Fellowships and Candidacy: Growing from the Challenge

HHMI EXROP Class of 2014. I’m in the bottom right with the green bracelet.

14 min read

June 15th 2020 I learned that I was awarded the 2020 Howard Hughes Medical Institute (HHMI) Gilliam Graduate Fellowship grant. News of the award both revived and resolved some complex emotions. I take the time now to reflect on the year leading up to applying to this fellowship for the second time, and figure out how in the world I might have deserved this award (since, apparently, I do deserve it). At the end of this blog post, I have some takeaways for the graduate student beginning to think about fellowship applications and starting to face one of the largest challenges of graduate school: The Candidacy (prelim) Exam. I hope students and advisors alike will find this post useful when thinking about what the process might be like for them or their students.

Beginning to Reflect

In 2014, a junior in college, I attended the HHMI Exceptional Research Opportunities Program (EXROP) orientation. This was one of those reality-bending, fortune-augmenting moments that seemed to really change the course of my life. I remember sitting in an auditorium, learning about Howard Hughes, HHMI, and the purpose of the money Howard Hughes left. Then I learned about this fellowship. It sounded so regal: The Gilliam Fellowship. As someone who looked for goals to commit to, I knew I wanted it as soon as I heard about it. That last year, only about 7 or 9 people, I can’t remember, were awarded it and it seemed really prestigious. I wanted to be one of those people. Funny enough, looking back I appreciated my single-minded enthusiasm in reaching my goals, however I never thought, like I do now, that those goals were a little bit short sighted. Not to say they were bad goals! It’s just that now I don’t (truly) know what I want to do with my PhD. I have an idea of my choices, but my goals only reach as far as the end of the PhD. But anyway, here I am, ending my 3rd year of my PhD with the prestigious accolade I set my eyes on 6 years ago. Perhaps it’s a sign to fully commit to a long career in science. Seems like I’d be good at it. It feels good to get this - but the main feeling I have is relief.

You see when you enter into graduate school, you don’t realize it, but you are stepping out of a world with near-instant, quantitative, grades-driven feedback and into a world where you are your own evaluator. Yes, you do get graded in your 2 years of graduate courses and if you are fortunate enough to excel at those, good for you. Graduate courses overall kicked my butt. And yes, you have an advisor who gives you feedback, but if you’re like me, suffering from imposter syndrome despite your best interests, believing positive feedback is incredibly hard when it isn’t in the form of a letter grade. That’s an unfortunate result of our education system as it is now, but I won’t go off in that direction, I wanted to talk about the path to this award.

I felt relief because it was positive feedback in its most concrete form - money and prestige. Someone (many someones) evaluated my work and decided to give me money and prestige for it. That doesn’t happen often in graduate school, but when it does, it gives you so much validation, quenches the thirst for affirmation that even though you feel lost you’re still generally going in the right direction. I needed this. And this makes it easier to believe my candidacy exam committee, my mentors, my advisor, and everyone else when they say I’m doing a good job. I didn’t believe it until now.

I’m also a bit sad. Sad because I’ve struggled so hard to perform and question and read and write, all while being convinced that I’d be discovered and weeded out as an imposter. I feel like I shouldn’t have had to feel this way. It makes me wonder why I rely so much on external validation. But it makes sense that I do - I’ve been so trained to respond to external validation throughout all of my science education (kind words, letter grades, awards), that I rarely find within myself a kind of internal validation when I look at my own work and see a job well done.

But I digress.

Attempt Number One: First Gilliam Fellowship Submission

After leaving HHMI campus and going to Stanford for my HHMI EXROP experience, I fast forward to the middle of my 2nd year at the University of Pennsylvania pursuing a Neuroscience PhD, December 2018. I was terrified. Overwhelmed. And this was even while I was in a nurturing lab environment with supportive friends and a well-functioning graduate program. I felt these things because I had to begin preparing for the biggest exam of my life: the candidacy exam, aka prelims. The format of prelims was to prepare a document that followed the same guidelines as the National Research Service Award (NRSA) application, and give a presentation on that document. The content of the document was a plan for your entire thesis - what your big question is, what experiments you were going to do, and justifications for every single thing you propose. We had until May to prepare and I didn’t believe I could do it. I hatched a plan - I would push myself to try to make a proposal for the Gilliam Fellowship, due in January. I didn’t really believe I would be able to make something that would win, but it soothed my nerves because at the very least I had to make something presentable. So I talked with my advisor and a postdoc in my lab and came up with a general proposal plan.

