Sunday, 25 December 2016

It's been a while...

Since starting my PhD back in October 2013, I've managed to keep up a steady stream of posts. The last four months of my PhD did not make for great blog posts, however. I wrote chapters, handed them to supervisors, waited, and then made corrections and sent them back. The process was steady and uneventful. Having said that, there were events in my life that sometimes made writing and motivation difficult. I had to move house, a friend died, unpleasant events from the past reared their ugly heads. Of course these things will happen when you least need them to, so you have to be prepared for them by planning and being organised. Happily, I handed in my thesis on the 31st of October.

A few tips:
  • Give your supervisors as much time as possible to read stuff, as they have other commitments aside from you.
  • After sending your supervisors things to read, regularly remind them politely to read your stuff. Don't leave it till the last minute and then blame them or get all huffy and disrespectful.
  • Do the corrections one at a time, as they come back, on your working copy. You can occasionally (not too often) send around a revision. If you wait until you have all comments back before applying them, you will delay your submission date!
  • Let your supervisors know if there is any part in particular that you would like feedback on.
  • A completed thesis is a big file - don't compile chapters until you really have to!
  • Warn the printers that you will be printing your thesis, so that they can advise you if they are expecting a big workload on that day.
I took the advice to start writing early, and have been writing regularly since the start of my PhD. That includes writing for fun, writing blog posts, and writing science communication articles. I think that has helped me to get into the right mindset, and not procrastinate too much or be afraid to write.

This blog has been helpful in consolidating my thoughts, and logging my progress. Many of the posts now seem silly: I was so worried about aspects of my progress, not making enough progress, procrastinating too much. None of that mattered in the end. Of course, my thesis hasn't been marked yet, and I haven't defended it, so the outcome is still uncertain. But I managed to produce within 3 years and 1 month a thesis that my supervisors are happy with - despite the fact that I procrastinated, travelled, had issues, had a life, had hobbies and interests. In fact, I will dare to suggest that taking time out to do healthy human things assisted the process of writing. I have really enjoyed doing my PhD. My only regret is that I wish that I had collaborated more on projects with other researchers, but one must set up quite a few collaborations in order to increase the likelihood that some of them work.

I will add to this blog when I have defended my thesis, but until then, adios!

Saturday, 9 July 2016

The 20th International Congress of Arachnology

Four months before I started my PhD, I went to my first ever conference: the 19th International Congress of Arachnology (ICA) in Kenting, Taiwan. I presented a talk, and connected with a bunch of fellow idiopid researchers to share ideas. That conference had a massive influence on the start of my academic career. It also made me realise what a truly wonderful bunch of people the arachnologists are, and what an exciting world I was getting into.

Now, four months before I plan on submitting my thesis, I have just had an exhilarating week at the 20th Congress, in Golden, Denver. It was the largest assembly of arachnologists the world has ever known, and there were some inspiring presentations and discussions. My head is still reeling from it all. It was perfect timing for me; I now have some ideas about research fields and grants to apply for, and also some pointers on how to improve my thesis. Although right now I have my head buried firmly in the writing up process (hence my silence for the last couple of months), it was well worth coming. Life doesn't end when a thesis is handed in! There is plenty to do to build my career. Conferences and networking are fuel for a baby scientist's growth, especially in a close-knit community such as the arachnologist community.

I won't bore you with a day-by-day text wall, but here are a few cool things that I picked up from the human and arachnid components of the conference.

1. My usual strategy of orbiting the crowd and then diving in to hit a weak spot has, for the last few conferences, been made more successful by befriending someone similar to me on the first day. One looks a little less predatory and a little more social if one has a friend or two.

2. Having said that, I am always surprised that there are plenty of people who are fine with being on their own, and they don't seem like losers or unpopular people. It is fine at conferences to be by yourself sometimes, as long as you don't do it too much (when the conference is over, you don't want to have missed opportunities).

3. The best time to network is at mealtimes, when you find a space, sit down and munch while listening to people talking about their research. They are pretty much a captive audience and you can get to know them pretty well.

4. Different countries have totally different research dynamics and cultures. Each has its merits and its disadvantages.

5. Amblypygi (an order of arachnids that look terrifying at first but are harmless) are underappreciated powerhouses of sensory perception, neural processing, and cuteness.

6. Jumping spiders have eyes at the end of long tubes, and in translucent species you can see the tubes move around as the spider scans its surroundings. They only have clear colour vision on a small part of their retina, so they need the ability to move their eyes and focus on different parts of their environment.

7. Sometimes (often, maybe), technology progresses faster than our ability to use or understand it and its outputs.

8. Even analyses using rudimentary techniques, or those which produce inconclusive results, are informative and of some use, so long as their limitations are taken into consideration.

