Reflections on my PhD - Part 1: The End Goal(s)


Recently I have been thinking a lot about academic careers and the effort we all put in to give us the best chances of success. I realised that PhD work often makes up a substantial proportion of this, and despite the fact I finished my PhD almost two years ago I still haven't fully decompressed the experience in my head or thought about how it went - pretty weird for someone who runs a blog that was born through the desire to find out more about the 'PhD experience'. Even people who have had mostly positive PhDs go through stressful times and so I think it's worth exploring areas where I found it possible to make some changes that, in hindsight, made my life easier. Is this a slightly self-indulgent and somewhat ego-centric exercise? Perhaps. Is it a very anecdotal and personal experience? Definitely. But, are there possibly some things that might help people or be interesting to read about? Maybe. And so I thought, in the absence of many people reflecting about their PhD experiences in detail, why not put my experience and thoughts out there.


I've split my experience down into a few topics that may be food for thought if you're going to start a PhD or are in the middle of one. As with most things on the blog, these points just reflect my personal experience but I suspect that at least some topics might resonate with others, and might serve as things to think about in your own project. In this first instalment I wanted to talk about how, after struggling with a lack of direction and formal structure in my PhD, I tried to come up with a way of thinking about my work that would give me some structure and focus.


Many people enjoy academia because it's a chance to explore areas of personal interest without feeling like part of a corporate machine. Unfortunately, I quickly realised during my PhD that this lack of clear well-defined deliverables, metrics of performance, and formal structure, as well as feeling like I was out on my own trying to find something interesting, made me feel aimless and ultimately stressed. I think this feeling stemmed from the fact that everything leading up to my PhD, my school work, BSc and MRes were filled with quantitative (albeit of course artificial and flawed) measures of how I compared to others. As a chronic worrier, the absence of these stupid metrics left me perpetually concerned that I wasn't doing enough, or at least not enough of the right things, and left me not knowing if I was doing enough to set myself up for success, something, like many people, I obviously desired (despite not always knowing exactly what this would look like anyway). The best way I found to combat this feeling, and one I wish I had found a bit earlier, was to frame my desired future path as a set of key goals, with the focus of my PhD being able to achieve these goals, a bit like ticking milestones off a list. In a sense I viewed ticking off these goals a bit like a game, and while, like in any game, succeeding in academia requires luck, and of course you can't control many aspects of it (I think it's best to try to be a bit stoic about that component, although that's something I struggle with and a topic for another post), I think there are absolutely things you can do to give yourself the best chance for success. 


Some might view the whole idea of treating a PhD like a game to be played quite cynically, especially those who see academia as an all-encompassing lifestyle rather than a job, but I think the 'game' can represent a path to achieving whatever goals you want (and perhaps how unhealthy it is depends on how jaded and/or incurably competitive you already are). For me, thinking about my day-to-day work as a means to an end helped give me some direction to my day to day work as well as a degree of personal detachment that I needed when things got difficult. A lack of personal detachment, I might add, that I suspect is one of the main reasons that unexpected hurdles that crop up during a PhD causes so much anguish for so many students. The path to achieving my goals, or my personal 'game', ultimately consisted of me trying to put myself in as good a position as possible to get a postdoc fellowship at the end of my PhD, and to try to set myself up for making an academic career a viable option in the future (both of which I'd guess are pretty common goals). By treating it as a game to be played I felt like I had at least some power to change things in a system where lots of things feel chaotic and uncontrollable (like worrying whether your fieldwork will yield the data you need from enough samples, the manuscript draft you are working on will be approved by all your co-authors in the time frame you had in mind, or the paper will be reviewed favourably by reviewers). For what it's worth, even if this ability to change outcomes in science is an illusion I think it can be a healthy one to have day to day, and without it I would have really struggled to finish my PhD. 


Viewing my work as 'playing my game' also put me in a better frame of mind to understand how the competitive side of academia works. While it's super unhealthy to view your academic peers as directly competing with you I think it's safe to say that at every career transition that is absolutely the case and it would be naïve to think otherwise. Although I think it's safest and healthiest to imagine yourself playing your game against academia and not any particular people, at the end of the day there are points in your career (whether you stay in science or not) where you will have to be able to back yourself and feel confident with how your CV will will look lined up next to someone else's, knowing that you did what you could to give yourself the best options. Since so many things in academia have big time lag between starting them and finishing them I also think having the structure of defining specific goals as part of a game avoids the last minute scrambling to put something together when it's needed. Set the goal early and work towards it. Realistically you're not going to be able to write and publish a paper in the two or three months before the application deadline of your dream fellowship or job, and so I think it's best to think about personal goals ahead of time and structure your days/weeks/months/years as a way of working towards them. Of course it's worth saying that I have also met super talented people who seem to be able to follow their interests and still achieve amazing success without any apparent structure, but I would rather take a structured approach than rely only on luck or prodigious talent (which I'm very aware I do not have).


