Menu Home

Writing a Ph. D thesis

Usually what’s going through my head when I can’t think of the right words.

Ah, yes. The Ph. D thesis. It’s that thing that you have to write and submit, in order to be eligible to graduate and become a Doctor (but not the medical kind).

I’ve spoken to quite a few people over the years about writing a thesis. The general consensus has been pretty negative, in that everyone seems to dread/hate writing it. There’s even thesis writing boot camps for people to force themselves to make the time, knuckle down and write.

I’m the odd duck (*quack* 🦆). I actually really enjoy writing academic texts. It started with the Honours thesis, which was the first large chunk of academic writing I ever had to do (undergraduate reports don’t really count). When I forgot to eat, it wasn’t because I was stressed, but because I was so engrossed in the whole process that I lost track of time completely! That being said, sometimes it’s hard to pause the writing when you have a train of thought that you don’t want to cut short by getting up and finding food.

Obviously I had a lot of good guidance from my supervisor (thank you!), but I’m certain my enthusiasm helped streamline things a lot more.

Since then, I helped write a book chapter about Coxiella burnetii (unfortunately you have to pay to read it, but it’s called ‘Coxiella burnetii: Hiding in Plain Sight‘) with my fellow lab members, wrote two manuscripts for publication in a peer-review journal (one is published, the other is currently in the process of being published), and am now in the midst of writing my Ph. D thesis.

So what’s in a Ph. D thesis? Because I certainly didn’t really know what it (traditionally) contains before attempting to write one myself.

Back in the day (that makes it sound like it was in ancient times, but I only mean a few years ago), the thesis was published as a physical, bound book. You could choose the colour of the cover and the embossing, so that it felt like it was individualised. Nowadays everything is digital so you have to pay extra to have the thesis printed in such a way. As a bookworm who still loves physical copies rather than eBooks (it’s just… that smell), I’ll definitely pay the extra to get mine printed.

FYI, mine will be a dark blue with silver embossing combo. Haven’t quite decided on what specific dark blue, though.

The first few sections are filled with the administrative stuff. The title, an abstract, a declaration of independent work, preface detailing any publications you’ve achieved throughout your candidature (especially if they form part/s of your thesis), any significant contributions from other people, an acknowledgements (the juicy part that’s probably the most personal section of the thesis), table of contents… All that stuff.

The official, numbered chapters begin here. The overall structure is somewhat similar to what is in a scientific manuscript, but there’s a whole lot more going on in a Ph. D thesis.

Chapter 1 is the Introduction/Literature Review.

There’s numerous subsections in here that aim to give the reader all the information required to not only understand the importance of your work, but to also showcase your knowledge. You’ve dedicated a solid number of years to this, so you need to show that you know what you’re talking about.

For instance, mine has a general flow like this:

  1. Put disease into historical context
  2. Showcase the disease (where is it found? How does it spread? What are the symptoms? How do you treat it?)
  3. Showcase the pathogen itself (what kind of bug is it? What does the infection cycle look like? Are there any ‘virulence factors’, which allow them to take over the host cell more efficiently?
  4. What’s the current gap in knowledge that I’m going to try and explore in my thesis?
  5. What were my aims for my thesis (what was I trying to accomplish)?

Chapter 2 contains the Materials and Methods.

This chapter contains subsections outlining how every single experiment was performed. Ideally it should be written in such a way that anyone reading it with a similar background could perform the experiment.

For me, it’s sort of broadly ordered like this:

  1. Strains of bacteria used, specific tissue culture/mammalian cell lines used
  2. DNA-related techniques (ALL THE DNA)
  3. Some odd experiments
  4. How to grow mammalian cell lines and infect them with bacteria
  5. Giant section on how I looked at nutrients in bacteria
  6. Some odd experiments
  7. Protein stuff (protein purification, antibodies, protein gels, western blots…)
  8. Imaging stuff (looking at cells at the microscopic levels)
  9. Moth infections

Sometimes it’s hard to come up with an efficient way to order each subsection (especially those ‘odd experiments’). I feel like a well-written methods section should flow in such a way that each experiment can be explained easily because all the components have already been explained in previous sections (so the stage is already set), and you just add the variation you did that used said technique as a new subsection. For instance, I can’t explain the imaging section if I don’t explain how to grow mammalian cells and use antibodies beforehand. Sometimes you just have to write out everything you need to put in there, and re-arrange the order until it looks the most logical.

Chapter 3, 4 and 5 contain the Results.

