Writing a Science PhD

Jennifer Boyle, Scott Ramsay

• Publisher: Bloomsbury Academic
• Year: 2019
• ISBN:
  9781350315365
• Edition: 1
• Topic: Study Aids
• Subtopic: Study Guides

This practical guide will help scientific researchers navigate the core stages of their PhD writing journey, from refining their research question to structuring, editing and proofreading their thesis. The authors, both of whom have first-hand experience of working with PhD researchers, set out what's expected from PhD writing, help readers to establish good practice, and provide tips on how to overcome common roadblocks during the writing process. Chapters are enriched with insights from nature editors and student researchers. Looking beyond the PhD, the book also features a chapter on writing for publication, which will help researchers to think about how to translate their research into high-impact journal articles and papers. This is an essential companion for all PhD researchers in the sciences.

CHAPTER 1 What the PhD Is, and What It Isn’t

Many students we talk to tell us that they spent a lot of their first year confused about what they should have been doing, or wondering whether what they were doing was ‘right’. Many felt other students simply knew more than they did about everything from internal university procedures, to writing the literature review, to managing supervisory relationships. We’ll try to give you an idea of what these are each likely to require of you.

We’ll discuss what students tend to assume, and how this aligns with what institutions actually want. We’ll examine topics in the context of how they’ll introduce you to, and acculturate you in, the wider academic community. This chapter will also ask you to consider how ‘embedded’ you feel in your department, and get you thinking about what you might do in order to feel more of a part of that wider research community.

We’ll also look more specifically at the thesis itself and explain how it differs from undergraduate work in terms of depth, scale and content. We’ll also try to make sure that you understand the importance of relating your work to the wider literature base, and of reflecting on the novel contribution you’ll make.

Expectations

The PhD is the highest level of degree that you can undertake, and almost certainly the most demanding piece of work that you’ll have taken on in your life so far. It’s an independent research project, and, as such, it’s the means by which you demonstrate your ability to manage a research project and enter the academic community.

The Quality Assurance Agency for Higher Education (the QAA) is the body which maintains standards within Higher Education in the UK. Their qualifications framework formally describes the PhD as follows:

Doctoral degrees are awarded to students who have demonstrated:

• the creation and interpretation of new knowledge, through original research or other advanced scholarship, of a quality to satisfy peer-review, extend the forefront of the discipline and merit publication

• a systematic acquisition and understanding of a substantial body of knowledge which is at the forefront of an academic discipline or area of professional practice

• the general ability to conceptualise, design and implement a project for the generation of new knowledge, applications or understanding at the forefront of the discipline, and to adjust the project design in the light of unforeseen problems

• a detailed understanding of applicable techniques for research and advanced academic enquiry.

Typically, holders of the qualification will be able to:

• make informed judgements on complex issues in specialist fields, often in the absence of complete data, and be able to communicate their ideas and conclusions clearly and effectively to specialist and non-specialist audiences

• continue to undertake pure and/or applied research and development at an advanced level, contributing substantially to the development of new techniques, ideas or approaches.

And holders will have:

• the qualities and transferable skills necessary for employment requiring the exercise of personal responsibility and largely autonomous initiative in complex and unpredictable situations, in professional or equivalent environments.

If you search for postgraduate codes of practice and associated regulations on any university website in the UK, you will usually find these guidelines in slightly varying wording but with the same underlying principles. You are developing the ability to act as an autonomous researcher, with the guidance and support of your supervisory team.

Some practical realities of PhD study

Insights from a journal editor

PhDs are where true science happens, or so I thought. Before I began my PhD, I had illusions of grandeur, of scientific breakthroughs and – I kid you not – Nobel prizes. The general topic of my research was black holes. It doesn’t get grander than this! And yet, the first task I was assigned was to read a bunch of papers – literature research. The next steps included wading through hundreds of references, collating information from different sources and eventually building a database – not very grand, not very ground-breaking. It was instead often boring, usually tiring, at times even defeating. In retrospect, it was also important: a basis without which any further progress could not have been accomplished.

