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The End of 2020

Updated: Jan 1, 2021

Killian Court After Snowfall
Killian Court After Snowfall

This year has certainly been an eventful one. The current pandemic has changed the way we live our lives in so many ways. I’ve written about my experiences up to my arrival at MIT for the start of my third year in the PhD program in my previous post. Here’s a little bit of what I’ve been doing since.

Upon arriving to Boston after my long road trip across the country, I found that I was struggling to find a new rhythm in a stationary place. I suppose I had gotten used to life on the road and traveling where I wanted, socially distant of course. I missed it in a way. The real struggle came in meeting my basic needs which were very dependent on policies of the Institute. Initially MIT had closed both gyms on campus as had most other gyms around the Boston area due to government orders, but when the order was lifted for gyms to reopen, MIT chose to continue restricting shower access. Taking a shower on campus was no longer going to be an option for the foreseeable future. In addition, the building I work in had locked all of the kitchen spaces to prevent people from congregating, but it also prevented me from using the refrigerator or washing my dishes if I ate in my office. Given how I had developed a rhythm and made things work on the road, I really didn’t like being back on campus with these restrictions in place. I understood their necessity, but it was making my life more difficult.

All the while, I was facing a few milestones that I needed to meet within the first few months of the semester. The first requirement was to give a presentation to the department (over Zoom) in an event called “CogLunch” on my chosen topic of research, and the second requirement consisted of the qualifying exams (written and oral) which would determine if I would advance from PhD Student to PhD Candidate. If a student fails the qualifying exams twice, they are released from the program with a Master’s degree. The qualifying exams are daunting under normal circumstances, but with many of my basic needs not being met, it felt nearly impossible to focus long and hard enough to perform well on the “quals”.

I reached out to my advisor and let him know of my situation. While he was understanding, there wasn’t much he could do other than ask my committee for a little more time for me to complete my milestones. They allowed me to move my oral exam date from October to November. It didn’t solve my plumbing concerns, but it did relieve me of some of the time pressure I was under. My committee consists of three professors (including my advisor) that continuously evaluate my progress throughout my tenure as a student. They decide if I advance to candidacy, continuously evaluate my scientific acumen, and ultimately decide if I will graduate to a full PhD when I defend my dissertation. The committee holds a significant amount of power over my academic progress.

To go back a bit, my initial meeting with the committee in the spring was in an event called a “Pre-Quals Meeting”. I will admit my performance was anything but spectacular. Since I had been on the road throughout March and April after the shutdown, I had little time to prepare for the meeting in May. My theory was weak and my literature review had been rather shallow. I was told by the members of my committee that my research idea was not “MIT quality”, which was a bit jarring to hear. Another said its scope was “punctate”. “This will not get into Nature or Science.” I didn’t realize I was supposed to aim so high. Those are undoubtedly the most reputable journals in science. I also felt frustrated because I didn’t have any real guidance on their expectations, but I suppose the Pre-Quals meeting ultimately served that purpose. I needed to improve greatly if I was going to pass quals. At least this time around I was able to access my office to prepare for these Fall milestones.

My advisor also shared a scientific paper with me that was supposed to help with my literature review, but, in a surprising way, it ended up positively affecting my life. The paper discussed methods of coping with anxiety. In the study, each person had been diagnosed with generalized anxiety disorder, or GAD. They were separated into three groups that were instructed to exercise three different coping strategies when presented with an anxiety-provoking statement such as “What if I lose my job?”. The three strategies were 1) to “observe and accept”, known as the acceptance condition, 2) to “worry as usual”, the worry condition, or 3) “don’t think or feel”, the suppression condition. They found that those in the acceptance condition had lower levels of distress to the worry statements when they were presented, and less activation in parts of the brain associated with emotional responses with greater activation in parts of the brain associated with emotional regulation. What does this mean? Changing the way a worrying situation is viewed has a direct impact on brain function. In other words, accepting the situation will help you get through it more easily, and it was shown using brain imaging!

This paper made me look at my own situation in a different light. Rather than focus on the things that I didn’t have, like a shower or kitchen, I began to focus on the things I did have. Even though the van wasn’t a full RV, I had built everything I needed to handle the upcoming winter. While the world was dealing with the pandemic with no real support, I had the privilege of being required to take a COVID test twice a week to access the campus. Even though stipend payments have had their hiccups, I had a secure “job” as a PhD student while many are facing layoffs and job insecurity. The kitchen was closed, but the bathroom sinks were open. Since I was one of the few people coming to the office every day, I bought a scrub brush and soap so I could wash my dishes in the sink. The gym showers were closed, yes, but I am a former soldier. I’ve taken bucket baths many times before. I had been on the road for months after all. On cold days I could make the water hot with a little propane stove. Things were okay. Not ideal, but sufficient. Within a month of returning, I had a new routine and a new attitude. Acceptance was the key.

