Digital Spring Cleaning

phdcomics save

(Source)

I cannot stress how important backing up files is. It’s one of those things that many people learn the hard way. I’ve lost enough bits of work over the years of doing school homework and undergraduate coursework on computers that I now have a slight obsession with saving my work every couple of minutes and also regularly copying my files into several different places. I still occasionally lose a bit of work, but mostly through unpreventable and sudden network/computer crashes. I have a serious fear of and aversion to this happening and use creative damage control options (once I even resorted to taking a photo of my frozen computer screen and using it to re-write a paragraph of work after restarting the computer).

I would much rather prevent the loss of any data, if at all possible. Some of my regular preventative strategies for minimising chances of losing work are:

  1. At the end of every day and sometimes throughout the day too, I will back up the most important files I have been working on by copying them into my dropbox folder.
  2. I tend to have a subfolder labelled ‘old drafts’ in any folder with ongoing work (e.g. paper I am writing, talk I am preparing or database I am using for analyses). This is just in case I accidentally or deliberately delete something I later decide I need.
  3. I also write a note to myself in my calendar to back-up everything (to a different drive, preferably more than one) about every 3 months.

I’m sure this all sounds great and hyper-organised but it is not a full-proof system. To begin with, I have a ridiculous amount of duplicated files all over the place. I regularly use lots of different hard drives (2 on my work computer, 3 networked drives I can access from any university computer, 2 drives on my laptop and one external hard disk) and about 5 memory sticks scattered about the place. Also, in addition to uploading files to dropbox, I still sometimes email things to myself (old habits die hard). It can occasionally be tricky to find something, especially if it’s something I haven’t worked on for a while.

I have gradually learned to label documents, folders and subfolders in a sensible and informative way but this just means that some files/folders have rather lengthy names. Sometimes I need to use the search tool in Microsoft to find where I squirreled away a particular document.

One helpful thing which goes some way towards mitigating the chaos is that I have one primary drive I use, where I keep all of my up-to-date files and I put back-up files in the various other places. Lately I’ve been trying to do some tidying up to sort through the mess. However, deleting files is a slightly frightening thing to do and involves double checking things really are duplicated or massively out of date. Generally, I just leave things be as I have loads of extra storage space anyway.

I have a similar approach to my emails. I like to keep my inbox relatively clear so as soon as I have read and replied to or otherwise dealt with an email, I file it away. I have a labyrinth of folders and sub-folders for my emails. I only wish our email client at work was as sensible as Googlemail so I could label/file emails under more than one category. I do tend to have to use the search tool quite regularly, so obviously my filing system isn’t optimal.

If anyone has any tips on keeping your digital stuff organised and backed-up, do share.

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A Framework for Mental Health Research (RDoC)

Although the Research Domain Criteria project (RDoC)  is not particularly new (the description of it on the NIMH website is dated June 2011 and it’s been on my reading list for at least a year), there has been a lot of attention drawn to it recently. This is partly because the DSM-5, the new psychiatric diagnostic handbook, is due to be published on May 18th, prompting Thomas Insel, director of the National Institute for Mental Health (NIMH), to recently write about the necessary next steps in mental health research (see here and here). I’m sure many others (for example The Neurocritic) have written about this recently. Having finally gotten around to reading about RDoC on the NIMH website  myself, I wanted to briefly summarise what it is and why it’s brilliant. If you haven’t heard of RDoC or keep meaning to look it up, this is for you.

The RDoC project is a framework for thinking about and researching all aspects of human psychopathology/mental health, without confining the research to existing diagnostic labels. The DSM-5 is the best thing we currently have for the purpose of clinical assessments and diagnosis, in the hope of trying to treat and improve the lives of people with mental health difficulties. But research suggests that it isn’t good enough.

In reality, mental health conditions overlap greatly, both in terms of clinical presentation, associated features (e.g. cognitive difficulties) and in terms of apparently non-specific risk factors (e.g. many genetic variants have now been shown to play a role in more than one condition (e.g. schizophrenia, autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD), all previously thought to be quite distinct conditions)). Even within a diagnostic category, there is a lot of variability in severity and also, you don’t need a diagnosis to have problems; symptoms below diagnostic thresholds often cause difficulties for affected people. It has become clear that mental health problems are not binary. Instead, there appears to be a continuous distribution of mental health difficulties, ranging from none to very severe.

