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What it was like to write a Ph. D Thesis

In a previous post, I detailed the general structure of a Ph. D thesis, complete with a basic guide on what each chapter contains. But when you get down to it, how do you actually start writing such a massive chunk of text? Here I’ve outlined the general process I followed for each Chapter- hopefully they might help someone who is stuck writing at home during this pandemic.


As a general workflow, writing text has always worked like this for me:

  1. Plan and structure the chapter (manuscript) with my supervisor. Write it all out in dot point format so you get a general idea of where things need to go and what needs to be said. This is where we discuss the general flow and tone required.
  2. Write a rough draft of the chapter (or a manuscript subsection).
  3. Send it to my supervisor, who will then edit said draft.
  4. I get the edits back, and I will go through each comment and address them. If I don’t agree with or understand a particular comment, I’ll discuss it with my supervisor and figure out how to move forward with it.
  5. I send this new draft back, and the editing process continues, or…
  6. I keep this edited file as my final draft for said chapter (or manuscript subsection), and move onto the next chapter, without my supervisor looking at it again. Repeat steps 1-5 until all chapters (or subsections) are finished, and compile into the one document (for a manuscript it’s already in the same document).
  7. (Optional) Have this fully compiled document present with so many formatting issues you want to throw the laptop against a wall. Fight through it. Google is your friend.
  8. Send this full version back to my supervisor, who will do a final edit.
  9. Incorporate all comments, and now I have a final, full draft!
  10. (Optional) Read the text again and discover more spelling/grammatical errors, and drive yourself insane trying to fix them all.

My supervisor and I generally rely heavily on Microsoft Word. I draft a chapter/manuscript, I save it onto a shared folder or send it to them. They can then either print it out (used to do this) or use Track Changes to edit and leave comments as necessary (we do this more now). Track Changes is handy because any edits done are highlighted and coloured, and any comment left can be addressed and responded to within the document. Technology is a beautiful thing.


In terms of what Chapter to start with, while I’ve previously made some comments, I’ll summarise it again here.

The easiest one to start is the Methods section. Hopefully you’re keeping up to date with your Lab notebooks so that somewhere you have a detailed and well written protocol for your experiments. If written well, these can directly form subsections for your Methods. Ideally you want to just be doing this as you do experiments, because you don’t want to leave this last minute. Thankfully I had an electronic Lab notebook, so for some experiments, all I had to do was copy paste from these straight into my Word document. Sure, I had to change some symbols, but the bulk of it was already written, which saved me a lot of time. For the most part, though, you’ll have to re-write a protocol to better suit a Methods section, but at least you’ll have a template with your Lab notebooks.

When you do a Ph. D (or Honours), you will inevitably have to write a Literature Review. In Honours, I had to write one and send a full draft to my supervisor in early July. For a Ph. D, you had to write one for your Confirmation meeting (12 months after you start). A Literature Review will become your Introduction, so having to write one early is a nice way to get started with the writing process. Obviously this will need to get updated when it’s actual Thesis writing time (projects change, the literature is constantly being updated- you have to keep on top of it), but it’ll be good to have some foundations laid sooner rather than later.

Next are the Results Chapters. These usually start with the making of Figures. Every time you do a big experiment, and you get some useful (or maybe not so useful but it’s what you gotta run with) results, you should begin compiling it into a publication format figure. For instance, here’s a graph I made previously:

This is actually from my latest publication in Infection and Immunity (I’ll write a post on it once it’s available in print).

On its own, the graph is a little useless. No one else knows what’s being depicted, and a figure will typically contain multiple graphs and/or graphs accompanied by images. One graph on its own isn’t quite enough.

Generally speaking, I’ll discuss what the overall figure layout is going to be with my supervisor, before I actually go ahead and make it in Adobe Illustrator.

We usually discuss and jot down ideas for how each figure is going to be placed. This one is from my first publication, in Biochemical Journal. Also- I really need to work on my handwriting. It’s terrible!!

Once you compile all the figures, it’ll look something like this…

Growth curves of WT (solid black circle), 0265::Tn (white square box) and 0265::Tn pFLAG-0265 (solid square box) C. burnetii in HeLa CCL2 cells (A) and THP-1 cells (B), n = 3. Error bars represent standard deviation. Immunofluorescence (IF) images at 3 days post-infection for HeLa CCL2 (C) and THP-1 (D) cells. Cells stained with LAMP-1 (green), C. burnetii (red) and DAPI (blue). Scale bar = 10 µm. * indicates CCV. (E) Survival of G. mellonella following infection with WT (solid black circle), 0265::Tn (white square box), 0265::Tn pFLAG-0265 (solid square box) C. burnetii at 106 GE. A PBS control (white circle) was also included. Results are shown as a representative of two replicates, each with 12 larvae per condition.
You can see how the earlier sketches contributed.