The day came when I was called to make my first presentation about my PhD research. This was my chance to shine, I thought. My slides were impeccably designed, dotted with big question after big question, fundamental unknowns about the Universe, scientific conundrums … and about black holes. I was already at slide 25 (of a 30-minute presentation) before I ‘stooped down’ to explaining the literature search I had done, the information I had collated and the database I had built. Needless to say this particular version of my presentation was never seen by anyone other than by my PhD supervisor. After slide 5 or so, she had already concluded that it was all wrong and I had to redo it, I had to sharpen it, I had to focus the slides on my work, my research.

This clash between my expectations of what doing a PhD would entail and what my PhD was actually about followed me well into the second year of my three-year graduate programme. It was a dissonance that made me feel at the same time inadequate – am I failing to do ground-breaking science? – and unfulfilled – when will the menial tasks give way to true science? And while I cannot preclude a major scientific breakthrough happening in your PhD, I can certainly tell you that usually a PhD is nothing more than an appetizer, a training course meant to teach you how to do (independent) research, a bite-sized – your bite size mileage may vary! – problem to sharpen your scientific skills on.

One should not regard doing a PhD as inventing the wheel, but perhaps more like measuring the curvature of a wheel. Or rather, the curvature of a very specific segment of a wheel. One wheel of a many-wheeled vehicle. And that’s okay!

Dr Marios Karouzos (Senior Editor, Nature Astronomy)

Uncertainty

The PhD is not supposed to be the perfect research project. It is a research project. You’ll develop the abilities and the skills we’ve described above over the course of the whole PhD. As such, you should recognise that it is a learning experience. You’re not expected to demonstrate proficiency from day one, so don’t be afraid to acknowledge when you’re unsure of things.

You’ll encounter gaps in your knowledge, seemingly insurmountable problems, unexpected results, and roadblocks that force you to completely rethink your approach. The QAA guidelines above refer to these as ‘complex and unpredictable situations’. This does not mean that your research is going badly. This just means your research is like the majority of research being carried out everywhere else.

Look at this real-life example of a ‘complex and unpredictable situation’.

Insights from a journal editor

I started my PhD studies with a research project on the adaptive immune system of zebrafish. These small fish had been studied for decades in the field of developmental biology, as their high-throughput potential and transparency made it possible to do large functional studies, but they were mostly ‘uncharted land’ in terms of our knowledge of their immune system.

My supervisor and I set to explore the main organs of interest from an immunology perspective and attempted to establish disease models in the fish that would have relevance for higher organisms. However, after several months of roadblocks and unexciting results, we decided to scrap the project and set on a different research direction, changing to a more conventional animal model in the field and to more cutting-edge questions.

This was a radical decision. At first I was shocked and very worried: we lost several months’ worth of time and effort apparently for naught, and it wasn’t clear to me if changing projects would set us in a more productive path. But by the end of my studies I came to appreciate the importance of that decision. The change meant that I acquired a broader set of skills and experience, and put us on a research track that followed fresh discoveries in the field and made much better use of the local technical expertise. The new project was fruitful and led to a publication.

Dr João H. Duarte, (Senior Editor, Nature Biomedical Engineering)

The example above not only gives a good sense of the type of situation you might encounter, and how these difficult situations are actually the ones that help you develop most as a researcher, but it also highlights the importance of a good relationship with your supervisors.

Guidance

Your main guides throughout your PhD will be your supervisors. While many institutions are likely to have guidelines on roles and responsibilities in the supervisory relationship, there can be large variation within that relationship. To take an example, ‘regular meetings’ might mean very different things to different people: a daily 20-minute conversation, a weekly meeting, a formal monthly meeting or a two-monthly Skype meeting, depending on your respective commitments. Some supervisors will see it as their role to offer career advice from the outset, and others might expect you to ask them if you want guidance in that area. Some supervisors might want to give you detailed feedback on every aspect of your writing, and others simply might not see this as part of their remit. We’ll think about how to negotiate these differing expectations in Chapter 14.

