Generals: summary and advice

Sometime within the first two years of a North American biology PhD, grad students take an exam that determines whether their research ideas hold water and whether they should continue with their PhD or leave. No pressure! This rite of passage is called the generals,  qualifying, or preliminary exam ("generals," "quals," and "prelims"), and it's analogous to a Masters defense in the European system. The specifics of the exam vary greatly between universities but tend to involve a written literature review and thesis proposal, as well as a multiple-hour oral exam by the thesis committee. (Sometimes there's a written exam, too.) The committee, which consists of 3-5 professors who read your proposal, will ask you questions for around three hours and then decide whether you should stay.

Preparing for generals in the month leading up to it was easily the most stress I've experienced in grad school and some of the preceding years. Yet, it didn't have to be. This post is a summary of what my generals was like and some advice based on what I learned. 

What my experience was like

Prelude to the prelims

I opened a Word doc called "draft 1" in Summer 2014, about a year ahead of the exam. This doc just served as a place to paste quotes from articles and write a sentence or two of methods when I didn't have any other work to do. The amount of writing in the 10 to 6 months pre-generals that made it into the final document was tiny, maybe 1-5%, but my mentality was that any bit I could add now would be an hour saved in the frantic last days before submission.

A lot of my thoughts on what exactly I wanted to study changed over the months, especially when I got preliminary data in November. It's one thing to say you're interested in collective antipredator behavior and another to specify that in chapter one, you'll study how alarm propagation in golden shiner schools changes under predation risk, and why this is important. For me, the stress began mounting as I prepared my second-year talk a month before the exam. (2nd-year Princeton EEB PhD students give a 25-minute talk to the department on their research plans.) How silly would it be to stand in front of the colleagues I respect and see every day and to fumble around with half-finished ideas? No, I needed a presentation that reflected how seriously I took my work, how much I had thought through my ideas, and how I wasn't walking down a research dead-end.

(Note: despite losing quite a bit of sleep the night before as I gave the presentation a much-needed redo, the talk went well and I got good feedback. I've used the talk multiple times since then to quickly show research plans to collaborators and colleagues and get discussion started. No need for all of these paragraphs to be somber!)

The last month

The talk symbolized an important transition in the PhD: I was no longer just interested in ideas; I had to be able to convince others that a potential project was not only possible but also worth studying. Over the next month, I read and wrote constantly. I wanted to make sure the ideas followed airtight logic, which meant spending a lot of time crawling through articles to find that one paper that showed that fish at the front of the school tended to be the hungry ones, or was it just the edge and not necessarily the front, and is the species closely enough related to golden shiners to be relevant.... Again, it's one thing to have a general idea of the literature supporting your ideas and another to have the details, and there are a lot of details about your species' life history, the methods researchers in the past have used that you plan to use, and the theoretical and empirical justification for your research avenue. With a week to go before the exam, I submitted a 46-page PDF to my committee and had to let out a laugh at the relief that it was no longer in my hands. (Note: many of those 46 pages were the 180 references!)

Over the next week, I just wanted to take the exam. I felt as ready as I could be, and I filled my time by skimming a behavioral ecology textbook and a few articles to make sure I was familiar with common topics. My exam was scheduled for the last day in the two weeks of generals dates, so I watched five of my cohort members celebrate the passing of their exams and grilled them on the details. All of them said it wasn't as bad as they'd worried, but they were glad to be done.

The exam

As is the unofficial tradition here, I brought some breakfast food for my committee and a short presentation with the major justification and goals for each chapter. (The exam started at 10am and went through lunch.) Before we started, I left the room and my committee discussed my proposal and what they wanted to ask me about. I returned, began my presentation, and was asked immediately why I was interested in heterogeneity, which was in my title. I answered, and then... the details get pretty blurry!

What I do remember is that the committee was very fair throughout the exam. They raised concerns, listened to my justifications, and told me when they disagreed with my reasoning, but they also told me when they thought an idea in my proposal was exciting, and they offered suggestions on how to make the experiments stronger. The mood was formal but almost relaxed, and it felt like a discussion on finding the best way to have an interesting research trajectory that could teach us something. I passed, but my committee asked for me to resubmit the methods section of my proposal, which we agreed needed some work, in a few weeks. I appreciated it, actually, because while I would incorporate their feedback anyway, it was a good additional incentive to synthesize it in one place.

And then... it was over! Really over. After the celebration that Friday, I had an incredibly quiet, anticlimactic weekend where I had to relearn work-life balance. When I took away the work I'd been doing for hours every day the past month, what was left? My favorite hobbies, including drumming to songs I love, had been largely neglected because I was "too busy," but doing nothing but hobbies on my free time felt strange without structure to my days. Once the concrete motivation of a pass-fail exam was removed, it took about 2 weeks to fully reignite  the curiosity and excitement for my project and to find a sustainable work-fun pace, where I wasn't working until 9pm every night, but I was still making progress every week that I was satisfied with.

