The Final Hurdle: Dr. Nikko Torres tells us about his PhD Defense

Written by Andrew Zhai

Take a moment and think about some traditional milestones in life and how long they take to occur. It takes four years to graduate from high school. Four years to earn a bachelor’s degree. Couple’s date for an average of three years before getting married and then it takes an average of three more years to have a child. These are all hugely significant events, and no shortage of stress, planning, and worry goes into each.  Now let’s consider a typical Ph.D in the biomedical sciences, which usually takes around seven years to complete. More time goes into earning a PhD than choosing the person you want to live the rest of your days with and then creating life with that person, and it all culminates in a 3-hour exam known as the defense.

The defense, at least here in the biochemistry department, consists of a 45-minute public seminar followed by a closed-door Q&A exam with a committee made up of head researchers. However, preparation begins well ahead of this when the candidate is given six months to write and hand in their written thesis, which is the thing being defended. And although it represents the final hurdle for every graduate student, everyone’s experience with writing the thesis and defending it is different; some adhere to a regimented writing schedule while others prefer something looser, some exams follow a strict format while others resemble more relaxed discussions.

There’s a stereotype that scientists have a one-track mind, too zeroed in on their work to be concerned about other things. Nikko is, I think, proof against that misconception.

Transcripts sat down with the newly minted (since February 2017) Dr. Nikko Torres to ask him about his experience with the PhD defense, from thesis writing up until the exam. Nikko completed his PhD work in the lab of Dr. Grant Brown examining the effects of DNA damaging agents on yeast and human cells, and how those cells react to that damage. I met Nikko during my first year of graduate school and he has always been able to provide a unique perspective on any topic that I throw at him. There’s a stereotype that scientists have a one-track mind, too zeroed in on their work to be concerned about other things. Nikko is, I think, proof against that misconception. Our conversation jumps from his defense, to music, to cooking, and if we had the time I would have asked about how he is also a karaoke megastar, or about his love of rock climbing. Here’s how he climbed that metaphorical rock that is the PhD defense.

Transcripts: Can you go over your thesis, in broad strokes? What was it that you were defending?

NT: I was looking at how the DNA in your cells become damaged and repaired. I started by taking an external view of the cell and the different kinds of damage that can occur. If we attack the DNA in different ways using different kinds of drugs, are they robust enough to survive? What we found was that you could not necessarily predict the effect that a combination of drugs would have based on their individual effects. Some combinations had a synergistic effect. After that I shifted to looking at how the cell defends against those types of damage from the inside, focusing on the molecular machinery that helps repair DNA. How do those machines re-arrange themselves following stress? So that was the last seven years of my life, summarized in under a minute.

Transcripts: At what point did you know that you were ready to start writing your thesis and defend? Was there a specific end-point that you were working towards?

NT: For me it was a process that I communicated about a lot with Grant. It’s a process that is variable for everyone, but in my case, at every point we were asking each other “Do you think this is enough for a thesis, even if it’s not ready for publication?” There was a lot of negotiation involved, but it was a balanced negotiation from both sides.

Transcripts: So it wasn’t immediately obvious?

NT: No. I will say though, that at some point while working on your project, most graduate students seem to develop a confidence that you can go into a room, and answer questions about your work. So the point where you feel you are ready for the actual Q&A part of the defense is more concrete.

But for the thesis, in my case, things were not so cut and dry. I started graduate school under the supervision of two professors. When we found that you could not necessarily predict combinatorial drug effects from our test, we decided not to pursue it any further. It was at this point that I switched to working under one project supervisor, which led to a switch in project as well. However, at this point we did not have enough time to develop a full story, and so the issue of deciding when to stop and defend became much hazier. When I felt like I had done enough, I communicated that.

Transcripts: You are given about 3 months to write your thesis. What were those months like for you?

NT: For me writing started off slowly. I started doing a little less lab work. The first step involved cannibalizing parts of old reports, presentations, and posters to start nailing down a skeletal layout. After that I started with the introduction chapter, just to test the writing waters.

Transcripts: Everyone says the intro is the hardest part.