Expectations of independence

No matter what level of support you have from your supervisor(s), a PhD will involve more independent work than you’re used to from your undergraduate studies. The guidelines we quoted above repeatedly highlight the importance of independent critical skills and personal responsibility. While your supervisors might provide guidance when it comes to carrying out the literature review, for example, and while your institution might offer additional training in how it should be produced, you’re still expected to be able to critically evaluate what you find, and to be able to offer ideas on how your research project fits in to the wider field, how it relates to existing work and the impact it is likely to have.

If you come from a different academic culture, you might find that this new set of expectations takes some additional adjustment. Equally, it’s important to remember that your supervisor knows and expects that your relationship is a teaching relationship – although you will, by the end of your studies, communicate on a more level playing field. It’s important that you ask your supervisor questions when you need to.

A new relationship to broader, ‘real-world’ research

You might also have to get to grips with thinking of your work in a new light: the impact it will have on the wider academic community. Publication is increasingly a reality for PhD students throughout their studies, and thinking about how you communicate with a variety of different audiences (particularly if you undertake interdisciplinary work, for example) is likely to take some adjustment.

It is common for students to feel quite lost at the beginning of the process. This is a typical comment:

Insights from a researcher

I arrived a little later than I had expected and then had to spend some time sorting out accommodation, so I missed a couple of induction talks. I’ve had mostly email contact with my supervisor, until we met for the first time last week. They’ve told me about the first year requirement, which is writing an overview of the relevant literature – and encouraged me to get started on that. They’ve said they’ll look at it once I have a decent first draft – but I’m not really sure what a ‘decent’ first draft would look like, or how much detail they’re expecting of me.

What the PhD isn’t

A PhD isn’t a research process where you can rightfully expect to arrive at the answers. As we mentioned from the national guidelines we outlined above, you’ll be working at the forefront of human knowledge and understanding. Things won’t go smoothly, and your supervisor won’t know the answer to all of the questions or solutions to all of the problems that you have. If they did, there probably wouldn’t be much of a need to be doing the investigations.

The PhD also isn’t a guaranteed track to a certain number of publications. No one can predict how well your research will go, and if you’re working with a very highly integrated research group then it may be the case that your research contributes a small piece of a much larger puzzle. In such cases, you might find that your experiments go well enough only to produce a figure suitable for publication right at the end of your time in that lab, and that a good paper suitable for publication in a journal with a high impact factor depends on the inclusion of a colleague’s work. If this happens, you might find yourself waiting until after you’ve completed your PhD and moved on before your supervisor feels that the whole lab team are ready to submit their work to a journal. On top of that, there’s no guarantee that the paper will be accepted. If it is, you’ll undoubtedly be asked to make a number of revisions as a result of peer review, and that might involve more lab work. If you’ve moved to another lab, you might be waiting for someone else to repeat and refine the experiments you had originally carried out. In short: publication can be a long, complicated, slow-moving process, and signing up for a PhD is not necessarily the same as signing up for one or more entries on your publication record.

Your thesis

There’s a high likelihood that your thesis will be the longest single piece of writing you ever produce. It’s not uncommon for a PhD programme to involve three to three-and-a-half years of research time followed by six months of writing-up time. Have you ever spent half a year working on a single file? An average thesis might be between 150 and 200 pages (A4 sized, with lines at 1.5× or 2× the standard spacing, and printed on one side of each page only) – or, if you pre...

Table of contents

• Cover
• Half Title
• Title Page
• Copyright
• Contents
• Acknowledgements
• Introduction
• 1. What the PhD Is, and What It Isn’t
• 2. Establishing a Writing Practice
• 3. Refining and Articulating Your Research Question
• 4. Finding Literature
• 5. Organising and Keeping Track of the Literature
• 6. Reading and Critiquing the Literature
• 7. Structuring Your Chapters
• 8. Writing About the Literature
• 9. Structuring Your Sentences
• 10. Paragraphs
• 11. Editing and Proofreading
• 12. Making the Document Look Like a Thesis
• 13. Writing for Publication
• 14. Common Roadblocks During the PhD
• Conclusion
• Appendix: List of Useful Software and Apps
• Bibliography
• Index