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Publishing my first scientific paper

August 22, 2014

As part of my blog catch up, here’s a much delayed post on my experiences publishing my first paper, earlier this year!


Any one who works in science will tell you that the currency of science, your worth, more so than any qualification, is your scientific publication record. “Publish or perish” they say as you wonder yet again how you’re going to fit in paper writing along side doing your research, finishing your thesis, teaching etc before you run out of money or sanity.

If, like me, you did a 3 year honours and a year taught masters, as is common in the UK, chances are you may only have one (if not no) paper to your name when you start a PhD – usually a reflection of your lack of independent research experience.

I’ve rectified that lack of experience during my PhD. I look back and I can remember when I applied for my PhD and was thinking “how can I write a proposal, I don’t even know enough about oceanography to know what questions I would need to ask?!”. Now the prospect of starting a new project excites me, I have so many questions I could ask, new topics I’m keen to work on. But until recently that much desired moment of seeing my name in print on a scientific paper had eluded me.

I think mainly it’s taken so long due to a lack of confidence in my own subject knowledge. Most of my colleagues had done 2 year research masters in remote sensing/optical fields before coming to their PhD. With my rudimentary knowledge of optics gained from working with ocean colour data products during my masters, I felt a little out of my depth for most of the first year of my PhD. Things picked up in the second year. With my knowledge base growing rapidly, I was asked to contribute to a couple of projects, including some data analysis for a paper and book chapter. With guidance from colleagues I began to see what it took to get your work to a publishable standard. By the end of my second year, despite submitting several pieces as a co-author, I still had not seen my name in print. The concept of trying to apply for postdoc work without a single publication, let alone a first author one was terrifying.

A second delay, I think, came from my research itself. I’ve been developing methods – more specifically, algorithms – to apply to ocean colour data (literally the colour of the ocean, for more info see here). The problem with this is that there’s often an end goal. In my case, I wanted to derive some information on phytoplankton (tiny plant-like organisms which live in the sea) to an acceptable accuracy. It’s not really the same approach as much of science – where you set a question (hypothesis), test it and report what data shows. I’ll freely admit it seems that publishing negative results, the “we don’t know”/”it didn’t work” answers in science is hard and I think in an ideal world this would be easier, if only to save postgraduate research students wasted time! The good news is, the difficulties I had with getting my methods to work, and explaining why in some cases they didn’t, has ultimately improved my understanding of my subject and lead to me finally publishing my first paper!

My approach had initially been to develop some algorithms to look at the size of phytoplankton in South Africa’s coastal waters – the Benguela upwelling region in particular, using ocean colour. Eventually I found myself more involved in a fundamental question: to what extent can we look at cell size using ocean colour data? Encouragement and support from colleagues and my supervisor assured me that this was a worthwhile question and with their help I reworked my research strategy. Combining modelling and in situ data measurements to develop and test our method proved very interesting and has given us a new structure to investigate a whole range of questions about ocean colour.

My paper was submitted to Optics Express; an open access, online publication. The review process was quick, with two reviewers responding with a few weeks of my submission. The first response was encouraging. It contained a lot of constructive criticism, which meant some work for me, particularly on making the figures clearer and simpler – something I had really struggled with. Ultimately this reviewer made it a much better paper, picking up on points I probably couldn’t have, after being so close to the work for so long. It seemed to me that this is how science should work. I felt they’d paid attention, engaged with the work as a concept and offered well thought through comments and words of encouragement. I don’t know who they are, but I’m grateful to them for not only for helping improve my work but also for providing an example of the type of reviewer I want to be. The second reviewer…well, luckily I had a glass of wine in my hand when I read their comments, and a supervisor who tends to read his emails at night to calm my mild panic! After re-reading the second review the next day I realised that this reviewer seemed to have misunderstood the paper and so I set about a) making my findings and their importance abundantly clear in the manuscript and b) carefully refuting their broad comments with all the knowledge I had. Rather than feeling downtrodden, as I might have expected given my previous lack of confidence, I was determined.

By the end of the review process, when my response and the paper were accepted, I felt something I’d not really felt at all in the PhD process – pride in my work. Meanwhile, two more co-authored papers and a book chapter have been accepted and I’ve got one more paper submitted and two in progress. I feel like an actual scientist now and it’s nice. It was particularly fortuitous that his happened in January as I began the final push to finalise and submit my thesis.

Some things I’ve learnt from this and will carry forward:

– Thinking about publications as an end goal. Whilst I can look back now and be happy that I got to freely follow ideas and develop knowledge during my PhD, in future I want to balance this curiosity with asking questions that should be more easily turned into publications.
– Co-authors: Very few people publish papers on their own. I think choosing co-authors well can make life much easier. I’m lucky to have an awesome supervisor and a couple of close colleagues who have collaborated on this and now other papers too.
– Reviewers are people too. I don’t know who reviewed my paper and why they responded the way they did, for better or worse. I do know that I put in a lot of work and thought a lot about my research before I submitted my paper. I think knowing when comments are constructive and should cause concern, and when comments are unnecessary/biased/wrong or even cruel etc isn’t easy and I imagine many young scientists like me will take negative or critical comments to heart. With this in mind, I intend to a) not take any comments too personally without assessing their context and b) make sure when I review papers that I provide constructive feedback without unnecessarily negative and cruel commentary.

As I mentioned, my paper is open access so anyone can read it and it’s available online here.

I also found this great piece on being a good reviewer, which I will definitely be when I get the chance to be on the other side of peer review.

What have your experiences of the peer review process been? Please feel free to comment below 🙂

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