Starting well: how to do a good first year in your PhD

When I started my PhD I was passionate about chemistry and I was excited about starting a research project of my own, that I could drive in the direction I wanted to. But I wasn’t exactly sure why I was doing it; I just wanted to. With the benefit of hindsight, I think that is not such a bad reason for doing a PhD. You should certainly not do one just because it is ‘the next step’ on the academic ladder, or because you can’t think of what to do next.

I recently noticed this comment on Pete Etchell’s (twitter) blog Counterblanced, asking for advice on the important first steps to take in a PhD, and thought: “That’s a good question”.

I remember being pretty worried in the first year of my PhD and thinking that I was getting nowhere. So here’s my advice (in a handy partner to this ‘How to write a thesis’ post) on how to start your PhD well.

I think getting to grips with what makes a good start to a PhD depends on understanding the goal of the process [1]. So here’s my tentative definition of what a PhD should achieve (comments/disagreements welcome):

Completing a good PhD will turn you into a self-reliant researcher with the ability and confidence to define and solve complex problems.

With that in mind as the basic goal, here are some things to consider during your first year:

1. Come to terms with the fact that ‘In your first year you break it, in the second year you fix it, and in the third year you get your results’.

This is a bit of lame catchphrase (I forget who first said it to me), but I found it to be frighteningly accurate. Please don’t expect to be a competent scientist immediately upon starting your PhD – that is what you will be at the end.

Instead, accept that for a significant chunk of your first year you will be making mistakes, learning techniques and probably not making much headway in terms of new work. If you are – great. But don’t worry if you’re not.

2. Learn how to manage your supervisor.

Academic supervisors can vary hugely in their ways of working, just like any other type of person. Generally the older and more established your supervisor, the bigger their group will be, and the less you will see of them.

It’s important you work out as quickly as possible how to manage your supervisor. A PhD is, to my mind, all about becoming self-reliant: being able to approach a problem yourself, think it through, decide on the best course of action and then get on with it. But to begin with, you will need some help from your supervisor.

They can be of three broad types: hands-off, hands-on or somewhere in between. Unless you are lucky enough to have the latter type, you will probably need to learn how to get the help you need from your guy without being swamped in ‘banter’ or being left without any guidance.

There is no easy way to do this, but once you get that your supervisor is a resource for you to use, not someone who is necessarily going to direct your every move (supervisor can be a misleading term), then you can at least start to deal with the problem [2].

3. Read text books, not just papers.

It can be tempting to think that now you’re a postgraduate you don’t need textbooks anymore. You possibly don’t need your undergrad. ones (at least, not as much), but advanced, subject specific text books will give you a great introduction to the literature in your field from the most prominent experts. You should start reading these straight away – I didn’t bother and I wish I had. Why was I reading random papers, hoping to hit on good stuff when I had a library full of books telling me what the important developments were?

Yes, read papers, but don’t think that you’ve left textbooks behind.

4. Conferences: when, where and how?

Most PhD students have a chunk of money set aside to spend on travelling to conferences. This is great, but since you will have a limited amount, it’s worth thinking carefully about how to spend it. You will often be able to go to small regional conferences with little expense, but when it comes to big international conferences my advice would be this: one near the start and one near the end.

These serve two functions. The one near the beginning of your PhD will help you get a good feel for who the main guys in your field are. This is much more illuminating than sitting, reading papers because you can instantly get a feel for the spirit of someone’s work from their talk. The one near the end is a chance for you to present your own work to an influential audience – this is important for your CV and for networking purposes. The later you leave this conference (within reason), the better chance you will have of gathering enough results to put together a substantial and interesting talk which people will remember.

5. Don’t repeat other people’s work (with caveats!)

One of the most unpleasant experiences of my PhD was trying to repeat the synthesis of a complicated molecule (it was about 13 difficult chemical reactions), which had already been published by a former group member. I was asked to do this at the beginning of my PhD, and I just didn’t have the skills to pull it off. The result was a feeling of complete inadequacy: “This stuff is published! It works! And yet and I can’t get it to work!?”

The problem was that – at that stage of my studies – the synthesis was too much for me. And further than that it was a loose-loose situation: if I made the compound I had done nothing new, and if I didn’t manage it, I looked silly.

The reason that you might get asked to do something like this is if a particularly interesting compound for your group has been used up and some new tests are required. If this happens, I would encourage you to think seriously about the cost-benefit ratio. How long will repeating the work take? And how likely is it that you will get a significant new insight from the extra experiments? If you feel like the ratio is unfavourable, go to your supervisor and explain how you feel – but be prepared to make a good case. And have an attractive plan for how you could better use your time.

