Reflections on the PhD Prospectus
More than just a milestone to check off.
Motivation for this piece comes from Claus Wilke’s essay, Most graduate students propose to do too much.
I’ve been thinking back recently to my PhD prospectus, which I completed years ago, and how it became the moment when I first felt myself shifting into the mindset of a real scientist. On the surface, the prospectus (or proposal) is just an hour-long presentation to your thesis committee explaining what you hope to accomplish for your dissertation. But it was the first time I had to articulate, in a deep and defensible way, what actually motivated my research. What gap in knowledge was I trying to fill? Why would any of it matter? At the time, it felt like another requirement everyone had to get through. Only later did I understand how much the structure of the prospectus quietly shapes the way you learn to think, at least it did for me.
For some context, I did my PhD in Biomedical Engineering at Boston University. In most departments across most universities, PhD students are required to complete a prospectus. It usually includes a written proposal, often in the NIH grant style with specific aims and a research strategy, and an accompanying oral presentation outlining the work you plan to do for your dissertation. These are submitted to your thesis committee, which includes your advisor and four other professors.
Different departments have different timelines. BU’s BME program required us to complete the prospectus by the end of our third year. In other fields, like computer science, students didn’t need to do it until six months before graduation. In disciplines where research depends on physical experiments, like biology or engineering, departments tend to require it earlier to ensure students have a clear plan and enough time to execute. In more theoretical fields, the experiments may be computational and short enough that a later prospectus still works.
Structurally, the proposal is often divided into three aims that map onto a larger scientific question. You introduce the big problem you are trying to solve, then describe three aims that collectively get you closer to answering it. For each aim, you lay out the experiments or analyses you plan to run, why those are the right approaches, and what results you expect to see.
Of course, I had talked through these questions many times with my advisor, and I could explain my work in broad strokes to friends and family. But until the prospectus, I had always implicitly trusted that my advisor understood the bigger picture and that I was working on something worthwhile. The prospectus forced me to answer a harder question: Did I believe in and understand the research strongly enough to convince five experts that they should believe in it, too? And you can’t convince anyone of anything until you’ve convinced yourself.
Connecting the dots from what I did every day at the lab bench to how that might create meaningful knowledge to push the field forward, and maybe even help the world in a concrete way, was transformative. It made me think ambitiously. I suddenly saw a whole arc of research far beyond what I could realistically do in the three years I had left. But I wanted to do it anyway. And so, I proposed the entire thing.
What the project was isn’t nearly as important as what happened next. I gave my presentation, it went smoothly, my committee congratulated me, and then promptly told me to cut half of it. One member even joked that I’d outlined the work of two, maybe three, PhDs. The exact work isn’t important because every one of my peers got the same feedback. It seems to be almost universal: PhD students propose wildly ambitious projects, and thesis committees guide them toward something more realistic.
Why do students over-propose? One reason is that students fear coming across as unproductive so end up proposing more to look good. I don’t find that very compelling as the primary driver. I think most students want to do the work they outline, or at least think they want to. A more convincing explanation is simply being naive about how long it takes to do research, especially in the biomedical sciences. The planning fallacy is deep-rooted in science, from graduate students to PIs. But PhD students might be especially vulnerable to this because they just haven’t failed enough yet to know how long their work might take.
But I think the deeper reason is that, at the prospectus stage most of us simply haven’t yet learned how to think deeply about a scientific problem. I don’t mean that we don’t know what’s important, or that we can’t outline the logical steps of a project. I mean something closer to understanding what it really takes to know the truth in science and to get to the bottom of a natural phenomenon. I’m still learning this myself, seven years after my own prospectus. It’s a lifelong process.
And that’s why we propose broad, ambitious ideas: they feel exciting. Broad claims feel consequential. Narrowing a question, cutting away good ideas for a single sharp, answerable problem, requires a kind of discipline and experience you just don’t have yet. The prospectus is, in many ways, the first real lesson in that. In the traditional academic path, it’s also the first formal moment when the scientific community gives you feedback on how you think as a scientist.
This implies that the prospectus serves a very important role in the development of a scientist. And that’s what makes it a powerful but underrated teaching tool. The committee’s job is not just to keep you from overworking yourself. It’s to teach you how to frame a problem, how to identify the core question, how to think from multiple angles rather than chase multiple directions. It’s one of the rare moments in graduate school where you are forced to move from “I’m doing experiments” to “I’m building a coherent research program.” I wish I could go back and appreciate this, instead of treating it like another box to check on my way to adding Dr. to my name.
At the same time, I sometimes wonder about the message embedded in the ritual. When every student is told some version of “you’re doing too much,” does that gently nudge people toward safer, smaller science? Does the instinct to protect students from failure also unintentionally train them to think less ambitiously?
Ambition and feasibility are both essential scientific virtues. The trouble is that graduate training tends to over-index on feasibility, because feasibility keeps students sane and ensures they graduate. But the scientific enterprise thrives on the opposite: people who are willing to try things that don’t fit neatly into a 3-5-year timelines. If the earliest training moments consistently reward the safest version of the idea, then young scientists may absorb the wrong lesson, not that ideas must be rigorous, but that ambition is something to be contained. We need training structures that can teach focus without extinguishing the spark that leads people to ask the biggest questions.
Doing a PhD is not the only path to developing this kind of depth. Any sustained effort, paired with real feedback, can reshape how you think. Looking back, I’m grateful for the prospectus because it forced me to see what it actually means to pursue a question with depth. Beneath all the logistics and forms that made me a “PhD candidate,” there was also a shift from doing the work to understanding it.