The RDoC framework is about cutting across these diagnostic labels and looking at the underlying dimensions of behaviours and measures of neurobiology. The idea is that recruiting participants to a study on mental health based on their diagnoses and then trying to determine how they differ from “healthy” controls in order to inform research on diagnoses, is actually a little circular. The alternative approach, suggested by the RDoC framework, is to recruit participants with a range of related problems (e.g. all types of mood disorders) and look within this group.

RDoC

(Example of the 2 main dimensions of the RDoC Framework)

The framework divides up mental health into a list of constructs (such as ‘Responses to potential harm (Anxiety)’, ‘Reward Learning’, ‘Cognitive Control’ or ‘Social Communication’) within more general domains (e.g. Cognitive Systems). It then divides research approaches into units of analysis (e.g. Genes, Molecules, Cells, Observed Behaviour etc.). Two other dimensions are ‘Developmental Aspects’ (how these constructs change over time) and ‘Environmental Aspects’ (how the environment affects and interacts with the constructs).

The hope is that considering mental health in terms of these dimensions rather than diagnoses, will serve as a research framework for improving our understanding of mental health and creating better diagnostic categories for the future. This framework seems to me a much more valuable way of doing research in this area. It reminds me of a great blog post by Dorothy Bishop from 2010, in which she argued that neurodevelopmental problems should be considered on a number of developmental dimensions, rather than as discrete clusters of difficulties (i.e. diagnostic categories). I was very inspired by this way of thinking when I first started my PhD and so I think it’s great to see that the NIMH is encouraging researchers in mental health to adopt this way of thinking.

Learning how to say ‘no’

(Image source)

One of the things I absolutely love about academia is that I am never bored through a lack of having anything stimulating to do. Outside of academia, I have experienced a job in which sometimes I had no appointments and no outstanding work I could do. I really struggled with this and tried to make work for myself and look like I was busy. But this felt more stressful and tiring than actually doing real work and it probably looked a bit odd when I was trying to tidy the office every single week… Fortunately, nowadays my to-do list always has a lot of really interesting things to be getting on with. Even the slightly more tedious things on there are at least satisfying to complete and tick off the list. If I ever feel like I’m at a point where I have tackled all the ‘Really Important and Urgent Things’ on my list, there is always the other half of the list, with all the ‘Things That Would Be Interesting and Useful To Do At Some Point’, or indeed the enormous pile of reading material next to my computer, which never seems to shrink much.

I love being busy, but as with all things, there is a point at which the stress flips from being motivating and positive to a bit overwhelming. Finding a balance and trying to maintain it is crucial for your mental well-being. When things start getting to be too much, it becomes clear that some things need to fall by the wayside if others things are going to get done to a good enough standard. But how do you choose what these things are and how do you say ‘no’ to the things that you’ve judged as less important?

I try to always be available to help anyone who would like my help, partly because when I first started my PhD I was always seeking other people’s advice, partly because I still do this a bit and partly because I genuinely like to help others when I am able to. When my PI asks me to help with things that aren’t directly related to my PhD, such as doing a literature review on a specific topic, giving a talk, attending a meeting, or doing an analysis on something she’s just thought of, I wouldn’t even consider saying ‘no’. But there comes a time when you realise that taking part in an hour-long monthly teleconference you never say anything at would be better spent doing something else and just reading the minutes when they come through by email.

So how do you identify the things that really will lead you off track from your PhD for too long and how do you say no to them? I’m probably not the best person to ask as I will say yes to things 99% of the time and if I don’t end up doing them it’s most likely that they are still on my to-do list and I still intend on doing them, but I was assured that they weren’t really that urgent…

A blog post from last year by Arthropod Ecology contains what seems like good advice on this subject:

“You will always be asked to do more than you can do, and at some point this can break you.  Stay somewhat selfish, and say no to things that take you too far from your career goals.  The key step to getting an academic post, and keeping it, is often research productivity, and so at the later stages of your PhD and early on in your academic position, keep focused on research and try to manage your time to keep that part of your portfolio moving forward.  I think it’s too easy to let research productivity slip when you are balancing other pressures of Academia.”

