Angus Ferraro

A tiny soapbox for a climate researcher.

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My thesis: friend or foe?

Bound and ready to submit!

Bound and ready to submit!

Last Monday I submitted my PhD thesis. I walked over to the Examinations Office in the centre of campus, up a few flights of stairs, handed a big old pile of paper over to the secretary there, signed a form, and that was it. I started my PhD in October 2010, and according to my notebook I wrote the first few tentative words of my thesis in June 2012.

I have heard others tell tales of the looming monstrosity their thesis became in their life, constantly bearing down on them. The folk wisdom of the PhD student is that your thesis is your enemy, and that every day you have to do battle with it, to subjugate it and wrestle it into some kind of coherent shape. To be honest, it never felt that way to me. I followed the standard routine chapter by chapter: outline, concept map, make figures, write text, proofread and edit, send to supervisors, revise. When I started blogging I had planned to use it to describe the process of writing a thesis as it happened: a ‘stop-motion’ thesis, as I called it then. It turns out that the process is a largely uneventful one, churning through the routine described above.

Occasionally this process broke down. There were times when I felt mentally and physically sluggish, so I took a short break – an afternoon off, perhaps – to refocus. It helped that I was still doing little bits of analysis quite late into my PhD. I had done enough to be content, but had a few extra things that were worth doing since I had some spare time. These tasks were pleasant distractions and allowed me to keep my mind active without stressing it out with major pieces of work with real and imminent deadlines. My thesis was never my friend, but it wasn’t my enemy either.

So, for me at least, writing a thesis hasn’t been an epic climactic undertaking. It’s been built up bit by bit, and I’ve worked without putting myself under crippling pressure. I think the academic environment here at the Department of Meteorology really helped: my supervisors provided encouragement, advice and calming words when they were needed, while the rich programme of seminars and group meetings reminded me that I was also there to learn, not just to write a big book and plonk it on someone’s desk.

As I walked back to my office after submitting my thesis I did feel noticeably ‘lighter’. Although it hadn’t been a stressful experience, getting rid of it still felt good. I am now free to do things for their own sake, rather than the artificial goal of a document for examination.

On the subject of examination, I still have my viva (or thesis defence) ahead. In the UK this takes the form of an oral examination by two examiners: the main one from another institution and the other from one’s own (who also takes the role of a moderator). The candidate is quizzed on the details of their thesis in order to check whether it really is their own work and whether they have the depth of knowledge befitting a PhD. It doesn’t sound like a pleasant experience but at the same time I’m looking forward to discussing my work with others. Much like the process of writing is pleasurable if one puts aside the fact it’s for a thesis, I hope the process of discussion my work will be pleasurable if I put aside the fact it determines whether or not I get a PhD!


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New chapters and foreign lands

By January of this year a major chunk of my PhD work was winding to an end. I had spent a long while looking at the effect of stratospheric aerosol geoengineering on the circulation of the stratosphere, which will form the second (and probably biggest) of the three results chapters in my PhD thesis. At the start of my project I had spent a lot of time reading about stratospheric dynamics and it’s now a somewhat familiar area to me. Well, almost. I still find some chunks counter-intuitive, and sometimes downright baffling. But at least it’s baffling in a familiar way.

We are always reluctant to move away from the familiar. But the work for my final results chapter required that I take the plunge into material and theory that was very much unfamiliar. I was going to look at the impacts of geoengineering on the tropospheric circulation. I eased myself into it by thinking about the tropospheric jet streams first. I at least have some grounding in this area. The dynamics of the midlatitude jet streams is somewhat similar to the dynamics of the stratosphere, and my undergraduate degree in Meteorology has quite a heavy emphasis on the theoretical underpinning of it all. The work on the jet was a nice transition.

Recently (over the past month or so) I have been thinking about precipitation. Especially tropical precipitation. Now, the Earth’s Tropics are meteorologically very different from the midlatitudes. In the midlatitudes the Coriolis Force is a significant effect and weather is determined by large scale wavelike motions producing depressions and anticyclones. Rainfall is mostly frontal in nature. In the Tropics the Coriolis Force is negligible. As a consequence we don’t usually see very large horizontal temperature gradients. This means we don’t see large, rotating weather systems. Rain comes from convective storms, on a much smaller scale than midlatitude frontal depressions. There is so much moisture in the air in the Tropics that the vertical temperature profile pretty much everywhere shows evidence of the release of heat when water vapour condenses to form rain. This forms a characteristic moist adiabatic temperature profile (see image below). Without a strong Coriolis Force this temperature profile is spread over the Tropical belt, so we see it even outside the rain-producing regions.

In order to interpret my model results I had to learn to think differently. Intuitions learned from midlatitude dynamics don’t apply this close to the Equator.