I see now that the second hardest part about writing the proposal was that I did not really know how to write something if I could only understand two thirds of it. I talked about the plan over and over with my advisor and the postdoc on my lab in order to uncover the parts I did not understand. And when I felt like I got most of it, I had to then write it. This was the hardest part. The best test of whether or not you understand something is to communicate it well. For that I read my advisor’s 10 Simple Rules for Structuring Papers and tried my best. What helped my writing the most was bringing my writing to my advisor, sitting down next to him, and rewriting/editing the document while my advisor explained why he changed what he changed. It was emotionally difficult to do paired writing at first because I had to watch as the words I proudly crafted and put to paper were being rewritten, better, before my eyes. But I realized early on to acknowledge my ego, let it say its piece in defense of my writing ability, and then let it pass on by so I could focus on why the words replacing my own not only made sense but were more compelling. I credit those paired writing sessions, coupled with my attitude adjustment, for my ability to write scientific prose as well as I do now. When it was time to submit my proposal to Gilliam the first time, I submitted something I was proud of. Now, 1.5 years later I know I can do much better.

Preparing for the Exam

After I submitted my Gilliam submission in January, I had to immediately forget about the fellowship and try to improve on the proposal I had written. As I read more papers and sat down to write my thoughts on the ideas I already put to paper, I realized my ideas were either unoriginal, or logically flawed. This became a disheartening theme. It’s rather daunting to realize that you are trying your best to contribute to a field that already has hundreds, if not thousands of people roving over the literature and finding holes to fill. I found that I had a lot of difficulty reading papers and got discouraged a lot. I put off working on it and focused on my classes. 1.5 months went by and on March 1st, it finally hit me that I only had a little more than 80 days left. That’s when I got serious, and felt a touch of low-level, ever-present panic. The prelim was a crisis that crept ever-nearer and I had to be ready.

That’s when I started doing what kept me going all the way up to the exam date. I started a daily journal, called “processing”, where I kept track of my “processes” throughout the day. I narrated my actions. Here’s an example beginning entry in March:


    Had meeting with Konrad about my CAJAL application and the significance document. I liked the meeting.

    The larger structure of the significance should be:

    Identification of questions
      The Existence Problem
      The Inverse Problem
      The Learning Problem


The magic of the processing document was that it didn’t really matter if I was focused on a scientifically productive task - what mattered was that I was constantly writing. I made it so if I never stopped writing, it would be relatively easy to write reflections on papers I read, think “aloud” about my ideas, and write my proposal. It worked wonders. Some days I only wrote a couple of sentences because I could not focus. Other days I wrote entire sections of my proposal document. I still use this system to this day.

While I was reading and writing my proposal, I also consulted with my prelim committee. I went to them with my big ideas and they gave me focus, as well as a good set of expectations for what I would see come exam day. My project was very theoretical. One big question I kept getting was “What is the biological question you are trying to ask?” This question came from the experimentalists on my committee. This challenging question made me more aware of the tension between the theoretical and experimental subfields. I began asking ever more basic questions about my own process of writing the proposal. Things that were assumed in my previous life as an experimentalist were put under the magnifying glass. “What is a hypothesis?” “What exactly is the scientific method?” “Are my hypotheses falsifiable?” “What is the difference between a question and a hypothesis?” “How is falsifiability different from verification?” and so on. This made my thinking a bit more precise. Soon I was able to answer the questions my committee gave me.

May 14th, 2 weeks before my exam date, I discovered a major breakdown in the logic of my proposal. I realized there was a confounding variable that I could not control for in my experiments, and when I realized it, the flaw seemed glaringly obvious. That’s when I really panicked and lost my nerve and confidence. I was so disappointed in myself. I convinced myself that I would not be able to defend my proposal, let alone make a brand new set of experiments to defend in 2 weeks. It seemed that, just as I had struggled with much of my graduate level coursework, I was struggling with the prelim, while my classmates all seemed to be finishing on time. I was heartbroken and felt ashamed. I canceled my exam and appealed to my committee to take it in the fall.

Starting Again

By that time I was pretty burnt out on the stress I was putting myself through. My Gilliam application had been rejected. I went on vacation to Europe and came back refreshed. I found my determination and decided that with every passing day, I would think and read, pressing on ever forward to my new exam date in October. I was armed with a clearer understanding of the scientific method, an already rich bibliography, and some burgeoning ideas that I had faith could be clarified with the time that I had. I also had the support of my committee and advisor who believed I was doing alright. Moving forward, I realized there was no “track” for me to be “on.” My path in graduate school was my own, and whether I finished my exam in May like everyone else was irrelevant. What mattered was that I reached the milestone of defending my prelim proposal. I was on my own schedule.

July went by and I accelerated. I worked out equations. I drew diagrams. I wrote the code to get some preliminary data. And I raced myself, because I had signed up for a summer school in August and I wanted to be able to focus on that completely, not worry about my exam. In August, my life went on. I went to the Cajal Computational Neuroscience Summer School in Lisbon, Portugal and had the time of my life and learned a lot. But most importantly, I got a lot of feedback on my ideas from various computational neuroscientists. They helped me clarify my ideas even further. And I made new friends.

By the time September rolled around, I was very sure that my ideas were logically sound. I had vetted them by talking to various scientists outside of my lab. Most importantly, I talked to nonscientists who highlighted the most fundamental questions (“So why is that important? Why are you doing this? What are you trying to do by answering this question?”) Soon, I could explain my project in a few sentences instead of a few minutes. I was ready to write and make my defense presentation. That month I wrote every day, getting comments from my advisor and friends. My writing had improved greatly. I kept checking in with my committee to make sure I knew how to deal with their questions, theoreticians and experimentalists alike.