What did all of this mean practically? Well, through taking the advice and insight of people I looked up to (and ignoring those from some I didn't), I made a mental list of things that I felt would help me achieve success and set these as the main goals in my personal 'game'. Day-to-day when I was at work I kept these goals in mind as something I was taking small steps toward, rather than a structureless four-year block of time where anything could happen. Broadly, my goals could be broken down into three main topics, meeting people, writing papers, and acquiring skills. Here I'll go through each of these goals describing what I aimed to do and my post-PhD reflections on how I think it's best to work towards each:


1) Meeting people

I think it's no secret that knowing people in science is valuable. It is a great way to get a sense for the work being done in your field, to foster new ideas and approaches, and to get an insight into the unspoken parts of academia. This includes who you should or shouldn't work with, which institutions are good or bad, and advice on what conferences/workshops/seminars are worth attending or applying to. On top of that, it's a way to find mentors and make friends in what can otherwise be a bit of a lonely professional setting - perhaps even more so in recent pandemic times. I have relied on the friends and mentors I have found numerous times when applying grants, writing papers, or just developing project ideas. Having the idea of meeting people as a core aim of my work made it easier for me to approach people after seminars or at conferences to discuss science or even just chat over a coffee, particularly early on in my PhD (although I know people who are more shy might still find this a big challenge). I was also lucky that my PhD supervisors not only encouraged me to meet people but also facilitated it during conferences by introducing me to their friends and mentors. I am still shocked to see people not introduce their students/postdocs/collaborators to as many academics as possible and honestly see this as a huge shortcoming as a mentor (more about this in Part 2 which will come out soon). If you know someone, even vaguely, and you have the chance to introduce them to one of your peers, friends, or colleagues, then just do it, it's such a fundamental way to have a positive impact on their career and the academic community in general (of course the same goes for giving people a heads up as to who to avoid in these settings - look out for each other). 


2) Publishing 

While this may be obvious, and despite the fact that there is a big component of publishing that is out of your control (including the availability of co-authors/collaborators, time, help with learning to write papers), I think there are almost certainly things you can do to set yourself up well for success in publishing papers. The most important thing in my mind is to come up with a vague chapter/publishing timeline with your supervisor(s) and mentors as soon as possible in your PhD. Of course this can and will change (and getting data and analyses done is a whole other thing - again though this should be discussed with supervisors), but for me having the structure of knowing roughly how the next few years could be broken down into manageable portions in my mind was key to being motivated and knowing whether i'm on the right course. This is not contingent on your perception of the 'impact' or novelty of these mini-projects. In my case we decided early that my PhD would be split into two main parts, the first being the production of new genomic resources and the second a large population genomic analysis. This meant that as I worked on one chapter I was able to gauge whether I was on track and what my time frame for the other parts of my project needed to be to hand in. It also meant that I could start reading around to see what kinds of papers people were publishing the same kinds of questions and the analyses and even figures that make up these papers. This can be done in advance of even getting your data and just gives you an idea of the end goal you're working towards. Of course the details of the paper and the angle you will write it from will change with your analyses but I think it's often the case that once you have some idea of what's required to have a publishable unit then the path to achieving that is less stressful. 


Another key component of publishing is of course writing. I strongly believe that writing gets easier the more you do it and with that in mind it is best to start writing early and regularly, even if that is just writing short summaries of key background papers for your PhD, the introduction or background to a paper you're thinking of writing, or even non-academic writing like blog posts, tutorials, or even work diaries or fiction. I know writing isn't easy for everyone but it is absolutely inevitable that you will have to write a lot, and so writing and getting feedback on your writing as soon as possible before you're in the time crunch of your PhD is extremely valuable. I have seen way too many people sit on great work, eventually missing the window of time in which it would have gained even more attention by being at the cutting-edge because they put off writing - this is a real shame. If you know you struggle with this maybe you can find a trusted writing partner to exchange drafts with - getting feedback from someone you trust can help break the deadlock when working on a manuscript.


