrowing.

My first thoughts were that of horror and panic as I imagined a classroom full of half awake, hungover, dead-eyed students staring at me blankly while I struggled to remember the difference between the different forms of rhabdosome in graptolites. Luckily, however, it was explained that this was a true introduction and most of these students had absolutely no prior knowledge on the subject so I was to keep it basic – Panic over, I'm good at basic.

A couple of mornings and my trusty undergraduate textbook of Rhona M. Black, The Elements of Palaeontology (1970) was all it took to throw together half an hour covering such basics as:

•       What is a fossil? And the differences between body and trace fossils

•       Why are we interested in them? What are uses? (biostratigraphy, palaeoenvironmental reconstruction, oil exploration, etc.)

•       How do fossils form? (Moulds, casts, etc.)

•       What conditions aid fossilisation? - Preservation potential, lagerstätten, bias in the fossil record

And of course plenty of pretty pictures of the various types of common invertebrate fossils to (hopefully) keep everyone interested.

When the morning of the lecture came, I was surprisingly chilled out about it and – aside from blank faces and awkward silences whenever I asked the room a question – all went quite well. Nobody threw anything, fell asleep, or walked out early – they all even stayed long enough to practice drawing and labelling an ammonite (even if a few did just draw random spirals instead of actually looking at their specimen properly). The follow up practical was pretty good too, an hour of drawing various common fossil specimens in the lab resulted in some nice sketches of trilobites, crinoids and echinoderms – here’s my example sketch of a Micraster I did to show what was expected:

My sketch of a Micraster cast

So, all in all, it was an unexpectedly enjoyable experience – now I just need to (finally) finish my thesis and find a university that’ll pay me to do more of it…