Anyway, I need to get all my thoughts together and get back into thesis mode. Conferences really take it out of a person!

Tuesday, 12 April 2016


I have been cruising around in my warm fuzzy cocoon of writing (which is so nice and entirely predictable, although pretty slow going) and making trees (which are improvements upon my already pretty finished phylogenies, so I can't go wrong). Until a few weeks ago, I was gently (but increasingly obviously) avoiding any other kind of analysis. There are big scary computer programs that I have to fight with, and I feel so tired after grappling with BEAST. But also I was afraid that anything I did would just retrieve the information that my data were inadequate and I'd need to start again. Before analysis, I don't know whether my results are useful or useless. They happily exist on my computer as big files filling up my hard drive and making me feel accomplished. But a PhD is not assessed by how much hard drive space your data takes up. A PhD is assessed by the defence or viva and a thesis, which has to be written, and cannot be written without results.

Analysing my results determines the usefulness of my data...opening the box determines the fate of the cat.
Luckily, I managed to get over this elephant in my own personal room. I started gently, downloading and exploring the programs that I had to use, and running through tutorials using the examples given. Then I tried to make my data look like the examples. Then I ran my data through the program and expected failure. The first few times, there were hiccups - usually a grammatical error, such as a space in the wrong place. After correcting them, I got some pretty cool and exciting results (well, I find them exciting, and perhaps one or two other people in the world would too, after I've explained to them at some length why they are exciting), and managed to make figures out of them. I was pleasantly surprised that my data meant something.

Now data analysis is addictive, and I keep trying to improve on previous runs of analyses and tests. I do not believe that data analysis can ever be completed; only abandoned.

If you're in the above situation, I would encourage you to face your fear and take the plunge so you can get on with your life, and also to save every version of your results and keep it somewhere safe on your computer, cos it's awkward when it gets deleted or overwritten by mistake.

Wednesday, 23 March 2016

Clean lines and organisation

I haven't posted here for a couple of months, mostly because this blog has been helping me to write consistently even when I had no thesis writing to do. Now, I am writing every day anyway, so I don't need to write for the sake of writing. However, this blog has been so useful to me in terms of tracking my progress and realising how insignificant most seemingly catastrophic events have turned out to be, that I cannot abandon it. I would definitely recommend any new PhD student to write a blog, even if nobody ever reads it.

Every PhD blog has at least one post about advice for new students. New students get a LOT of advice. Much of it is useful, but much of it is also useless. Each student and project is unique, and they need to figure most stuff out on their own. The generic advice often given by universities (write a little every day, find a good work-life balance, talk to your supervisors etc) usually holds true and is good to stick to.

However, there are two things that I would add to the university spiel. Firstly, get some bloody exercise. The bodies of PhD students become stagnant, decrepit, and downright unhealthy from three years of sitting at a desk indoors and prioritising study over everything else. Exercise helps you to avoid health issues that can stem from this lifestyle. It helps you to integrate yourself back into society if and when that time should come. But your body also houses your brain, which needs looking after if it is to remain sharp and useful. Yes, study is the most important thing in your life right now, but you can't study without taking care of the things that help you study, like your brain. Taking time out to exercise makes you feel good, helps you sleep well, and forces your brain to divert its attention away from how best to compoverise the distribution of the arcbenders in R. It forces you to focus on yourself.

The second important thing that I have learned is about organisation. I have a diary, a to-do list, and a three-month plan in addition to the mandatory PhD timetable that I constructed for my proposal (and the slightly less naiive one that I made for my 18-month report). To start with, I figured each task would take a small amount of time and I could progress in a modular way. However, over the time I have been here, things have tended to not work or blend into each other, and it all took a lot of time. To start with, this really panicked me and I thought I was not working hard enough. But that is a self-centred view and one that entirely disregards the nature of science and the universe. It is all new stuff that I am doing, and some of it will go wrong. I would encourage new students to be as organised as you can possibly be, and more organised than you have ever been in their lives - you need to know what you have done, what is left to do, and each little step leading up to completion. You need to know exactly what the next steps are. Every PhD is composed of data collection, data analysis, and writing; these steps tend to bleed into each other and that is ok. In fact, it is vital for the PhD to work - when you start analysis you will realise there is a bit more data to collect. You also need to be writing the entire time, not just after you've done the analysis. So although you need to be extremely organised, you also need to be aware that stuff goes wrong and just because you say you will have a completed phylogeny in two weeks does not mean that it will be so. Everything takes a lot longer than you expect.

Right, on to finishing the calibration of my phylogeny (something I meant to complete about a year ago). Wish me luck ;)