Advice for PhD students

1) Start writing early 

This one might seem obvious, but not in the way you'd expect. I found it really helpful to have a place to store thoughts as far as a year in advance of the exam. The actual format and details of my project ideas changed up to the days before the proposal was submitted, but it was good to have something down before the pressure started building. This was helpful when I started writing the "actual" proposal because it felt like I was adding to a first draft of ideas instead of starting from scratch.

2) You're smarter than you think. It'll be alright
Writing a proposal for your PhD plans can shake up your confidence. You're constantly looking at holes in your logic that you're trying to fill: how long to wait between trials, is your species really the best for this question or are you just using what the lab studies, are your questions interesting to anyone besides you? These questions didn't seem too important before, but now your proposal feels bland without them. You need to deeply commit to your ideas to understand them well enough to convince others (and yourself) that they're important. There's a lot of self-doubt involved, but you're doing better than you think. There's a lot to learn, but you've also learned a lot in the past year and a half. Keep at it. One of my favorite quotes really applies here: "The reason we struggle with insecurity is that we're constantly comparing our behind-the-scenes to others' highlight reels." Everyone had to figure out the details of their projects, and it's natural to struggle a bit as you learn everything you'll need.

3) View the exam as a discussion
Your committee wants you to do well. Your department is training you to become a knowledgeable scientist, and the reason generals is hard is that there is a lot of nuance to doing good science. Disagreeing with each other is inherent to finding the best possible path to new knowledge. Your committee and you have the same goal, for you to do a PhD that answers interesting questions, and there's no point in being scared that they'll ask you something you don't know the answer to. (Spoiler alert: this is guaranteed to happen.) Take notes, ask them questions. This is probably the only time in your career that you'll have five incredibly intelligent people closely examining your work and giving you feedback for hours. Take advantage of it.

Good luck!

-Matt

PhD: 1st-Year Reflections

The first year of the PhD is over. Kind of. It's not technically your second year until the new first-years arrive in September, and the work hasn't suddenly stopped with the end of the semester, unlike in many course-based humanities PhD programs. If anything, this summer is when I'll actually make any progress on experimental ideas I've been developing since I first e-mailed my advisor two years ago. But enough time has passed that I think I can share some reflections on my first year that can hopefully help someone else starting or considering starting a PhD in biology.

A quick bit of background about Ecology and Evolutionary Biology (EEB) at Princeton to help frame this post, since EEB programs vary hugely across universities: 

- You are admitted to the department, not to an advisor

- There are no lab rotations

- You finish most of your course requirements in your first semester

- You teach a maximum of 4 semesters and you start immediately

During my first semester, I spent most of my time as a TA for a huge introductory bio course, read articles for the two graduate-level classes I was taking, attended weekly colloquia by visiting speakers, and read as many articles as I could to develop research ideas. In my second semester, I did a tropical ecology graduate research course in Kenya, analyzed the data and wrote up a presentation, read more articles and two textbooks, performed pilot experiments to get experience working with fish, spent several months writing and revising a protocol for proposed experiments to be approved by animal welfare, and attended the weekly colloquia. (But mainly across both semesters: I spent hours and hours figuring out what experiments to do and how to do them!)

What I thought grad school would be like during college

"Grad school is where you show up at noon, plan some experiments, run them the next day, then analyze the data. A PhD takes 5-7 years because it takes a while to plan the perfect experiment, one that hasn't been done before and that answers a hole in the literature. During your first year, you do 5-6 experiments and publish at least one of them."

When you're doing lab reports during college, it's almost guaranteed that the Discussion section will say something like "the study would benefit from more data." We had three hours to do the lab; imagine how good the data would look if we had three weeks? Then, during your senior thesis, you continually imagine being able to do your research without juggling hours of lectures and homework at the same time. Grad school seemed like a big expanse of time to think about experiments, try them again and again until they're perfect, and then publish. Any sub-perfect experiments were the fault of the experimenter not being motivated enough.

What I thought grad school would be like during the Fulbright

"Grad school is where you show up at 10am and try to figure out why the pilot experiments didn't work. A PhD takes 5-7 years because ironing out all the details of an experiment takes weeks of pilot work, running experiments and analyzing the data can take months, and many experimental animals only have certain times of year when you can run experiments on them. During your first year, you spend half the time planning and the other half the time running the experiments and troubleshooting."

(As some background: I worked at the Max Planck Institute for Ornithology for a year after graduating college, collaborating with a PhD student on a study on sleep in great tits and doing a pilot experiment on social foraging in the wild.) The sleep study required weeks of reading articles and planning, with its pilot taking about a month to perform, analyze the data, and get ideas for improving the final design. Preparation for the experiment took three months, the actual experiment took two weeks, and analyzing the videos took four months. Grad school, it seemed, would be a cycle of preparing for an experiment, performing it (successfully), analyzing the data, and publishing.

What I think grad school is like at the end of my 1st year

"Grad school has cycles. Sometimes you show up at 10am, read articles all day, teach yourself R, and go home early. Sometimes you show up at 8am because you need to run three trials of experiments, and sometimes you swing by at 2pm because you were up until 4am writing revisions for a manuscript due to the journal that day. A PhD takes 5-7 years because literally everything takes longer than you think it will, and nothing works the first time you try."