The last aspect of publishing that I was aware of, and something I think everyone should have some say in is the approach of where to submit work. This, I've learned, is a balancing act (especially these days when discussions of which journals are good/bad are a merry-go-round) but I think for PhD students who will undoubtedly face competition for jobs/fellowships impact is still important. I don't just mean journal impact factor specifically (this might be more important to some than others) but ultimately if your work isn't read then it's hard to get credit for it or have much of an impact anywhere. I think most people would agree that work that is not accessible or read is not valued as much as work that is read and at a time when everyone is bombarded with papers it's worth thinking about the ways you can get your work in front of people's eyes. Journal choice is definitely something that can do that. I have found that looking at what kind of work journals publish and asking more experienced academics is a great way to see where to pitch a paper. Then from a list of suggestions you can see which journals satisfy all the things you want - e.g. if it is a society journal or not, open access or not, and whether the impact factor is 'right' (I'll try to stay away from the debate on what this means but most people can judge if they are writing a short descriptive paper or a huge multifaceted and comprehensive study with humanity-altering implications and can submit it to an appropriate journal), whether it is general or specific enough for the story you have, and whether any of the journals stand out as those you like to read. Then it's time to look at the author guidelines for that journal and start crafting the paper to fit those guidelines. If I can give my core personal tips for writing they would be:

- Start by putting your name and affiliation at the top of the document and add even a placeholder title as soon as possible. This means that rather than seeing a blank page or random thoughts when you open the file you see something already resembling a paper.

- Write down a bullet pointed paper first. For me this often means writing an introduction off the top of your head listing the key background topics someone needs, then informally outlining your results, and writing a list of talking points for the discussion section - then you can work on filling out each section. I find that having an idea of what to work on next and being able to flit between sections avoids writing paralysis.

- Write the methods sections as you do the analysis, add software names, links, and version numbers as you go

- Have a section at the bottom of your document listing your main take-home message and keep referring back to this as you write, adjusting the main text and/or this list of take-homes as you go


3) Accumulate skills

I think one inalienable truth is that as far as careers go, the more diverse your skill set, the better you are set up for success. In your PhD, these skills can include things like carrying out specific types of fieldwork, learning different analysis approaches, and even project planning and writing. One thing I knew I wanted from my PhD was to learn how to do bioinformatics but I was also aware that I didn't want to become someone who could do one type of analysis and then just do that in a bunch of different systems. I don't judge people who have taken this approach because they are often super valuable scientists who help develop these approaches but I do think this strategy makes things quite challenging down the road, particularly if there are many others like you out there or the field inevitably moves on making your skill set somewhat obsolete. Instead, I wanted to carry out a diverse range of analyses that allowed me to answer specific evolutionary biology questions and also wanted to handle lots of different types of sequence data. I felt like after my PhD this experience of handling different data types would be useful (which has proved to be true) and that after exploring all the different analyses I could do with different data sets I would have a broader set of options for postdoc fellowships or future projects. This one can be tricky since I have seen some people get put into one kind of 'box' either because of their group, which might be experts in a specific approach and so by default this is the skill they also learn, or by a group leader/PI who needs someone who can do one specific type of analysis across projects and focuses their efforts to train a student in that one approach. All I would say is that you should be aware of the kinds of approaches you'll learn during your project, think about how this set aligns with your interests and desired skill set at the end of your PhD, and if needed then discuss with your supervisor how you might be able to gain other skills. One way to gain skills outside of your day-to-day work would be to see if there is budget in your group or part of your PhD program for courses where you can fill in the gaps. Alternatively you can try connecting with other people in the department or even online and asking if they have any tips for learning some approach, they might be able to point you in the direction of tutorials, courses, conferences, or workshops that could help.


And that just about wraps it up - the three main goals of my PhD and how I tried to work towards them. How well I managed this I'm not sure, but undoubtedly I did more of each thing than I would have had I not viewed them as core goals I was working towards. One thing I learned about a PhD is that people who seek out specific things typically end up doing more things that satisfy them than people who are passive and would rather wait for things to come to them. If you can muster the energy to chase some specific and personal goals, and ultimately your PhD is a nice chance to be a bit selfish in this way, then go for it! If you're anything like me you might also stay a little more sane with the motivation and structure it provides.


Next time I'll be talking about the student-supervisor relationship (and possible conflict) so keep an eye out for that soon!





Comments