Completely serious – so far thesis writing has been one of the most relaxing things I’ve done since the pandemic started. I think it’s largely because I just get so in the flow and get distracted from all the other outer-world things that normally keep me anxious. And my mind gets so happy. Because it gets to just productively think. I expect it will get more stressful when I have to actually try to nicely piece together all this word-dump-ness I have written so far. But for now I’m really enjoying it. To the point I’m feeling guilty which makes my brain unhappy again. Why can’t my brain just accept that work can be fun and still be work?

More on the various aspects of the PhD-earning journey here: 

But basically, you do some classes and some teaching, then you do several years of research on some specific project, and then you write a thesis (aka dissertation) explaining what you spent all that time doing (and defend that thesis in front of a panel of profs). Your thesis isn’t just (or at least it shouldn’t be) just your lab notebook copy and pasted (and precisely formatted) into a big document that gets printed up and bound. Instead, it puts your work in perspective. It’s your chance to not just show them how hard you’ve worked but instead to show how all that hard work you did fits into the bigger picture. What was missing from that picture before you started? (this is the basis of your intro section). How did you fill in that blank? (results section). What’s still missing from the picture? Are there new pictures that now need to be filled in given what you found? How might they be filled in? (conclusions & perspectives section).

I really like getting to think big-picture and speculatively. It reminds me of when I was first starting out in my research and got to really explore mentally. But now, it’s less overwhelming because I can better understand the literature, and I feel like my speculations are at least seriously grounded in reality – and evidence I can use to back them up. So, this last section is proving to be especially satisfying. 

When I first got the “green light” to start writing my thesis, I was super overwhelmed. And I didn’t even know where to start. I didn’t even really know what goes in a thesis. And the instructions we got (aside from the super specific details about what font, font size, etc. to use) weren’t very helpful – basically, “there are lots of ways to do this and we’re super flexible as long as your thesis committee is okay with it.” I tried looking at a number of past students’ theses – which was super helpful but they were all super different. So I’m mainly trying to make it most like the last grad student from my lab because at least I know my PI (lab head) liked it that way. 

So, I had some guidelines and some examples, but I was still just totally overwhelmed. How the heck to start? I started by taking and using what I’d already written – in addition to my thesis proposal, I also had bi-yearly progress reports I had to write. So lots to go in for the intro and some of the conclusions.  And then, for the results, the paper I have in preparation will provide a lot of that. A cool thing about the thesis is that you get to include all the stuff that didn’t make it into the paper. So I put in that stuff from my past reports. 

At that point I had a super mashed up Frankenstein thing. But it served as a starting point. And once I started really working on it, things started to flow. Turns out, thinking about writing my thesis has been way more stressful than actually writing it!

So, fair warning that I’ve never actually written a whole thesis, let alone one that was accepted, but here’s what I’ve gathered about what’s important to keep in mind and do/not do. And sorry if I’m overstepping my expertise boundary, but I like to tell people what I’m learning so… Oh – and this video I found from James Hayton is really helpful for how to tackle thesis writing 

The basic layout of a thesis (order and precise contents my vary) is:

  • title page
  • potentially an abstract
  • acknowledgements
  • table of contents
  • list of figures
  • list of tables
  • list of abbreviations & acronyms used
  • introduction
  • results (several chapters)
  • conclusions & perspectives
  • materials and methods

For the lists of figures, tables, abbreviations, etc. LaTeX makes this super easy, which I’m loving.   

I had some intro stuff from my proposal, etc. but I’m having to add waaaay more. Because, the intro is actually a huge part of the thesis. It’s like a whole literature review article before your report. But you don’t want to just regurgitate all the facts that in some way relate to your research topic. Instead, you want to kinda put the readers into your perspective going into the project or at least, what someone could have known about the things you found out more about. What was still missing? And why was it important to know that thing? Why should anyone other than you care?

Working on the intro, one of my biggest problems has been that when I find a good paper I want to include findings from, that references something else, which references something else and I keep finding bazillions of cool (and relevant) papers to read (or at least skim). My desktop got so full with browser windows that I stuck some of them in a separate desktop, and then forgot what was on that desktop and… Thank goodness for Mendeley at least! Whenever I visit a paper that I think looks intriguing I go ahead and add it to my reference library.

The results section can literally include a paper you’ve written (as long as you wrote at least most of it yourself). If applicable, you need to specify what parts you did vs what co-authors did. The results chapter that’s my paper-to-published is in “we” (and I greatly appreciate all the crucial help and guidance my mentors gave me in planning experiments, etc.) but one of the coolest things about a thesis is that you – finally – actually get to say “I” when you mean it! 

The results is usually several chapters, which can be separate papers if you’re lucky enough to have several, or they can include aspects of your research that were kinda dead ends (I have one of these) and/or extra things that didn’t fit into the paper (I have one of these too). 

The results sections can each have their own methods sections or it can be at all the end. And they can have their own discussion sections. But the real meat of the bigger-picture discussion is in the conclusions section. There, finally, you can be speculative and creative.  I worried that it would be bad to introduce too many future directions things in my “conclusions and perspectives” section? If I propose a number of future experiments will it’ll seem lazy that I didn’t do them myself or something? But people (at least on Twitter) have assured me that that sort of thing is A-OK! Who knows, maybe someone will actually even try those experiments! (although our theses don’t get published online so probably no one will ever read mine) I hate the idea of my project dying when I leave the lab and all those ideas just floating around in the ether. 

Apart from getting to think creatively, I really like working on this section because it’s where I get to put my work into the bigger picture. And it makes me feel really accomplished. And like I fit into the bigger picture, not just my research. 

Speaking of my research, I’m waiting for some reagents (lab supplies) to come in, waiting on a dataset from an experiment, and waiting for feedback on my paper, so figured I should make as much progress as possible on my thesis while there’s nothing else I should be doing. Yet I’m still feeling like I’m doing something bad because I’m enjoying this way too much! Apart from everything I’ve mentioned already, it’s so exhilarating to really be able to see the finish line! I have loved grad school, but I’m super excited for the next step as well! (I’m planning to do a postdoc (more research in a different lab) in a lab I’m not ready to publicly announce yet, but which I’m absolutely psyched about!!!). 

Hope this post is actually helpful, or at least gives you a glimpse into my current life! I like to try to give people a view of grad school from a student perspective (and keep non-academia family and friends updated on what I’m up to – which is why I first started the bumbling biochemist in undergrad!) Working on this thesis has made me realize how far I have come as a scientist – but also how not-far I’ve come in terms of self-confidence… But faking it till I make it has gotten me this far, so hopefully it can take me through this final stretch!

more on topics mentioned (& others) #365DaysOfScience All (with topics listed) 👉  ⠀  

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