Learning new theory can be pretty intimidating. It’s difficult to know which paper to read first. Sometimes I find myself feeling paralysed. I have a pile of things to read but keep having to refer to different sources to understand terminology, or to get to the bottom of some ‘obvious’ physical understanding not fully explained in one piece of research. Then I took a different tack. I went to see one of the hundreds of other people working in the Department of Meteorology.

This department has experts on any conceivable area, and now, when I’m learning new theory, this is becoming invaluable. In a single hour with a researcher in tropical meteorology I ‘got’ it. I understood the fundamental differences between tropical and midlatitude thinking. Now I can read those papers with confidence. Now I understand the terminology, and a little of the intuition as well. Self-teaching works well (and is entirely necessary for a PhD student) but spending a little time with an expert can help one learn how to teach oneself. This is much the same as, how, when learning a foreign language, you must first learn enough to communicate on a basic level. Once you have that, you can begin to immerse yourself, to learn from conversation with native speakers. The amount of learning that goes on increases exponentially with time. You learn far more from native speakers. But you need to do that initial bit of work to access this higher plane of learning.

Talking of foreign lands, I will soon be off to the 2013 EGU (European Geosciences Union) General Meeting in Vienna. It’s a colossal conference (nearly 12,000 people attended last year) and I’m sure the experience will be educational, entertaining, confusing and exhausting. I’m sure I could list adjectives forever on that one. I will try to write some blog posts and Tweets during the conference, reflecting on what it’s like for a naive young PhD student to be launched into one of the world’s biggest academic conferences.

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Writing – don’t be shy

When I started my PhD I had a simple plan in my head for how I thought it would go.

Year 1: Preliminary research, setting up the problem and gaining the knowledge base required to analyse my future results.

Year 2: Results come flooding in.

Year 3: Begin by pulling together the material I have generated and putting it into coherent form. A concentrated slog of writing, then I would be ready to submit.

Like all plans, it turned out to be wrong. It was probably useful in some sense, but my project has not followed the trajectory I set out in my head late in 2010. I actually had a substantial chunk of results (enough to write a paper) by the end of my first year. My second year was quite a barren time in terms of results, but highly educational. Now, in my third year, I am writing parts of my thesis before the model runs which will provide the bulk of two of the three results chapters are even finished.

I ended up starting my thesis earlier than expected because I had had some setbacks with the climate model I was using. Reading’s IGCM is a useful model but it has little documentation. Learning to use the model had as much in common with the oral traditions of the Icelandic sagas as it had with modern forms of written communication.

The long and short of it is that I had a lot of downtime while I was waiting for model test runs to complete, restarting crashed runs and so on. It took me around nine months from being introduced to the model to completing the final ‘results’ runs. The final runs themselves only took a month to run.

I found myself with some time on my hands. I could have done some tangential reading, but I find it hard to stay focused that way, and I don’t think I’m particularly good at learning that way. I learn much better with purpose behind me. For example, I learned a lot about radiation modelling a few months ago when I was writing the section of my thesis describing the code I was using, even though I had been using it since late 2010. Having to write it down forced me to re-examine what I did and didn’t know and to ensure my knowledge was up to scratch.

Early on in my PhD, while I was doing ‘exploratory’ reading and research, my supervisors encouraged me to write little reports. They told me it was good practice. Not only did it make me learn my stuff, it also helped them stay up to speed with the literature using my concise reviews. Also, some (but not all) of it could end up being slotted straight into my thesis. I ended up writing a few of these reports in my first two years. Some of them aren’t much use. Either the writing is too sloppy, or the results and/or analysis has changed. But one – a review of microphysical processes affecting sulphate aerosols – was indeed suitable to go straight into my thesis. Bam. A whole subsection. Done. And I wrote it in my first year!

I was also fortunate enough to have some interesting results by the end of my first year. Encouraged by my supervisors, I wrote a short paper about them. It was exciting for a young researcher to have a publication in a fine journal like Geophysical Research Letters. Re-reading the paper today there are quite a few things I would have changed. The figures could be improved and some of the methodology is needlessly fiddly. Nevertheless, it was another opportunity to write up a chunk of my future thesis. Even better, the quality of the work was somewhat assured since it got through peer review at GRL.

I have a spare couple of days while I run some diagnostics programs on my model runs, so I am writing this material into my thesis. It’s not quite as seamless as I wanted. The style of a thesis is more conversational than a paper (which is a shame – papers seem to be required to be difficult to read sometimes), so need to change that. I also have no space constraints, so I can expand on discussion if I thnk it’s appropriate. But even though I need to make changes, the main ideas and the deep thought behind this chapter of my thesis has already been done. It’s a good feeling.

It is not always possible to write a paper during your PhD. Sometimes it only comes together into a nice story later on. Nevertheless, I think it’s a very good idea to keep writing during your PhD. It helps drill information into your mind and saves you some work later on. It gives you a bit of variety in your everyday work. Your writing will improve, and, who knows, you might even like it.

