On Writing a Thesis

If you spend any time around graduate students, you know the culmination of years of work toward a degree ultimately comes down to pouring the essence of that work into a giant written document very few will ever read: a thesis. Also known as a dissertation. (Due to my US-centric perspective, I treat the two as synonyms in this post.)

As it happens, I finished a full draft of my thesis yesterday. It has been a stressful, exhausting, anxiety-riddled few… weeks? months? Yeah. The “fun” isn’t over yet because there are certainly revisions in my future, not to mention the actual thesis defense, which will consist of a public talk followed by an indefinite period of conversation/questions/snake fights with my committee behind closed doors.

So that’ll be great.

But my goal today is to give future-thesis-writers a window into what my process looks like, and share the tools I used to make it slightly less painful than it could have been.

My thesis contains five chapters and three appendices in about 200 pages and roughly 25,000 words. (The word count is imprecise and rounded down because a thesis has lots of words that aren’t exactly part of the main text.) As I understand it, this is a reasonably typical length for astronomy, but I honestly don’t care, because I think I said everything I needed to say.

I have three pieces of unsolicited advice, which boil down to: know how you work, get tools you’ll use, and what I’ll call “think globally, write locally.” Let’s go.

Know how you work

Maybe you’re one of those people who likes to wake up early, gets important work done before the rest of the world is awake, has completed all your thesis research well in advance of when you’d like to defend, and has published four papers along the way. In that case, I say congratu-effing-lations, you have this in the bag.

For the rest of us, it’s time to take stock of how you work. Think about the last time you were really “in the zone” and got a lot of work done solo. Where were you? What was the environment like? What time of day was it? Did you have a certain beverage, view, or music at hand? Figure out what works best for you and structure your life around it. Maybe that means you need to unplug the internet, build a playlist, budget for daily coffeeshop purchases, work in pomodoros, disable email notifications, or embrace the popcorn workstation. Maybe it means you need to block out writing hours on your calendar, get a transit pass, find a standing desk, set weekly deadlines, or pull all-nighters every Tuesday. It doesn’t have to make logical sense and it doesn’t have to be a lifelong commitment; it just has to work for you for now.

If you’re having a hard time remembering the last time you felt highly productive working alone, or the specific circumstances, don’t despair. It’s never too late to try new productivity techniques. We’re all making this up as we go!

Get tools you’ll use

Writing a thesis is more than just opening a blank document and dumping your brain into it. There’s formatting and references and figures and tables and… so many pieces that somehow have to come together. Thankfully you are not the first person in the history of humanity to tackle these problems, and lots of tools exist to help. Good tools are easy to use and lighten your cognitive load so you can focus on the content of your thesis rather than the mechanics of writing it. But not every tool works for everyone, and sometimes you have to be patient with yourself and your computer while you try and discard one after another. After much trial and error, here are some of my favorites.

OmniFocus: The powerful to-do list app that basically changed my life. This is a place to write down action items for everything in your life, from errands to work to any random task or idea you need to get out of your brain. The degree to which I use OmniFocus to its full potential varies, but whenever I need to get something done I take the time to break it up into small, manageable pieces here. You can use it to set deadlines, start-later deferral dates, color categorizations, location- or person-based contexts, and so much more. OmniFocus is not free, it is only for Mac/iOS, and it syncs seamlessly between them. If you are thinking of trying just one of the tools listed here, it is the one I recommend most highly.

TeXShop, ShareLaTeX, and a LaTeX class file: If you want to write a thesis, you’re probably going to need some LaTeX. My editor of choice is TeXShop, which is free and lets you place writing (editor) and viewing (PDF) windows side by side. If installing LaTeX gives you trouble, I recommend ShareLaTeX, which is also free, works in any browser, and syncs with Dropbox (see below). You’ll also need a class file with various packages to tell LaTeX how you want your thesis formatted. Many departments and universities have official or unofficial class files that adhere to formatting guidelines. Ask around to see what older students or recent graduates from your department have used. In my case, NMSU graduate Jeff Coughlin created aastex-thesis (based on AASTeX v5) and a set of well-documented sample files that compile into a pretend thesis—about exowhales, no less!