The importance of learning to say ‘no’ will probably become clearer to me the closer my PhD thesis deadline approaches and my time feels more precious. At the moment, I’m generally happy to help others out, but especially if my help is likely to result in authorship on an eventual paper or a senior person thinking favourably of my apparent positive can-do-attitude when looking for a post doc…

Fitting the pieces into a thesis

I’m very excited that my first PhD paper has recently been accepted for publication, after a supposedly ‘minor’ (but actually quite tricky) round of revisions. My plan is for this paper to be one of my first results chapters in my thesis. I’ve also got some reasonable ideas and have begun on my next 2 chapters/papers. This feels pretty cool on the whole but being ever the pessimist, I can’t help but worry about something. I think I’ve been dwelling on the bigger picture lately because of watching a few of my friends recently submitting their theses and having their vivas (i.e. defences) as well as having had to prepare an overview of what my completed thesis might look like for my appraisal a few months ago.

The attitude in my department, and specifically amongst my supervisors and colleagues, is that I should be focusing on writing up my PhD results chapters as I go along, with the intent of submitting them for publication as soon as possible. I quite like this approach as it is very motivating and makes my PhD feel like a real contribution to science, rather than just as a personal learning process that has no benefit to anyone but me. However, one of the difficulties with this approach is trying to tie together my ideas and publications into a coherent whole, which tells a story with a logical progression of ideas. As far as I understand, this ‘story-like’ nature is important in a PhD thesis.

However, I’ve also been told that it’s generally fine to just have a collection of loosely-related published chapters inserted into the thesis exactly as they were published and to maybe include brief “link” chapters between them to tie them up a bit better. The Thesis Whisperer refers to this kind of approach to your thesis as a “patchwork PhD” but like the friend she refers to in her post, I kind of feel like this is cheating a little bit; I don’t like the idea of not having a seamless and logical argument threading through my work. I’m also a bit concerned that having a set of introductions, methods and discussions in each of the “Results” chapters will mean the thesis Introduction, Methods and Discussion sections will be very repetitive. I’m not sure that boring my examiners with repetition is the best approach to convincing them to happily accept me into their midst…

So although I am not quite halfway through my PhD time-wise, I have already begun worrying about the structure of my thesis. I’m not really sure how I might link up my 3 planned results chapters so far and it feels important to address this issue now, before they’re finalised. Additionally, I feel the need to plan my next analyses in light of trying to have a coherent end product. It feels like a tricky thing to tackle but I guess this is a more organised approach than trying to find a way of trying to fit the pieces together once everything is all written.

The self-reliant part of the journey

I often hear that mentorship is a key ingredient of success, and not just in academia. I’ve certainly found that when in doubt, getting advice from someone who knows more than you is the best and fastest route to figuring out a problem. As PhD students, we have supervisors, advisors or tutors to help keep us focused and approve what we’ve been doing. However, supervisors are really busy people with a million and one responsibilities. At a recent talk on tips for successful PhD students, the top tip was to nurture your relationship with your supervisor. The speaker pointed out that you should be the driving force behind initiating meetings and interactions with your supervisor and you should not expect them to take the lead, as they are likely to be too busy. To be honest, the speaker basically said that you may need to resort to “gentle stalking” in extreme circumstances of busy/disorganised supervisors…

I haven’t ever had to resort to anything like that but then, up until now I have been supremely lucky, having weekly hour- or even 2 hour-long meetings with my main supervisor. These have really given me the chance to ask the sorts of things I might otherwise spend fruitless days trying to figure out myself without every really getting anywhere. They’ve also been a brilliant motivating force; by the time all my various Monday meetings and seminars are done, I really need to get moving if I want to get enough done to have something useful to say by the following Monday meeting.

(Image by Tim Hamilton)

Sadly, the good times have come to a halt. As of next week, my supervisor is off on maternity leave for the better part of 2013. Although I am not in any way being abandoned (I have 2 other supervisors whom I might see every now and again and there are other people I can go to for help if need be), I will not get the same level of support that I’ve been virtually spoiled with this last year.

The first year of being a PhD student is perhaps the most crucial for having nurturing guidance and support in finding your feet. Now in my second year, my analyses and ideas are in motion and I have a plan of what I will be doing next (though this is more likely to change than not). I’d like to think that I’ll be completely fine but part of me is worried that I’ll go off on a tangent or get things wrong without someone to look over my shoulder more; this is probably another form of imposter syndrome rearing its head. Hopefully, I’ll adjust to the change ok and muddle through somehow. Maybe it’ll even be good for me, by forcing me to become more independent?