NT: Depending on your style, some people write it last. I had to do it first to get into the mindset of writing. It helped me understand where to start, and what I had to work with. It helped me see the bigger picture and set the frame for the results section and then the discussion. The introduction is where you need to consider how your work fits into the larger body of science and the work that’s already been done in the field.

Coffee or beer? You be the judge.

Transcripts: The two parts of your thesis deal with different aspects of DNA damage. Was it difficult tying those two together?

NT: It was definitely a challenge framing it into a coherent story, but in the end it was a valuable experience. Being able to make sense of and draw connections between seemingly disparate elements is, I think, one of the most important skills that you pick up during graduate school

Transcripts: What were you listening to during the writing process? Did you have a song that got you into the writing mood?

NT: It depended on where I was writing. I would usually find a distant spot to write so that the act of biking there would give me a mental break. If I was in a coffee shop, I’d be listening to whatever could drown out the music being played on the speakers, which tended to be low BPM electronic music. Something to keep me on tempo while typing. I listened to a lot of Tycho and Boards of Canada. When I was designing figures I just listened to whatever I wanted to. Something like Grimes, Carly Rae Jepsen, or Solange. Whatever was new that was not one the radio…not that radio music’s not great!

I left the room, didn’t have my phone on me, and just stared out of the window and zoned out

Transcripts: OK, let’s jump ahead. You’ve completed your thesis, edited it, and handed it in. You’ve studied meticulously and it is now the night before your defense. What was that night like?

NT: You’d think it would be this momentous, scary moment, the night before the defense, but honestly I was just tired. I went through my presentation once or twice and then cooked myself a very elaborate meal. I wanted to do something different so I made sure to make everything from scratch. It was a jambalaya, so a big mix of a bunch of different ingredients. After that I just started to look up random tidbits and facts, anything that I thought had even a minuscule chance of being asked. At this point a mini-panic set in and I didn’t really sleep. I slept two hours total, which is something that I would advise against. But It wasn’t until the next morning that the full-on real panic creeped in. Scheduling a defense is always complicated, so I was stuck with a Monday 9:30 am time slot. It also happened to coincide with a giant snow storm and one of my examiners couldn’t physically be at the exam. We had to Skype him in.

Transcripts: How many of the random tidbits and facts that you studied came up during the questioning session?

NT: They weren’t asked directly, but I ended up mentioning a lot of them to answer the very broad stroke, general questions that were being asked. For example, my exam committee would ask “Why do you think protein localization is important?” and in response to this I would reference the specific studies that I looked up beforehand. None of the questions asked were about specific details. They all dealt with the big picture, and I think this style of questioning is more conducive to having a discussion instead of just a very formalized Q&A, which is what most people probably imagine a defense is like. It’s also, I think, more interesting for all parties involved to have a more relaxed discussion about the Big Picture of science, and how your work fits into that, instead of being quizzed about details.

Transcripts: What are the moments after the defense like?

NT: The exam committee asked me to leave the room while they voted on whether I was ready to append those three consonants, PhD, after my name. Since the defense was more of a relaxed discussion, I felt very comfortable afterwards. I left the room, didn’t have my phone on me, and just stared out of the window and zoned out. I wasn’t nervous about the thing at all.

Transcripts:  Now that it’s all over, if you look back at the whole affair, what were you most worried about, and did that worry materialize?

NT:  Before I started writing the thesis, I was worried about the actual exam session. But then while I was writing the thesis and giving practice talks, I became less worried about the exam and became more worried about the seminar part. Since the seminar is open to the public, I was concerned with how to present a coherent story that would be understandable and engaging for all the people in the room. I assumed that after the second slide most of my family and parents would tune out, which is fine, and they did! But I wanted to tell a coherent story, which was hard because I knew how disparate the parts of my thesis were. It was hard to gauge people’s reactions while giving the seminar, so even today I’m not completely sure if I accomplished that. That’s the thing with the defense, you spend almost half a year prepping for it and it’s over just like that, it’s a blur.

Header illustration by Nikko Torres.



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