Hockfield Court at MIT with Fresh Snow
Hockfield Court at MIT with Fresh Snow

With my daily needs met, I began to focus on my academic progress. As you may remember from prior posts, I was involved in quite a few different projects before the pandemic, but as the qualifying exams approached, I needed to focus more closely on my research proposal and less on other projects not leading to my dissertation. I had always been proud of my ability to juggle multiple projects at a time, but I was beginning to learn just how much work goes into research development rather than implementation. At Stanford, I learned how to run multiple clinical trials at a time, but developing the theory behind a trial is an entirely different dimension of research. It requires quite a bit of time and effort to fully develop an idea that is supported by the evidence. This was precisely why I wanted to earn a PhD. The time had come for me focus deeply on the area of research of greatest interest to me: understanding combat-associated PTSD.

The key component of the qualifying exams is the written portion. The word “exam” makes it sound as if it were a traditional multiple-choice exam, but this was not the case. The written exam is a document (around 12-15 pages) based on the National Institutes of Health (NIH) grant submission process. NIH funds the majority of the scientific research in the country and they have a very precise process for grant applications. The neuroscience department has chosen to use this format as the written exam in an effort to help prepare us to write grants as full scientists. I think it’s a great way to test our mettle since grant writing is the primary way most scientists fund their research activities. The oral exam is a presentation to my research committee of the written document formatted as a typical scientific talk followed by a discussion of the research. Since the CogLunch was also a presentation and scheduled before the oral exam, I framed the CogLunch event as a trial run for my oral exam.

It takes a large amount of time to prepare for quals, so I had been slowly working on the theory since early summer. I was trying to see how I could work on the topic of PTSD in a new way, but I was coming up with a few theoretical dead ends. During the summer, a friend of mine spoke about empathy in a way that got me thinking about a possible link between empathy and PTSD. It seemed to me that empathy seems to be a requirement for the development of vicarious trauma, or trauma due to an event that occurs against another person. If someone doesn’t care about the traumatic event or the person to which the event occurred, they are not likely to develop vicarious trauma. Upon digging a little deeper in the literature, I found that the topic of empathy is fairly well-researched, with many competing theories already in existence. The majority of the work is done with doctors and nurses in medical settings with such hot-button topics as compassion fatigue and empathy burn-out. Given the wealth of research already on the topic of empathy, trying to tie empathy and PTSD might end up being a much more difficult task than originally envisioned.

Later into the summer when I spent a large amount of time alone in the West, I started to feel something change within me as I continued to isolate. I mentioned in my prior post that I had three events that made me realize that isolation was not a good thing. As the pandemic wore on, I started to think that loneliness could make other mental health issues worse. By the time I arrived back in Boston, I wanted to dig deep into the literature on loneliness and see if there were any holes in our knowledge that I could work on. This was my primary task within the months of September and October.

The leading theories on loneliness look at the concept from an evolutionary perspective. Human beings are social creatures, which means we must be connected to other human beings to thrive. People are able to handle short periods of isolation, but as isolation wears on, we all get a strange feeling to seek out other people. Being alone doesn’t feel good. The evolutionary theory examines the feelings associated with loneliness as a signal to the conscious self that one must seek additional human contact. Much in the way that the feelings of hunger and thirst alert us to seek more food or water, loneliness alerts us to find other people. However, the mere presence of people is not enough. We must develop meaningful relationships to those around us. The late John Cacioppo, a researcher who performed the greatest amount of work on the topic before his death, succinctly described the concept of loneliness. He defined loneliness as "a distressing feeling that accompanies the perception that one’s social needs are not being met by the quantity or [more importantly] the quality of one’s social relationships". The key component is the perception part. Someone can be alone without feeling lonely, and someone could be surrounded by people and still feel lonely. Perception of a social need not being met is the key.

In linking the idea of loneliness with PTSD, there are some interesting correlations between the two concepts. Chronic loneliness, or prolonged social isolation, causes a state of hypervigilance or a heightened state of awareness of one’s surroundings, much like PTSD does, but you don’t need to experience chronic loneliness to understand this type of hypervigilance. Here’s a common example: imagine walking home on a sidewalk on a dark evening all alone. These days, it might be too easy to slip on some headphones to quell one’s feelings of uncertainty, but if you’re alone and without distractions, you’re likely to pay much more attention to your surroundings than if you were walking with someone. That hypervigilance seems to be necessary when alone, but for some reason it goes out the window when in the presence of others. This phenomenon of hypervigilance extends throughout the animal kingdom. Even fish in the sea perform something similar. It is much riskier to swim alone than with a school of other fish. From their behavior, we might be able to infer that they experience some form of loneliness if they stray away from the school, which my make them feel insecure, and causes them to quickly rejoin the group. It's a stretch to say the fish "feel" loneliness, but their behavior implies some evolutionary link between staying with the group and staying alive. Maybe it's the same with people.

