The Third year Slump

My, it has been a while since we’ve posted here! Sorry, Helicuties, third year has been off to quite a rocky start. We both spent most of the beginning of our third year troubleshooting protocols that just weren’t working no matter what we tried. Frustratingly, the protocols that we were struggling with had so many different variables to take into consideration, making it extremely difficult to optimize within a reasonable amount of time.


Super blotchy Westerns with missing lanes and smears! The second blot Phuong ever run (the first one didn't have any lanes at all, not even a ladder!) How do people get these to look so perfect?!

In Phuong’s case, she was grappling with getting her target bands to appear on her Western Blots. Western Blotting is a common technique used in the field of molecular biology to identify the presence of target protein in a sample. Due to their prevalence in experimental research, the published methods that Phuong used as references were vague in detail, assuming that knowing how to run a Western Blot is common knowledge. It was not, in Phuong’s case. She had never run a Western before, nor was she even trained as a biologist before joining her current lab! It was very frustrating and demoralizing to see beautiful figures of perfectly run Western Blots in papers, and not having any idea how the authors were able to do them. Like many things in experimental research, the Western Blot technique is very finicky depending on what specific tests you want to run. Even incorrect loading of your samples into the gel can cause a disruption in the way that your samples run. On top of that, Western Blots take a couple of days to run, so one failed blot meant half of a week already down the drain! It’s easy to see now how one experiment can suck up MONTHS of a researcher’s time.


The smiley-face of doom when running a gel (the dye is supposed to run as a straight line down the gel)

Ayumi was working on a fluorescence quantification assay. No one else in the lab was working on this at the time, so she often felt pretty lost. The results returned by early assays made no sense; they were greater than was even possible given the starting conditions! From the specific fluorescence detection instrument to the type of 96-well plate used to fresh vs frozen samples to time spent on the plate, if felt like every little change resulted in massively different results. It took months of optimization to find a technique that matched quality control samples before she could actually analyze real study samples, and at that point one of her study sample groups had gone “bad” (frozen for too long), so she had to redo an entire pharmacokinetic study. Luckily, her PI recommended she work on other projects to take some time to cool off between experiments, and that helped her a great deal with burnout. She did manage to create a protocol that worked, and is on her way to publishing the results. Her PI reports that this frustration is a necessary part of the graduate experience, and she concurs. However, she does not plan on doing any fluorescence work for a little while because she is sick of it!


Something We didn’t know before starting grad school is how long protocol optimization took! When we were undergrads, our mentor always had pre-prepared step-by-step protocols to follow. And what do you know, they worked every time! Now as grad students, we realize how much we took our mentors for granted and all the work that must have been put into each protocol we received in undergrad.


Collectively, we spent a lot of time questioning our abilities as scientists. You know that saying, “Insanity is repeating the same thing over again and expecting different results?” Experimentalists walk a fine line between sanity and insanity when optimizing protocols, and this was very disheartening as PhD students who are still trying to figure out their dissertation projects! Imposters syndrome hit us both hard. What made it worse was hearing that one of our close friends had left the PhD program (they mastered out, which is totally a career option for those of you who aren’t sure that a PhD is for you!).


Ayumi and I on a cry-der date where we cry about grad school together over some yummy apple chaider tea

Although it felt like a very isolating experience, many grad students we’ve spoken to had… interesting… third years as well. In fact, there is a name for it! The 3rd Year Slump. The excitement of first year has passed, the stressful, fast-paced nature of prelims, quals, and classes are over (at least until generals!), you’ve got that dead look in your eyes, and now you have roughly 3* more years of pure research. It’s no joke. Your 3rd year is also the point in time when you’re still figuring out the direction of your research, having just passed your preliminary exams just a year ago (or less!). For both of us, we are fortunate to be at a point in our projects where we’re working on publishing our research! It’s super exciting to see the progress we have put into our research to get to this point in just a year (during COVID no less, how awesome are we?!). Of course, this also means that we are in the thick of writing, and hitting writer’s block after writer’s block.


Even staff in our program know about the third year slump.


“We often hear from student’s in their third year that it can be somewhat unexpectedly challenging. The first two years are distinguished by clear milestones such as completing coursework, choosing a thesis lab and passing qualifying exams. By year three, students are suddenly focused solely on their research, which is inherently open-ended. Both the uncertainty and lack of structure can be overwhelming. The good news is, as the year progresses, students figure out how to build in more structure while also enjoying the freedom that comes with driving their own research project.”

-Corin Shelley-Reuss, MolES Events & Communications Specialist


Even though we have been tragically busy this past quarter and are super behind on updating this blog, we miss you all! We are alive, but are definitely past the ‘honeymoon period’ of our research. We appreciate a year of support from you all, and are excited to get back into the swing of things this new year (it is crazy how 2021 flew by). We have lots to update you in the future of all the things we’ve learned in 2021: sharing grant/manuscript writing experiences, mentoring stories, and (I still can’t believe this) being contacted by our DEI and science education hero, Dr. TK Francis! We hope you all had a wonderful (or even okay. We will take okay) rest of your year, and we are looking forward to reconnecting with you in 2022!


*please please please no more than that!