Graphing time

Graphs are awesome. They can convey so much information at a glance. I was inspired by a recent blog post by Heather Doran, in which she included a pie chart breaking down what doing her PhD thesis looks like. So I decided to make my own chart of what I spend most of my time working doing (minus lunch and the odd tea break that is).

graph

Part of me was very tempted to actually try to keep track for a few weeks and use real data for the graph but really, I’ve got plenty of more useful things to be getting on with! So this is more a hypothesised subjective feeling of what it is I do. It is probably quite different from the beginning of my PhD this time last year (I think the reading/taking notes bit would have been more than half of the pie then) and probably equally different to what my PhD life will be like in a year.

Balanced feedback

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I recently wrote about taking the time to reflect on PhD progress and mentioned that I had my end-of-year appraisal coming up. I’ve had it since and I think it went fairly well on the whole. Despite this, something about the experience has been bothering me. This something is a more general feature I’ve noticed about academia.

When I arrived on time for my “mini-viva”, my panel asked me to wait outside the room so they could have a quick chat beforehand. Though friends had mentioned this happening to them, I thought it a little strange; the panel could easily have met slightly earlier or just told me to show up later. Waiting outside, I could hear bits of what they were saying through the closed door, even after moving to stand at the far end of the corridor. This was both a little embarrassing and intriguing as it gave me some idea of what to expect. They started out their chat by briefly saying they think I am definitely on track (yay!) only to proceed to try to come up with negative things they could say about my report. I got the impression that although they thought things were going well, they didn’t want me to feel that I could rest on my laurels (as if I would!) and that there was room for improvement (obviously). So, although the actual interview was fairly relaxed, it had a definite feel of questioning and (constructive) criticism about it, with me attempting to defend my work (presumably as practice for my real viva in >2 years’ time).

I know that although I’ve worked hard and my supervisors said they were pleased with my progress, my work to date is far from perfect and at the moment, that is still ok. And I understand that the job of the panel was to draw attention to any imperfections, check that I understand various important issues and make suggestions for improvement. I’m actually really happy with how my mini-viva went and I received some useful feedback and suggestions for what to do. My panel were not mean or rude and certainly did not seem to be trying to poke unnecessary holes in my work – in fact, most of the issues they brought up were things I was already aware of to some extent. However, they seemed to shy away from saying anything overtly positive, so that it took some reflection afterwards for me to decide if it had actually gone well or not.

The thing I am trying to get at is that I get the impression that there is a general shortage of explicit positive feedback in academia and a tendency to be overly critical. Granted, a healthy amount of scepticism and constructive criticism is an essential component of science. It’s also vital to learn how to take such criticism and advice without taking it personally. As early career researchers, we are explicitly taught and encouraged to look for flaws in and criticise previously published studies. Our supervisors and colleagues edit our work and return it covered with tracked changes in all the colours of the rainbow. Journal reviewers can seem to go out of their way to be hostile and rude in pointing out limitations, even those that we have already acknowledged and discussed in our manuscript. Understandably, Q&A sessions after talks tend to focus on what has not been done or addressed fully. From my limited knowledge, grant committees appear to be the fiercest of all critics. There is always room for improvement – this is not a bad thing, just a statement of fact.

The not-so-great thing about this attitude is that there can be a lack of positive feedback, leaving us PhD students attempting to infer what more experienced researchers think is good or interesting. Once all the reports, essays and exams are done with at university, there is little in the way of formal feedback in academia. There are no grades and it can be tricky to know how well we are doing. Perhaps, ideally supervisors and mentors should offer encouragement and praise where deserved, but really, there is no reason others cannot do so too. I think that drawing attention to strengths is an important way to balance criticism of limitations. It’s not just polite but also pleasant when someone from the audience starts a question after a talk by saying “I really liked how you did X, but can you tell me more about Y” or when a reviewer says “this study makes an important contribution with regards to X, however there are some limitations which could be addressed…”.

Many PhD students suffer from imposter syndrome. This is why feedback should be a combination of positive and critical comments. Nobody (certainly no PhD student) always does perfect science but if you have got as far as successfully enrolling on a PhD programme, you obviously have potential and this potential needs to be nurtured. Occasional affirmation from those you look up to can go a long way towards boosting confidence and feeling like you are on the right track.