6. Collaborate

Is there something your group can do really well, but which in itself isn’t going to furnish interesting results? Maybe you just have a rare HPLC-MS, and others in your department are jealous? Why not offer to run a few samples? You never know where it might lead.

To illustrate: a story. A labmate of mine noticed that our group was pretty good at making more-than-averagely-complex macrocyclic organic compounds (like these). These compounds are only really interesting if they are functional (they do a useful job), but there is quite a time investment in making them in the first place. My friend decided to look for opportunities to use his expertise in making these types of molecule, and apply it to what other people were trying to do. In the end, he spotted a guy in Italy who was working with some interesting components which could act as starting materials for our synthesis. He contacted him, and a collaboration followed in which my friend quickly churned out some interesting molecules and sent them back to Italy.

The net result was an impressed supervisor, a new contact in Italy, an interesting paper and a whopping smile on face of the guy in the next fumehood.

7. Ask you supervisor for opportunities to write.

If you are looking for a relatively academic career (and let’s assume you are if you are doing a PhD) then writing is going to be a hugely important skill in the future. Supervisors often get requests from relatively minor journals to do reviews in their pet subject, but may not always have the time to write. That’s where you come in – you can write the draft of the review and practice your writing skills whilst also getting yourself a nice publication.

8. Tailor your off duty activities to the skills you need post-PhD.

There’s plenty of time to do ‘extra-curricular activities’ during a PhD; from demonstrating in undergraduate practical classes to public engagement activities. There are so many opportunities for PhD students that you really must make use of them to help you with your future career. Everyone else will, so don’t miss out!

But don’t do too much – don’t neglect your research. Instead choose what you do carefully and tailor it to what you want your future CV to look like. A PhD is a training exercise. Make sure you get the right experience for what you want to do.


1. This, like my last post, is slanted towards a science PhD, and may not be true of all doctorates, like mickey-mouse English ones (joking, joking!!)

2. To be clear, I’m deliberately not making any comment about my supervisor personally here. It would be easy to find out who I worked for if you wanted to, and he is an eminently clever and talented man to work with.

Posted in Chemistry, Science | Leave a comment

Five tips for thesis writing

It’s what I call ‘Das meisterwerk.’

OK, I couldn’t resist it. There seem to be lots of these ‘the xx top tips for writing your PhD thesis’ posts around (I noticed this one via Twitter the other day which has some nice general tips). In the end I just had to write my own. If you happen to be reading this and genuinely wanting advice – rather than a bit of a laugh – you should know that I did a chemistry PhD, and so this post will be slanted subjectively towards that subject area. Just saying.

1. Write as you go.

This is a common tip, but worth repeating, especially for the tedious bits, like the experimental section. And do it properly. If you don’t, you’ll spend ages finishing off bits and looking up tiny pieces of information that would have been fresh in your mind when you did the experiments (up to 3.5 years ago), but now take 30 minutes of sorting through files of data to locate.

2. Understand what the examiners want to see from you.

A thesis can seem like a daunting prospect, so it’s worth getting clear in your mind what you actually need to achieve. This doesn’t need to be the best work of your life, especially since probably only about four people will ever read it!

If you understand what’s required of you, it’ll transform you into a much more confident thesis-writer because you will know that passing your viva is completely do-able. When the examiners look at your thesis and viva performance they basically want to see that you have:

  1. Actually done the work in your thesis (you have).
  2. Understand your research (you do).
  3. Critically assessed how your work fits into the context of other research (see below).
  4. Made clear the sources of information you’ve drawn on (have you referenced? Then, ‘tick’).
  5. The ability to put forward arguments in writing (your supervisor and labmates will help with this).

When you look at it from that perspective, it doesn’t sound too daunting, right? So as long as you haven’t copied someone else’s work, you understand what you’ve done, and have some basic research skills, you’ve covered most of these points. Hurrah! The hardest bit of the thesis (in my opinion) is critically evaluating other people’s work (point 3). That, and using it to place your own research in context. More on this below..

3. Write the introduction AFTER the results and discussion.

This might sound crazy, but trust me. You need to know what the main message of your thesis is before you can see where that message slots into the preceding literature. Know, really clearly, what your unique insights are by writing your R&D chapters first. Then you will be much better placed to decide what literature you need to write about, which you can merely need to be aware of and which you can forget about.

Then all you have to do is say what the strengths and weaknesses are of the relevant work in your field. And there you go: you have critically evaluated the relevant literature. And when you go in to your viva you can do so with confidence, because you are sure you’ve fulfilled the requirements to be a doctor.

4. Think carefully before using Endnote.

Endnote is just a real pain to use. The only advantage it seemed to have, for me, was that it meant you could find a reference on Web of Science and click a button to automatically add the details to your Endnote library.