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Don’t stick to the plan

Plans are useless, but planning is everything.

– Dwight D. Eisenhower

I failed to take my own advice today. I wrote a substantial part of my thesis section on a climate model I am using without planning it. No outline, no concept map, nothing.

Sticking rigidly to the plan rarely works because you made your plan in your head and the real world doesn’t work the same as the one in there. That doesn’t mean planning is useless. Aspects of your plan might go awry, but it is unlikely to be entirely wrong. The plan helps formulate the problem clearly in your head and provide a path forward. You might deviate from the inital path, but it helps to have a few points of reference along the way (especially at the start).

In my defence, this section was a simple one. I was comparing the output from the IGCM‘s simulation of the present-day climate with observational and reanalysis data. I had already made all my figures; all I had to do was talk about them. Model assessment is rarely an exciting part of scientific writing. It is necessary, but there are no exciting results to present and discuss. This section answers the question ‘is the model alright?’. The answer is ‘yes, just about’.

In my thesis I have to be more rigorous than that, but the writing is more or less a simple description of the plots and a little discussion of whether the biases in the model are serious problems or not. I had put a little thought into this already and had a list of a few references I needed to include, so in a sense I had planned a little bit.

To write a detailed plan and concept map like I did for, say, the ethical and social subsection, would have been like using a sledgehammer to crack a nut. The ethical and social section was a foray into an area outside my expertise and was something which required a structured argument. The section on model assessment was comparatively simple to write. I noted this in advance and changed my plan accordingly. The section might need some proof-reading as a result, but in general the ‘Models & Methods’ section of any thesis is ‘menial’ work which doesn’t require too much difficult thought.

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Thesis writing: getting started

It is very important to make your thesis look readable. The quality of your writing determines how readable it actually is, but if your text is presented in a sloppy fashion you may lose your reader early on and struggle to engage them again. Your material is going to be technical and quite tricky to follow. It is your job to make the communication of your work as painless to the reader as possible.

LaTeX – nerdy at first, seamless after a while

I use LaTeX to typeset my thesis. There is a lot already written about LaTeX on web, so I won’t bother with that. The main difference is that you use ‘tags’ or ‘markup’ to create formatting. LaTeX documents are plain text files which contain instructions for the LaTeX program. You then tell the LaTeX program to convert those instructions into the finished document. Formatting is no longer your direct responsibility. Want a heading? Just write \section{Title}. LaTeX will format it accordingly. It takes a while to get your head around. I learned it over a few days while I was on placement at the Met Office in 2009, and have barely used a wordprocessor since. I use LaTeX for typesetting proper documents and plain text for everything else.

The main advantage of LaTeX is that images don’t madly jump around the page like they do in wordprocessors, and there is a facility, called BibTeX, which makes referencing and creating bibliographies a breeze. Seriously. It is so much better than anything else out there. I use Mendeley to generate my reference list which slots straight into my LaTeX files. It’s beautiful. There are also plenty of LaTeX thesis templates out there. Here in the Department of Meteorology PhD students ‘inherit’ thesis templates and make their own modifications. There are a few floating around, each with their own distinct lineage. The one I use has a very elegant structure, with files for each chapter kept separately. It’s quite nerdy, and actually typestting it involves running a custom-written program which does all sorts of complicated stuff, but the outcome is pleasant.

The blank page

Now onto the more difficult point: how to actually get started writing. There has been so much written about the terror of the blank page that I feel this might be a little superfluous. Nevertheless I might be able to offer a few comments.

When I get the ‘blank page fear’, it is because I have not planned what I am going to say. Work that out first. What’s your goal? If you don’t have one, don’t write anything just yet. You will have no idea what to write until you have an idea of what to say. When you are talking to people about complicated things your speech will become more measured. In informal conversation words just come to you, but when it gets important, words have to be carefully selected. The same thing has to happen with your writing. Work out what you need to communicate first. Draw arrows around your concept map so you have a sense of what you’re going to write about first and how that leads to the next thing.

When you do start, you will feel tentative. It is the same feeling as when there is a long silence in a conversation and the silence becomes quite tangible. You will be reluctant to break that silence and your first words will be halting. You will tempted to write something like ‘One of the most important things…’ or ‘There are many factors contributing to…’. This is dull. If you are telling me this in your first sentence I already know it is going to be an important factor. So by all means start like this to get things flowing, but you may want to go back and revise it to something more vigorous.

Vigorous openings – an example

One argument for geoengineering research (though not necessarily deployment) is that there may come a time when deployment will be preferable to any other option. If mitigation efforts continue to fail and the threat of climate change is severe, the risks associated with SRM deployment may become preferable to the risks of unmitigated climate change.