Dropbox: You probably don’t back up your work as often as you should, and even if you do, it’s probably not every time you hit “save.” I initially uploaded my thesis files to ShareLaTeX, linked that to Dropbox, and then did most of my writing in TexShop. So long as I was online, the latest versions of all my thesis files were automatically synced with the cloud. This offered peace of mind, because if my computer spontaneously self-destructed, I could have continued working with ShareLaTeX on any computer with internet access.

TextWrangler: My go-to text editor. You can use alt/option-click to select a rectangular block of text (a column), it has brilliant find-and-replace, and it lets you remotely edit files over ssh. I use this for everything, including python programming, formatting LaTeX tables, and keeping a BibTeX bibliography file up to date. TextWrangler is free and for Mac only.

Papers: The absolute last thing I want to actively think about is how to cite a paper or format my bibliography. BibTeX handles some of this, but it can’t help me find the paper I’m looking for or open several in tabs for me to continually reference. Papers lets you save PDFs in a special folder, automatically organizes that folder and imports information about that paper, and makes it easy to copy a BibTeX record into your bibliography file. From there, you can customize a natbib keyword, run a series of LaTeX-BibTeX-LaTeX-LaTeX commands in TeXShop, and carry on writing. Papers also syncs between devices (Mac/Windows/iOS) so you can read papers on the go. It’s not free, but they offer student pricing and it is well worth the investment.

SnagIt: This is just a fancy screenshot program. I use it to grab a figure from a paper, save it in the “figures” subdirectory of my main thesis directory, and add it to my thesis. It’s not free, but there are many other perfectly good screenshot options out there.

Evernote: My research notebook. My workflow is essentially paperless, so anything I need to jot down goes here. I write a brief summary of what I did each day for my own personal reference. Quick calculations, the location of important files, and notes taken during meetings all land in Evernote. It’s free and syncs between all my devices which makes it a handy reference during meetings and conferences.

RescueTime: A neat little free app that runs in the background on my computer and tracks how much time I spend using different applications. It keeps you honest and lets you compare hours spent on different tasks from week to week.

focus@will: Various types of music and ambient sounds that help get you in the flow of working. I use this when I just can’t concentrate and/or when I want music but don’t want to spend time deciding what to listen to. It’s a subscription service with a free trial period. [post edited to add this one]

Slack: Did I mention I’ve been finishing my PhD remotely over the last year? This means my collaborators are never “just down the hall,” and Slack bridges that gap for free. I’ve become at least as good of a communicator from afar than I ever was when I could theoretically walk to a colleague’s office. For example, during a virtual meeting, everyone can easily share plots and other files in real time.

“Think globally, write locally”

One of the most challenging parts of a thesis is figuring out just how to pitch your epic, unprecedented contribution to the field. There’s no getting around it: this is important, and part of the game is convincing others your results matter. But if you don’t have it figured out yet, there’s no reason you can’t start writing your thesis anyway. I essentially arrived at my conclusions as I was writing, for two reasons: the final numbers pertaining to my stars weren’t ready until days before my draft was due, and the process of writing about those numbers helped me clarify the story they could tell.

I can’t work if things aren’t organized, so the first thing I did after I had a set of mostly-empty LaTeX files in place was come up with chapter and section titles. I decided, quite arbitrarily, that I was going to have four chapters: Introduction, That Paper I Just Published, and Applying Stuff I Did In That Paper To Similar Situations (split into two logical halves), and three appendices. Then I created sections, and subsections, and even a few sub-subsections. Once all this was written down, I had a clearer idea of what my thesis looked like globally. Then I could pick a smaller “local” section I was ready to work on and get a finite piece of thesis done in one writing session.

That’s not to say the chapters and sections couldn’t change! They most certainly could, and did; for instance, at the eleventh hour, it was decided I would write a fifth chapter entitled Larger Context And Summary Of This Entire Damn Thing. More or less. But by that point, it was clear I had some things left to say which did not fit in the other four chapters, and adjusting course made sense.

With tools in place to handle formatting, citations, figures and tables, colleague communication, a to-do list with bite-sized pieces, and an outline as a jumping-off point, all that was left was the writing. I know enough about how I work to block off large chunks of time in the afternoon and evening during the last few weeks, which culminated in one final writing push from 10pm-5am on Sunday night. It sucked, but it worked. At least, I think it did. My committee will have the final say on that in the next couple of weeks.

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Not my favorite way to spend Easter weekend, but I think the bunny had it worse.
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