But there are actually tonnes of other great reference management software systems out there, like Zotero and, even better, Mendeley (these are both free). Endnote cost me a chunk of money, and in hindsight I think I would have been better off without it.

5. Plan in things to do while you get other people to check your drafts.

You will definitely have to get one of your esteemed labmates or postdocs – and eventually your supervisor – to check your drafts. (This is why point 5 in section 2 shouldn’t get you down too much: you’ll get help!) But be nice to these people – they’re your friends – and don’t expect them to have it read overnight. Allow them a couple of weeks to get through it, and use the time to try planning your post-PhD life. I’ve known people who have felt pretty empty once the four-year project suddenly ends. Or just take a break; you deserve it.

So actually, writing a thesis that will hep you pass a viva is not so hard. I’m not saying it’s easy – it takes work, sure – but my landlord was wrong to assume “Wow, you must be a super brain,” on hearing I had passed my final exam. You do not have to a genius to be a PhD. I have seen plenty of non-geniuses do it in my life in the lab.

So what about all the (much) cleverer people than me who get PhDs and are geniuses? Is it fair that I have the same qualification as them? I’ve always thought that their publication record and how they conduct themselves in interviews will stand them in good stead. I’m sure that is true, but now having PhD under my belt – and knowing that I remain a non-genius – I can’t help but feel a modicum of guilt.

Posted in Chemistry, Science, Science and society | 6 Comments

Might a soul be defined by information?

Perhaps because I’m a Christian, the ‘hard problem’ of consciousness (that is, the fact that scientists don’t really know how to define it) seems to blur into the problem of ‘what is a soul’. If we have one at all, that is.

I think I have a soul. I am sure I am the same person now that I was when I was six. Even though all the matter in my brain (and throughout my body, come to that) has swapped over several times during that period, there is still something essentially ‘me’ about me. Listening to Travis, having spots and doing a degree all happened when I was a materially different person. But I’m still tainted by all those things, for better or worse.

So clearly, the matter we’re made from doesn’t define us. But at same time, our mind, soul, consciousness – call it what you will – must be intimately linked to physiology. When we die, and the flow of sodium ions in and out of our nerve cells ceases, the soul has gone. Of course, that’s not a scientific fact because it’s hard to define what a soul is. But it does seem to be a self-evident truth.

Last week I went to see a talk by physicist and Christian John Polkinghorne. He was a pleasure to listen to. He was lucid and simultaneously abrupt; at one point cutting off a questioner saying, “Yes, all right, I really think you’ve said enough, thank you.”

Polkinghorne offered a thought which I found characteristically simple and insightful of a brilliant thinker. He suggested that the soul is simply encoded information. Perhaps that is obvious – I don’t know – but I find concise and thoughtful definitions to be like gold dust.

So I started to think: what if we could somehow grasp and chart all the information that makes up a person – the memories, experiences, thoughts and ideas? If we could do that fully and properly, would we have captured their soul?

Before the end of this century, suggested Polkinghorne, we may know the answer. He was musing on the accession of disciplines like systems biology and complexity science. These are starting to help scientists get a grip on the enormously complicated information management systems that help our bodies do things like remain at a constant temperature, grow and divide, and generally behave in an intensely living sort of way. (See this article by Sir Paul Nurse, for some ideas on how systems biology might mature further).

Polkinghorne reckoned that if scientists successfully pursue systems biology, and manage to understand the feedback loops that control cells, information will eventually become a “central concept” in science. It must be information that ultimately drives the clockwork of biological systems, and perhaps it will end up sitting up alongside energy in the hierarchy of things scientists care about.

Complicated as a cell is, it is simple compared to a human mind. But if we could develop the “theoretical approaches” and “management of information flow” that Nurse sees as necessary to understand biological systems, we might find ourselves equipped with an instrument for measuring the information encoded in biology. Perhaps it will be an instrument for measuring a soul too.

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In which Bristol Bright Club doesn’t quite know what’s hit it…

Bristol Bright Club were kind enough to invite me along to perform at one of their regular comedy nights recently. I was flippin’ terrified, but I think it ended up going fairly OK – certainly nothing like as bad as I thought it might be.

I thought I would post the (by now familiar) amusingly-budget-video recording of the night here, for your enjoyment. I’d also like to know.. what do you think?! Should I ever try this again? Or shall I stick to writing serious stuff!?

NB. There was actually more of this, but since it contains personal material I decided to edit it out. Plus, frankly, I’m sure that was more than enough to be going on with!!

Posted in Amusingly budget video, Chemistry, Comedy | 2 Comments

Keeping warm and keeping on

From Cheltenham Science Festival.