Come October I was ready. Every time I practiced my presentation it got shorter and shorter. My graduate program community came to one of my practices and gave me useful advice (“If you don’t want to explain it, don’t put it in the slides!”) and gave me clear warnings of what to look out for. Most importantly, the practices taught me how to think on my feet. After these, I realized in several ways my proposal was flawed, but defensible.

Attempt Number Two

Exam day, I was nervous, but excited. I knew I was prepared, not only due to the hours of reading and thinking, but also due to the mental adjustment. I knew my committee was cheering for me. They were going to do their jobs and challenge me, but they weren’t there to make me feel bad about my work. I knew they knew I put in the time to think about what I was going to present, and they were going to test me on that. An important thing to realize about the prelim exam is that it is a conversation. You know your project best. You will get questions you don’t know how to answer, so in those cases, admit that you don’t know and then give thinking aloud about it your best shot. The first 5 minutes of the exam my knees were shaking and my voice quaked, but once I realized the world wasn’t ending, and the questions were not suddenly exposing me as an imposter, I started to actually have fun.

After my exam, as I waited in the hall for the committee to come to their decision, I was full of joy and exhilaration. The questions I answered badly weren’t answered too poorly. The questions I didn’t know the answer to I admitted I didn’t know and gave them my best guess. And overall, I retained command of my presentation. As far as I knew, from my own internal validator, I had done a good job, and I expected the committee to see it that way.

I passed. With flying colors according to the head of my committee.

I took a break, then refocused my energies at the old target: The Gilliam Fellowship.

My ideas were good ones, well defended, and clear. My challenge was to frame the proposal for an audience I didn’t know. So I asked friends and faculty in different parts of the neuroscience field to read my proposal and let me know what didn’t make sense. I had a shorter page limit, so I refined my language and removed relatively unnecessary verbiage. In a way I felt like I was putting my proposal in a crucible and refining an already finished product. The end of December came quickly. The day before the deadline, a particularly talented friend of mine helped me rewrite the very beginning of my proposal, arguably the most difficult part. Once I changed that, that was it. I was done.

I submitted the application, and went on to the next thing, forgetting about it until now, 6.5 months later.

My tendency to put in my all into something, then move on to the next thing without processing or reflection, is definitely reinforced in my PhD. There’s always something to do next. But getting this award made me put on the brakes and just reflect. It’s funny how PhD requires you to think a lot, but you can get away with not thinking about your journey as you go through it. From my first submission to Gilliam to the last submission to Gilliam, I’ve had an incredibly eventful, rollercoaster of a year full of growing pains and re-evaluations of my science, my goals, my processes, and myself. The Gilliam fellowship merely signposted an incredible year of development for me. I’m thankful for pushing myself to apply both times so I could get such concrete validation of my growth.


Apply to fellowships - Fellowships are challenging to apply to. You have to understand enough, think enough, and write enough to communicate your ideas to people you will never see. The fellowship applications will force you to clarify your thinking as well as orient your audience so that everyone is on the same page.

Have a daily ritual - Days go by quickly. Whatever you decide to do to make sure you are making even the tiniest of steps every day; just do it. Don’t even think about whether or not you will do the daily ritual. Commit to it, and all of those days of incremental productivity will add up.

Question your understanding of the scientific method - I was quite surprised and angry that I didn’t actually understand the logic behind the scientific method. Going back to the history of philosophers of science helped me understand what the method was and what logic gives it its strength and staying power. I highly recommend brushing up on it, it will give you a framework within which to think and develop your ideas and experiments. I started here.

You are on your own path/schedule - Even though you matriculate with a cohort of students in graduate school, everyone’s path and interests are very different and everyone has different strengths and weaknesses. When strategic, decline to compare yourself to others and just focus on what you are doing. You’ll find that you’ll feel better about the progress you do make instead of wondering why you aren’t doing enough.

Talk to everyone about your ideas - You’ll find that no matter how comprehensive your thoughts are on your ideas and experiments, someone will be confused by a hole in your reasoning that you have missed. Talking to people outside of science is good for this.

The candidacy/qualifying/prelim exam is an opportunity - I never would have gotten this fellowship if it were not for the struggle, effort, and challenges I faced while preparing for this candidacy exam. It’s all worth it. But most importantly, you will come out stronger and more precise than you’ve ever been. This is why it is part of your training.

A takeaway I have from talking to many different upperclassmen in my program is that every year of PhD is very hard, just in different ways. The challenge of the 2nd year, which expanded into my 3rd, was bounded by fellowship applications that gave me the special opportunity to see how I have grown. I recommend everyone apply for fellowships - not just for the prestige or the money, but for the opportunity to grow.

Ilenna Jones
Ilenna Jones
Research Fellow

My research interests include neuronal biophysics, dendritic computation, and neuroscience for AI.