Now when it comes to PTSD, the traumatic experience and subsequent changes in behavior occur under their own mechanisms, but current science doesn’t take into account the effects of loneliness on the development, maintenance, or exacerbation of PTSD symptoms. When traumatic events occur in the combat zone, soldiers are still connected with other soldiers who experienced something similar, at least for some period of time after the event. Symptoms of PTSD certainly exist in the combat zone in the most severe cases, but many end up experiencing a “late-onset” type of PTSD where symptoms begin to show only after returning home. The process of coming home is challenging for many, and as soldiers leave the military and become veterans, the connections to those who understand their experiences are slowly lost. Talking about traumatic events with non-military friends and family isn’t an option for many and as a result, veterans can begin to isolate themselves from others. I think it’s within this isolation that many of the issues we see today, especially suicide, come about. However, at this time, there is no psychological paradigm that accounts for the lack of social connection in mental illness. We are social beings, but our scientific perspective doesn’t account for our social needs! I think this is a big issue. I think it could be profound and important. I think I found my research topic.

With a general idea of how I wanted to proceed with the research, I needed to formulate a good way to present these concepts at the CogLunch event. The task was to present my research idea within a 20 minute timeframe, so I couldn’t spend lot of time talking about background information, but I needed to support all of the ideas I had in my proposed experiment. It took about a couple of weeks, but I was able to put together a 30-slide presentation on the topic of PTSD and Loneliness from a cognitive neuroscience perspective. I felt pretty good going into the talk, but the real fun started when I finished. It was a mediated Zoom meeting, so I couldn’t see the audience, but people “raised their hand” and asked several questions. There was even a question from a doctor at the Boston VA who was attending the talk. This was great! Apparently, they publicized the event to people outside of the department. With public enthusiasm, I felt more than ready to tackle the most important and grueling aspect of the milestones: the written exam.

The Neuroscience Building at MIT
The Neuroscience Building at MIT

This turned out to be a monumental task, and I was ready. I had never written a full NIH grant before, and since grant applications are the way scientists fund their research, it seemed like a really good time to learn. The NIH website was helpful in a technical sense, but since there are so many different fields of research, they have to water down their site to apply to all fields. There’s no neuroscience-specific template. My advisor offered a copy of some successful grant applications that he submitted and this was exactly what I needed. The grant application is formatted like a story, sort of. There are three “specific aims” that explain what the goals of the research are, a background section that explains why this research needs to occur, a methods section that explains how the research will be carried out, followed by an analysis section that explains how the collected data will be statistically analyzed. My type of research could be classified as cognitive neuroscience whose main tool of investigation is functional MRI or fMRI. This introduces some special complications in study design that need to be accounted for. I could rely on my prior experience with clinical trials, which were primarily in the department of radiology, to help me design my study. After about another two weeks, I had a working draft of my written exam that looked much better than what I had in the spring. I took a few more weeks to polish it up and by the first week of November, I had submitted my final draft to my committee. Written exam completed.

With the CogLunch and the written exam completed, the oral exam was much easier than I expected. I had practiced several times, wrote a script to help keep me on track, thought of as many questions that could be asked, and I prepared for them. On the day of the oral exam, I wasn’t nervous (okay maybe a little) when I got started, but by the time I ended I was feeling pretty confident. The prior meeting with the committee didn’t go as well as I had hoped, but this time was better than I could have imagined. One professor commented that I had come a significantly long way since the pre-quals meeting, while another professor stated that “this is MIT quality work” and “I can’t wait to see what you find”. The committee was genuinely excited about my research proposal. This was great! At the end of the meeting the committee unanimously voted to advance me to Candidacy. I had passed! I am now a PhD Candidate!

It felt great to put these milestones behind me, but it was really just the beginning. The point of the rite of passage is simply to see if students are ready to actually do the work of a scientist. The real work comes in the implementation of the study and the subsequent analysis and publication of the results. This is where my prior experience with clinical trials really helps. Implementation. This is something I know how to do. The analysis side of things is something I need to work on a little more, so, after quals, it was recommended that I take a course in cognitive fMRI analyses. I had taken an fMRI course before, but it was more focused on the physics of how to obtain good data as opposed to the theoretical implications of designing an effective fMRI experiment. This will be something I will do in the Spring semester.