“Is it possible to continue living in a civilized society, transporting ourselves around and still manage to avoid destroying ourselves and the world around us?” It’s not everyday you’re asked this question by Kryten. But Robert Llewellyn, the actor who played the mechanoid being in the TV series Red Dwarf, was on hand to pose it to an audience  in Cheltenham earlier this week.

Llewellyn and Roger Kemp, an engineering expert from Lancaster University, both agreed that it is “possible, but difficult” to keep ourselves warm and still maintain a semblance of modern life.

In an energetic talk, Llewellyn put the case that we need to get over our addiction to burning things. “We just need to stop thinking: ‘Yeah, let’s get just all the oil of the earth that we can, and let’s even burn sand to get tar out of it, and let’s just keep burning things at all costs!'”.

He said the exhaust gasses in a average household boiler can be used to spin a turbine and generate 2500 kWh of power per year. This is not insignificant; an average house uses about 3300 units annually. This kind of solution might be a good way to keep warm whilst avoiding destroying the planet, he suggested.

Llewellyn has recently met a man who developed a glass manufacturing process which used no burning at all; counter-intuitive, since glass making is normally a process which requires immense heat. The new idea used an enormous lens to focus the Saharan sun onto the sand, turning it into glass. Llewellyn said this highlighted the need for a radical re-think of the way we do things.

Kemp and Llewellyn cited three factors as stumbling blocks to this kind of radical approach to keeping homes warm sustainably. To blame were disjointed policy approaches, a lack of skills among tradesmen and a general sluggish attitude in the wider population.

The lack of skills was an especially difficult area, said Kemp, as there is no single approach to make houses more energy efficient. A typical plumber does not have the know how to install a heat transfer system properly. Training more people in these skills would help, but since so many different approaches are needed for different houses, the study time required would be long.

“Most of the houses that will exist in the UK in 2050 have already been built,” said Kemp. And there are a whole range of houses, with different properties, which will need an assortment of technologies to keep them warm without costing too much.

Llewellyn informed festival goers that he has already started to embrace an attitude of non-combustion, as far as possible. “I drove the 26 miles to get here in a ridiculous-looking electric car,” he said. “Not at very great speed, but at least I didn’t burn anything to do it!”

Posted in CheltSciFest | 1 Comment

Bioluminescent algae enter our homes

From Cheltenham Science Festival.

Rachel Armstrong’s vision is of a futuristic city lit by coloured tubes of light weaving organically through the rooms and spaces. The tubes are twisted into bizarre shapes, which can change colour to reflect moods. And they light up as people pass through the spaces, reacting almost intelligently to the presence of humans.

The power source for these tubes is not electricity but bioluminescent algae.

“The wicked thing about algae is that they luminesce in response to vibrations,” said Armstrong, at an event entitled ‘Future Buildings’ in Cheltenham yesterday. This would mean that not only would bio-powered tubes be low carbon, but they would also switch on in response to people moving around close to them.

Will future buildings really contain biological power, and perhaps even living structural components? Armstrong hopes so. Better integration with synthetic biology could “re-infuse our living spaces with the emotion they lack at the moment,” she said.

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CDTs: where’s the evidence?

In 2008 the EPSRC decided to slash the number of PhD project studentships it funds by 33% and switched £300 million of its funding to Centres for Doctoral Training (CDTs) instead.

Many senior scientists were angry about this, and I personally felt a bit disappointed in this decision. I felt like the EPSRC were taking a swipe at project PhD students like me. In the end, I went on an unattractive rant, which I’m not massively proud of, but which does explains some of the issues.

I wanted to find out if there was any evidence that CDT students would be ‘better’ than project studentship PhD students. For example, the business skills that CDT students are supposed to develop might provide the UK with better economic returns on the investment in PhD students. If that is the case, then perhaps the EPSRC has made the right decision.

The ESPRC provided me with this report which analysed a four year PhD prgram in neuroscience run as a pilot scheme similar in nature to contemporary CDTs in the 1990’s. One key point is the following:

For example, the programme’s management committee looked at the productivity of ex-students nine years after they started their PhDs and found that scientists who trained on UCL’s four-year programme published approximately twice as many papers as scientists who had been accepted for the scheme but opted to go elsewhere for their training.

But I wasn’t completely convinced. Does publishing twice as many papers automatically mean that CDTs should completely replace project studentships? I wanted to do some more digging and the Times Higher Education were kind enough to host me while I did it. My report is published today, and was co-written with Paul Jump.

I have no wish to criticise the EPSRC or any CDT, but I do think this switch from project studentships to CDTs is important enough to get talked about more. I look forward to the comments under the THE article…

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