Something I didn't quite grasp during my senior thesis and the beginning of the Fulbright was how much others had helped in making the experiment work out. It's the difference between trying to find a store in a huge city you've never been in versus someone giving you a crude map and telling you roughly where the store should be. My advisor in college steered my thesis ideas towards a project that would answer a question regardless of what the results were, and my collaborator in Germany was the equivalent of a 4th-year PhD student in the U.S., meaning she'd had a lot of experience with figuring out the right way to do an experiment.

What my 1st year was like: 

You frequently feel like you know nothing

An incredibly common feeling in grad school is "hm... I'm not sure how to do this." The first reaction is to ask someone else, maybe an older grad student in the lab, or your friend who's a lot better at R or Matlab than you are (hi, Sinead). You just don't know the answer right now, so let's find it and move on. For our generation especially, Wikipedia and Google make the answers to most of our questions separated by merely seconds from when we decide we want to find out. Grad school, on the other hand, is about constantly being in this zone of wanting to know an answer but not having it. That's what research is; if we knew the answer, we'd have passed the info along to someone else (government organizations, the medical world, conservation groups, engineers, etc.) and be focusing on finding the answer to a new question.

As frustrating as it can be not knowing how to fit a quadratic curve on a scatterplot in R or who to e-mail for ordering new syringes for the lab, it is very satisfying the next time you have to do it and you know exactly how. And as you read more articles, go to more lectures, and talk with more people, you start seeing the same concepts reappearing... but this time, you understand them a little better.

You spend a long time figuring out how to find the answer to a question

Do you remember those "If you had a million dollars, how would you spend the money?" essay prompts in high school? One of the biggest hurdles I've had in planning experiments in grad school is getting out of this mentality of infinite money and time. You read about experiments where the authors make grandiose claims out of six data points and you vow to never publish something so ridiculous. If you're going to do science, you're going to do it right, even if it means fewer publications during your PhD. Your experiments will have at least 30 individuals, each assayed on multiple days to control for between-day variation in behavior, and each individual will be exposed to 5 treatment groups to see the full effect of the variable on behavior.

Those are fantastic intentions, and you can often make it work. But it's really difficult. If you're like me in college, "really difficult" sounds like something that applied to people who weren't you; you've faced "really difficult" before and gotten an A in the class. Let me reiterate: it is really freaking hard to do this.  

Here's an example from this week: I've started a pilot experiment to figure out how the social environment affects how skittish a fish is in a new environment. The idea is to use 8 fish in 3 different groups of 60 fish. Due to poor planning, the videos ended up really dark, and it's impossible to distinguish who's who in the video. Not only can I not use the data; if it wasn't for some quick thinking by marking all tanks where fish had seen the experimental tank, I might have had to scrap the experiment! (In animal behavior research, novelty to an environment is often extremely important.) So even though I've been planning these ideas for a few weeks, I nearly messed everything up within the first two days of actually doing anything. It always seems so obvious before you start, and then it never goes how you plan. (Above right is a video still from a trial I can't use.)

But... that's just how it goes. You can't get to the end result without making mistakes. And you can't make any progress if you don't try.  

You wait (a lot) for clearance to do research

Animal welfare committees are a crucial part of research by instituting ethical requirements for how research should be conducted. They ensure that the research has a bigger point and that your methods are the most humane way to get there (e.g. if mice have to be euthanized, what's the calmest and least painful way for the animals? If the crickets suddenly start dying during the experiment, what do you do?). If you're doing fieldwork, you need to get a license for the work; if it's in another country, you probably need a visa as well.

Ensuring that research will be done properly takes a lot of time. Animal welfare committees have panels of both scientists and non-scientists to get a range of perspectives on the ethics of the work, which means extra time is needed to exchange and explain the reasoning for different viewpoints. For fieldwork, a lot of people want government approval for permits or visas, and there are only so many people reading the proposals. The only advice I can give on this is to start early, be patient, and be courteous with your e-mails. The waiting time (on the order of months) can really help refine your ideas for when you actually start.

You start to understand what makes for an interesting scientific question

For the first few months of grad school, I told people I was interested in how group composition affects predator evasion behavior in schools of fish. It took a lot of thinking and discussing with others to refine those ideas into a broader framework with more applicability than one species of fish under one type of predation risk.

You spend a lot of time thinking in grad school. Your ideas have to stand up to hundreds of hours of mental chewing; the best ideas are the ones that not only hold strong but also generate new ideas the more you learn about them.

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Doing research has been challenging but I've been really happy so far. It's really quite amazing to be paid to think about and do experiments asking questions nobody in the world knows the answer to yet. I feel like the incredible amount of time stuck, trying to figure out an impasse, has taught me how to find the answers to things I don't know. This mentality has given me a lot of confidence to approach things I might have shied away from before because it seemed too difficult (e.g. teaching myself linear algebra, taking a metro or bus in a country where I don't speak the language, etc.). And most importantly, I constantly feel like I'm gaining a better understanding of how the world works, which only makes me more excited to see where grad school takes me.

-Matt