Now you can write in a figure legend. The figure legend should contain enough information that the reader can discern what is being presented, without having to look over the bulk text (because who has the time?).


Okay, so you’ve been writing out your protocols, written a Lit Review (and are somewhat keeping up with current literature), and are compiling results figures (it’s a slow process sometimes). You’ve got around twelve months to go before your thesis submission date- now is the time to really start writing.

I was quite lucky in that I had a manuscript written and underway, but pretending that you don’t, this is how you would tackle the thesis.

  1. Start finalising your Lit Review to turn it into your Introduction. It’s usually been a while since you’ve even looked at it (for me it was like, 1-2 years), so your project direction has probably changed, and new papers have been published that you need to incorporate. This can be quite dry, because it’s just a case of combing through the literature again (hello, Pubmed) and bulking out your first chapter. I went through the chapter subheadings with my supervisor again so that we were both clear on what I was going to write about (and how it would be ordered)- just so I didn’t end up writing lots, only to have them go, ‘actually… I don’t like the way it’s set up’. It’s good to have direction. Get a draft done sooner rather than later, and just send it to your supervisor for them to edit. That way you can get the ball rolling and move on to the next chapter. They can give you feedback about what’s missing or where you’ve written too much.
  2. Methods. You can actually work on this while you do your Introduction, or you can do this before. Entirely up to you, but I did this after the Intro just so I could be productive while being brain dead from all the reading I did for the Intro. Same deal as the Intro in terms of discussing the ordering and content in dot point format prior to writing it out. Then you can simply write out everything- because you’ve got a template protocol to go off, right?? Because you’ve been writing down your experimental procedures somewhere…? Right? You just need to make sure you put a no-break space (ctrl+shift+space for PC) between the number and the unit measurement symbol. E.g. 10 uL as opposed to 10uL, and all that stuff. Formatting… Yay. Once it’s drafted, you can send it back to your supervisor again for review.
  3. Results chapters. For a Ph. D thesis, this chapter, as mentioned previously, is like a manuscript draft. It has a mini introduction, the results section, then a discussion. The best way to gauge the content for these chapters is to look at published manuscripts. You need an adequate introduction to give enough information for your reader to understand the results (because by now they would have forgotten everything from the actual introduction- mostly because it was two chapters ago and also it’s ginormous). The results themselves will hopefully be about writing the bulk text of a subsection for each figure (which you’ve been making already…?) in the order that you and your supervisor agreed on. The discussion is directly in relation to your results, and not a broad one like what is contained in the perspective chapter of your thesis. Again, a manuscript is a good way to figure out what to put in here. For things like Honours, though, all you need is just the results subsections. Much easier to handle.
  4. Broad discussion/perspective. Once again, would highly, highly recommend discussing the outline with your supervisor, prior to actually attempting to write this. Given the contents of your thesis, what do the results mean? How does your work contribute to the broader field (and society)? Is this thesis, and therefore you, worth granting a doctorate to?? Usually involves a brief summary of the results chapters and the broad conclusions drawn, and then delves further into what that means. Hopefully these concepts are things you’ve already thought about and have been discussing with your supervisor/colleagues/strangers in the night throughout your entire degree. These big picture questions and answers are what makes a thesis, so it’s good to ponder on this chapter for as long as you can, and write bits and pieces before tying it all together.
  5. Addressing editorial comments. Hopefully by this stage you’ve accumulated quite a few chapters with a large number of comments that need to be addressed. Every time you submit a chapter for review to your supervisor, and you get bored of writing the next one, you can always go back to these edited chapters and start fixing it all up. But if you didn’t get a chance to do that until you wrote all the chapters out first (like me), now is the time to edit. It’s usually a lot of back and forth-ing between you and your supervisor, but hopefully you can fix everything and address every comment.
  6. Compile each chapter into the one document. This is where all hell breaks loose with the formatting. All I can say is Google is your friend, and good luck. Hopefully your citation manager (I use Endnote) doesn’t go berserk. Make sure all the Appendices are in order.
  7. Write an abstract. Now that everything is compiled, it’s much easier to write the abstract. I always leave the abstract until the very end, because I can’t summarise something that’s only partially written. Better to have a good grasp of the overall tone and conclusions before you write a summary.
  8. Add all the administrative stuff. Thesis title page, preface, declarations, table of contents, table of figures, table of tables… All the fun stuff.
  9. Read the whole, compiled draft and edit as necessary, then send to your supervisor. Waiting patiently for the edits can feel super weird, because you literally aren’t allowed to work on your draft until you hear back from them (because what would be the point?).
  10. Incorporate all final suggestions. Discuss any comments you’re not sure about. Fix everything. Read it, re-read it. Read it aloud. Get someone else to read it.
  11. Submit for examination. Pop the champagne and relax.

Categories: Ph D posts

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

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