Today I improved this opening couple of sentences by making the first bit a lot stronger.

Geoengineering research is justifiable only if a situation can be conceived of when deployment is a desirable option. The ‘arm the future’ argument for research (though not necessarily deployment) is that is would be prudent to investigate the full range of possible policy response to climate change, in case there comes a time when deployment is preferable to other options.

Weak, tentative prose comes from a mind lacking confidence. Practice by looking at examples of your writing and thinking about ways to make it more direct and assertive. Then apply it. I will write more about vigorous prose in a later post, but for now let me say that Strunk & White’s The Elements of Style is most useful. It is a concise collection of examples of how to make written English more readable. The precise rules aren’t important. The overall effect, driven by the examples of good and bad English, is vital.


Thesis writing: concept maps

A concept map for a section of my literature review.

In a previous post I wrote a bit about outlining: a useful and pretty basic technique for planning any body of writing. You set down what you want to write, in order. Then you write it.
It is quite rare to be able to structure the argument beforehand in this way. I use an outline for a very high-level overview of my thesis. It is essentially a table of contents. I find outlining too restrictive for planning the content of a section. I switch to a close relative: the concept map.

I doubt I would be alone in being initially disparaging of the ‘mind maps’ we are encouraged to create by enthusiastic teachers. I didn’t get the point. Back then I understood what I was writing with sufficient clarity to be able to hold things in my head. I did not need a map around my mind.

Things have got rather more complicated since then. I can’t hold a whole thesis section in my mind. The material is too detailed and subtle for that. Sure, I understand the concepts, and what material I want to include, and I might even understand how the concepts interact. This does not mean I understand intuitively how to write these things down in a coherent fashion appropriate for my thesis. So I revisited the ‘mind map’, which I prefer to call a ‘concept map’. They are surprisingly effective provided you actually need to use them to structure subtle arguments.

The image at the top of the post shows a concept map I drew for a relatively straightforward section of my thesis. I divided it into three clear topics. There isn’t much interaction between the topics. Then I scribbled down a load of things I want to cover. I’m not quite sure of the order of things yet, but by writing things down I can visualise how things fit together. I have included a few key references but it is safe to say I have not fully worked out how this section is going to work. The concept map is a freeze-frame of the state of development. I can add to it later.

The image below shows a very different concept map. It is for the ‘ethical and social’ section of my thesis, which is a brief section explaining some of the non-scientific issues around geoengineering. The subject matter is profoundly different from every other section and not something I am too familiar with. I recently attended a transdisciplinary summer school hosted by the Oxford Geoengineering Programme, and that gave me enough information to write down what I thought were the key concepts. Then I did a little reading around each to make sure I understood them properly, and added references in red. Finally I attempted to link some concepts together (arrows). There are four groups on the map below, though the one on the bottom and right is quite a loose grouping.

Concept map for a subsection of my thesis

Concept map for the ethical review section

Seeing all the things I needed to cover in this format allowed me to quickly test out different combinations in my head. Which concepts were related? What are the broad topic areas involved? What is the relevance of all this to my discipline, atmospheric science? The concept map is not just a planning tool; it is a thinking one. I should have taken snapshots as I built it up, because it would have revealed much of my thought process.

I suppose ‘mind map’ is not a bad phrase. These things do indeed act as guides, allowing you to forget banal things like remembering all the things you’re supposed to be thinking about and focusing on the significance of these things to each other and your thesis. I referred to the map constantly while I was writing this section of my thesis and I found it a pleasure to write, having got a lot of the nitty-gritty part out of the way. Having it set out in front of me freed my brain for the more exciting mental gymnastics of arguing persuasively and coherently and writing clearly.


Thesis writing: outlining

In a previous post I explained how I think your thesis starts taking shape before you even think about it. It grows out of every little choice you make. This is reassuring. It means you are working on your thesis all the time!

This is all very well and good, but at some point you will have to write something down. There are a number of first steps you could take. The first thing I did was to write an outline.

An outline, very simply, is the thing you look at to remind yourself what you’re doing.

My present thesis outline is below. There is a lot more detail early on and it gets fuzzy later. This is nothing to worry about. The point of an outline is to record your vision for your thesis. Once I had this in place I could visualise how it would work together as a coherent whole. It also made me realise how much work I had left to do! This highlights the close relationship between the project plan and the thesis structure I talked about before.

An outline carries as much detail as you want. You can add to it over time and modify it as your thesis takes shape. Mine began with a working title and the headings for each chapter. I later added details as to the content of each chapter. I can also add notes giving the deadline for writing various sections, and move bits around as my vision for the thesis changes. In some sections I have begun to sketch out what I want to write, at least in the form of the things I need to get across. I wrote these down in no particular order and with no thought to how I would get these points across. That comes next in my thesis-writing system, the concept-map stage.