This is where it gets a bit weird. Each results chapter, when written as traditional thesis chapters, contains a small introduction, then a normal results section, followed by a discussion section about the showcased data.

It can feel a little repetitive when you write a specific introduction for that topic. I found that mine was similar to an introduction for a manuscript. Short, succinct, and contains enough information to set the scene for the results that follow.

The results sub-chapter contains many sub-sections like a manuscript does. The general structure is identical to a manuscript, but you can also throw in ‘negative’ results, i.e. experiments that didn’t really work. Maybe it didn’t show any differences between the conditions, and didn’t really add to the broader story being woven for a manuscript. Maybe you realised that the approach needed to be revised, after you’d performed the experiment, so you have two data sets for before and after you changed the protocol. Either way, you can throw all of that in there and talk about the struggles, albeit in a professional manner. You don’t normally get to do that for a manuscript, so this bit sort of threw me.

The discussion sub-chapter (still within the overall ‘Results’ chapters) is a direct discussion of the results shown, which, again, is very similar to what is in the manuscript. But- you can also discuss things a little more thoroughly than what you would in a manuscript. I guess it’s because a manuscript is significantly shorter than a thesis, so you really need to choose your words carefully. A thesis, though, allows you to have deeper discussions about what your results might mean.

Each results chapter is a different aim of your Ph. D thesis. They might be a progression (I found A in chapter 3, so I explored this further in chapter 4 and 5), or part of a broader question (I looked at these three aspects of bacterial infection), but it doesn’t have to be one or the other (or either). Mine feels like two separate sections (one looks at what Coxiella eats, while the other looks at a particular protein that seems to be very important for Coxiella to replicate inside cells), but the overarching aim is to simply understand how they live inside the host cell (because under normal circumstances, anything that ends up in the recycling bin gets killed and dismembered).

You can also forgo all of this, and just insert a published manuscript, if you wanted to. This saves you from writing a results chapter twice. You can do sections, or you can also forgo writing a thesis in the traditional sense altogether and submit a thesis ‘by publication’. You just need three, peer-reviewed and accepted manuscripts. That can be a wee bit difficult to achieve in under four years (or less), so I think most of us tend to write chapters. It can be done, though.

Chapter 6 contains the broad Discussion/Perspective section.

This isn’t supposed to be a big section (apparently). I’m currently writing this bit, and it’s been the most confuzzling part to date.

The aim is to tie the significance of your work to your overall field (why does the work contained in this thesis matter?), but… I’m finding that it feels somewhat… unstructured- or at least, it feels less structured than the discussions featured in the Results chapters. It’s supposed to be broad, so the first part discusses the context of my work, my results, their significance to the broader field, and how it could impact work on the disease itself (I’m going for a therapeutics approach). I’ve read others that were more similar to manuscript discussions, so… I think there’s a lot of variation between theses. I guess it sort of comes down to what your supervisor expects, so I would highly recommend sitting with them and discussing what to put in there (discuss the Discussion, if you will).

After this, it’s basically the Reference List/Bibliography, then any Appendices you’ve included.

I’ve got an Appendix that lists the recipes for anything I’ve made (whether they be cultures to grow bacteria, or buffers used to run gels), big metabolic pathway maps I’ve drawn on Illustrator, as well as any publications I’ve gotten that formed parts of my thesis.

Apparently it’s supposed to be around 100,000 words, but no one really checks (unless it’s absurdly long or short). Especially with all the Figures and Tables embedded in the pages, it can be pretty difficult to count all the words in between.

So that’s a Ph. D thesis in a nutshell. I’m still enjoying the process of writing, but to fellow students who are slogging it out there, you can do it!! Even if it’s verbal vomit, it’s still something. Just write whatever comes to mind and edit it later, cause let’s face it- our supervisor/s are gonna edit the hell out of the drafts anyway.

Such reverence

Categories: Ph D posts

Tagged as:


A Ph. D graduate in Microbiology, residing in Victoria, Australia. Currently working in multiple locations but still in the STEM field. 👀 🦠 🧫 🧬

7 replies

    1. You’re very welcome! If you have confirmation reports and such (or progress review reports), they can also form your literature review and help you start writing your results (and figures) early, too! There may be slight differences between universities and departments, but hopefully the general set up is still the same. All the best with your Candidature!

      Liked by 1 person

      1. Yepp we do have annual progress reviews which we have write reports for so hopefully that will help me keep writing instead of having loads to do at the end! Thank you and all the best with yours!

        Liked by 1 person

Leave a Reply

Please log in using one of these methods to post your comment: Logo

You are commenting using your account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

%d bloggers like this: