In the backdrop of COVID19, I defended my PhD

In August 2014, I took a flight from Chennai to Houston, Texas, US. I was starting my PhD degree in biology at Rice University. I remember my first day on campus. Walking along a path lined with trees, I looked to the future and thought about my lab, the science, the people and the things to come my way. 

I chose to work on a fundamental problem in developmental biology – How does a pattern of distinct cell types form?

In my PhD project, I set out to understand the mechanism behind gastrulation – How does a group of homogenous cells organize into the three germ layers? The prevailing view in the developmental biology field is that cells choose to become different cell types depending on the levels of a key molecular signal. Using a stem cell model of human gastrulation, we measured and modelled the activities of three signals known to be necessary for gastrulation in mammals. Our results suggest that cells adopt different germ layer cell fates based on the dynamic interactions of the three signals, and not the level of any one signal in a cell.

Early stages of development, source: Wikipedia

Our lives start as a single cell – the fertilized egg, and by the time we are born, there are over 200 different cell types in our body organized in a layered pattern. The skin cells form the outermost layer; muscle, blood and bone cells form the middle layer; and cells of the internal organs like stomach and intestines form the innermost layer. This layered arrangement of cells can be traced back to an early developmental stage – around two weeks post-fertilization, a flat disc of cells organize into a layered pattern comprising three discs arranged on top of each other. Each layer of cells constitutes a distinct cell type corresponding to one of the three germ layers – the ectoderm (outer), mesoderm (middle), endoderm (inner). As reflected in the names, ectoderm cells give rise to the outer organs like the skin, mesoderm cells to the middle organs and endoderm cells to the internal organs. Because of its literal significance in our lives, this developmental stage has a special name – gastrulation.

It took 5+ years, many failed experiments, and numerous hours of reading, writing, coding and critical thinking, to finally get one inroad into the problem. After this, it was finally time to wrap up this journey. Beginning with, defending my PhD findings.

The date was set – April 1st, 2020. We started the multi-step process with the submission of a detailed report of all the work. This is followed by a public oral presentation and a detailed Q/A with the thesis committee. The committee consists of three-to-five professors to evaluate the scientific rigour of the research. I was familiar with the recent scientific literature and confident about my findings. Defense was going to be easy.

Similar to experiments, life rarely goes as planned. Ten days before the defense was due, on 20th March, the research laboratory – my home for the past six years, closed its doors. The university shut down for an indefinite period.

COVID19 had raised alarms in the US. Busy with my defense preparations, I had not spent much time thinking about the pandemic. Now it was impossible to ignore. The biologist in me delved into a series of questions – Which cells does the virus invade? How does the infection propagate within a cell, a person, and a community? At the same time, I was worried about the unprecedented socio-economic impacts of the pandemic – shut businesses, burdened healthcare and exposed social inequalities. As the death toll increased, I, like most people, became a helpless observer of the catastrophe. For the first time in many years, something outside my research threatened to consume me.

Images of Rice University campus by Ya He

As my thoughts slowly turned back to the defense, a host of covid-induced uncertainties struck me. Will my defense be postponed indefinitely? Or will it be held on video-conference? What if I or my thesis committee members get sick? At least four of the five committee members had to show up for defense, else I would have to reschedule. Imagining the worst but hoping for the best, I continued to prepare. A week before the defense, I sent my report to the committee members. Three committee members acknowledged the receipt. “At least three people might attend the defense”, I assured myself.

To my great relief, the university announced a detailed protocol for defense via Zoom, just a few days before my defense. After downloading the app, I acquainted myself with “best practices on Zoom meetings”. The untrustworthy Internet connection at home made me anxious. Thankfully, the university granted me access to a conference room on campus for the PhD defense. Only two people were to be in the room and at least 6 feet apart, as per the universal physical distancing guidelines. For moral and technical support, I requested my PhD advisor to be the second person in the room. He kindly agreed. 

While wrapping up my preparation on the night before the defense, I entertained another doubt: What will I wear?! For sure, a mask, I thought. The default dress code for such a meeting is business formal wear. But given the COVID-19  and the virtual nature of my defense, I would be excused even if I showed up in my pyjamas. To retain some aspect of normalcy, I chose formals.

On D-Day I greeted my advisor, from a distance of course, outside the conference room. Once inside, we logged on and prepared. Committee members (all of them, thankfully = no rescheduling!), lab members, and friends tuned in from the comfort of their homes. I realised that (virtual) conditions brought some relief for someone afraid of crowds and public speaking. I didn’t have to worry about eye contact and my facial expressions. We asked the audience to keep their questions for the end, and muted them during my presentation.

Images of Rice University campus by Ya He

The defense began. My advisor introduced me, “Sapna thinks very deeply about fundamental problems in developmental biology.” Coming from a man of few words, it was touching. I wanted to present my work well. I spoke about my work, uninterrupted, for about 40 minutes!

People clapped 👏. It was now time for a public Q/A. Strangely, no one asked anything. Or, so we thought. Then, my advisor and I got a string of private messages. We had forgotten to unmute people. We rectified it, apologised, and continued with Q/A. 

After the public Q/A, we asked everyone, except the committee members, to leave the virtual meeting. They obliged. It was now time for the committee to grill me. After an extensive Q/A, the committee asked me to leave the meeting, so they may decide my fate. Because I was sitting in the same room as my advisor, I left the room, like I would, in a regular defense. A few minutes later, my advisor came out and announced, “Congratulations Dr.” My committee members echoed the same. D-Day was done! 😀

I reached for my phone to share the news with my parents in India. The moment I held my phone, news about the rising COVID-induced deaths in New York greeted me. I was no longer an excited PhD graduate. I became a helpless observer to the destruction again. 

Gradually, I came to terms with my conflicting emotions and rang my parents. Their cheerful voices reminded me of the importance of that day. It was a step closer to my dream, a milestone in my science journey.

As I end this journey and look around, I feel even more sure of the fact that if there is anything that can get us out of this worrisome COVID-19 situation, it is science! And, I, as a scientist, can play an important role in it.

Author bio: Sapna Chhabra is a postdoctoral researcher in Biology at Rice University. She seeks to understand the simple principles hidden beneath the complexity of living organisms.

Acknowledgements: Images of Rice University and Sapna by Ya He, sourced from the author, featured image constructed by Hansika (TLoS).