Another study that I had been working on prior to the pandemic just so happens to be a project that aligns directly with my dissertation. The Brain-Body Study uses a fear-conditioning paradigm to relate how the brain and body respond to stressful events. A fear-conditioning paradigm is an experiment where two stimuli, in my case a photo and an electric shock, are paired several times so that the photo alone is enough to make the participant react as if they were shocked. My research proposal also uses a fear-conditioning paradigm, which I will explain in great detail in Part 3 of the What PTSD Means to Me blog coming soon, but for now, just know that two studies are using similar designs, which also means using the same equipment. Before the pandemic, we were working out some of the bugs in the shock delivery system and data collection equipment. We were unable to complete the debugging before the campus shut down. Since advancing the Brain-Body Study will also advance my dissertation, I decided to see if I could use the time to work out the bugs myself.

Thanksgiving wasn’t much different from any other day, and it served as a good time marker to get started on this small hardware project. Since the building reopened, only those that take COVID tests are allowed to enter. It is a bit of a hassle to submit to these tests, so most people that can work from home are doing so. Since we are still not allowed to scan subjects at this point, it makes for quite the open schedule at the MRI scanner. All of the fear-conditioning hardware is located in the console room, the small room where the technologist operates the scanner. Unfortunately, there wasn’t much of a manual on the fear-conditioning equipment, so I downloaded as many of the manuals as I could find and started to dig in. For both the electrical stimulation and the data collection hardware, the problem turned out to be a software coding issue. I’m not an expert coder, but I’m learning more and more with each new system I encounter. E-prime and BioPac are definitely an interesting combination.

Once the coding issue with the electrical stimulation was solved, I wanted to see if I could add features to this setup, such as creating digital signals to indicate exactly when and which type of stimulus was being presented during the experiment. It was a little bit of an extra thing, but I wanted to see if I could do it. After about two weeks of learning the Visual Basic language and learning how to communicate with external devices using this code, I was able to work out exactly what I had envisioned: digital signals to mark events. I feel quite proud of this rather small feat. I just think it’s cool I can program hardware! Below is the first successful test of the digital signaling setup with each stimulus type as a separate channel. Following from left to right, you can see exactly when each type is presented by the jump in voltage. 0V = off, 5V = on.

Digital Signal Markers Representing Different Stimuli
Digital Signal Markers Representing Different Stimuli

It has been pretty strange walking around the neuroscience building without running into people. This massive building seems practically empty with most of the people tucked away in their individual labs, myself included. Classes are all online, so there are no undergrads walking around. It’s ghostly at times. This Fall semester has been anything but normal, but I was still able to accomplish the things I needed to. I feel like the “acceptance shift” had such a profound impact on the way I viewed tackling these tasks. Rather than focusing on what I did not have, choosing to hold more value in the things I had made me appreciate just how lucky I am. Regardless of the current circumstances, I am pursuing a PhD at a great institution on a topic that I am passionate about. It’s pretty hard to get all of those in one, and I’m making it. I don’t know how 2021 will pan out. I certainly didn’t think the world was going to be taken over by a virus at the end of last year. At least I know I have a plan moving forward. No matter how this coming year turns out, I think I’ll be alright. I think we’ll all be alright. Better times are ahead.

The photographs I had taken on the road have finally been uploaded to the site. They consist of both of my cross-country road trips last year, the New Year’s trip to California and my COVID-shutdown trip. I had been meaning to make a gallery since I returned from the January trip, but then 2020 happened. In the last few days, I was able to create a few galleries on the site, but I’m not certain it will work properly on every web browser, so please let me know in the comments if you have any problems with displaying the images or any other web bugs. Take a look and let me know what you think! If you like an image, I added a “love” button at the top for you to smash! Feel free to share the images on social media or download them directly. Unfortunately, I need to shrink the images to limit the size of the files on the site, so if you’re interested in a full-resolution photo without the watermark (roughly 4000x2000 pixels) just reach out and I can share with you directly. You can send a message with the chat bubble on the site.

I plan to make a few more changes to the site this coming year. One thing I will continue is my Understanding PTSD series of posts. In 2021, I want to bring the science to the people through this channel. I want to highlight papers that I think are important by presenting them to you and offering a little bit of down-to-earth talk about their implications. My hope is that I can start to make the site more of a resource for people to learn more about PTSD scientifically and perhaps what we might be able to do about it. I also want to get back into my TBT channel where I present some more of the crazy things I’ve lived through. All of this will require more time and dedication to the site, so I hope my schedule will remain stable enough to complete these goals. Here’s to hoping for a better year.

Happy New Year, Friends!


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Excellent read. Been thinking about you as always. I'll try giving you a call in next few days. Happy New Year!

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