iGEM 2019 Reflection

Over this past weekend, instead of getting out to enjoy the last bit of nice, late fall weather here in Boston, I spent the weekend inside a convention center, frantically running from scientific talks to poster sessions and back. It was the 2019 iGEM Jamboree.

For those of you unfamiliar, iGEM (International Genetically Engineered Machines) is a worldwide synthetic biology competition in which teams, usually housed at universities, work on a project in the field of synthetic biology and then present their work at this massive conference. Participating on Purdue’s iGEM team as an undergrad was my introduction to the field of synthetic biology and how I first fell in love with research. Now, as an iGEM alum, I have volunteered for the past few years to judge the competition.

Although a bit blurred from all of the lack of sleep from this past weekend, my thoughts are currently circling around the idea of prolonged engagement with a community, which is what I want to write about here.

Growing up, I feel like there are few opportunities we have in our education to engage with projects or communities for extended periods of time. My undergraduate research project, which I worked on for three semesters, was the longest intellectual engagement I had until I started on my PhD research. My place on my high school track team, which I competed on for four years, was probably my longest engagement with any single community. Other people may have different experiences, but, partly of course with the nature of being young and not having that many years to use to engage, I found very few opportunities to understand the benefits that long-term commitment to a group can yield. Part of this is also informed from reading some of David Brooks’ pieces that came out in conjunction with his new book. He talks about how our societal definitions of success often involve a wide range of fleeting experience (e.g. living in fifty different countries or moving through twenty different jobs) when, in actuality, it is the people that settle and engage with one community for long periods of time that get the most satisfaction from life and have the most impact.

I am thinking about this in respect to iGEM because I feel like my engagement with that community is a preview of what long-term engagement could be like. As a judge, you get to see a little bit more of all the work the full-time iGEM staff puts into this community and you see how their work pays off year over year and how their ambitions are constantly pushing the community in new and different ways. Every time I attend the jamboree, I am reminded of the power of a vision and a handful of smart, hardworking people.

I am also thinking about this on a smaller scale, in respect to my own iGEM community. While I spent a lot of time with my former teammates in undergrad and consider many of them friends, we are currently spread out all over the country pursuing graduate programs and industry positions. This year, seven of us judged the competition and we got have a reunion of our team in addition to judging at the jamboree. It was really special to bring a subset of that community back together and this happened because of the opportunity to engage with and support the very community that brought us together in the first place. I could begin to see how this competition could bring us back together every year, ensuring long-term engagement with our smaller community and with iGEM as a whole.

But of course not all can go according to plan. At the end of the conference, iGEM HQ announced they would be headed to Paris in 2021, throwing the viability of our plans of continuing to judge into question. This is a great move for the iGEM community, as it moves the competition to be more accessible to the European and Asian teams, but I can’t help but be a bit sad that this developing tradition had a serious monkey wrench thrown in the mix just as we were making it happen.

I think my takeaway from all of this on the personal side is to look for opportunities to engage with the communities that helped raise you and make you who you are. My other takeaway is, if you are someone in a leadership role in a community, find ways for those who came before you to reach back and engage.

After the weekend, I tweeted a picture of the seven Purdue iGEM alums who came together to judge this weekend. The Twitter account for my undergraduate department reached out and asked for more details so it could be added to our monthly alumni update newsletter. Another community that helped shape me providing an opportunity to engage; I sent an email with the picture and details of the weekend right away.

Of Planners and Pipets: Struggling with Time Management in Graduate School

It is nearly one year to the day since I officially committed to the Sgro Lab here at BU. One year since I in earnest started in on my project. One year of working and learning and doing experiments and reading. And in this past year, I feel like I have made maybe one month’s worth of progress.

I gave myself a lot of excuses over the past year for why I didn’t feel like I was making much progress: I was starting a new project in the lab, I was working on an organism no one else in the lab was working on, we were a young lab and had not built up a lot of institutional knowledge, I was starting to mentor undergrads, I started TAing. While maybe these quelled some week-by-week anxieties about progress, part of me always knew they were excusing I was using to justify my lack of progress to myself.

As the fall and winter rolled by, I saw my lab mates making slow but real progress on their work, getting enough data to start going to conferences, while I was still working on validating the initial direction of my project. I started to wonder what I was doing wrong compared to them, I started to wonder why I was doing so poorly at grad school.

After some tough but helpful conversations with my advisor (kudos to her for her patience and persistence with me), I started to come to the realization that my time management and how I spent my time was getting in the way of making real progress on my work. I was initially in denial during these conversations because I thought I had always been good at time management. In undergrad, I balanced a full course load, the time-demanding job of being an RA, multiple clubs and organizational involvements, and still had time for going to fun and interesting events around campus. I had used calendars effectively since high school and always got my work done on time; I was a time management master!

The realization those conversations with my advisor helped me get to was that, in fact, I was not an effective time manager. This was because in undergrad, my time managed me. With all of the involvements and responsibilities, I had few windows to do the work I needed to do, and so I efficiently used that time. In graduate school, with few assigned blocks of time and potentially whole days of unstructured hours, my time no longer managed me. I got lost in sea of unscheduled time because for the first time in my life, I actually had to manage my own time.

Over the past few weeks, I have been trying new strategies to figure out how to effectively time manage while in grad school. There are challenges of knowing when to hone in on one project thrust and when to back out and support a full portfolio of thrusts, of scheduling experiments around lectures and office hours and seminars, and how to leave time for paper reading and more unstructured brainstorming, and I am nowhere near feeling fully productive with my use of time. But I feel like I have turned a corner in this realization of my lack of time management ability and the need to develop tools and strategies to get me on track on making real progress in the lab.

The realization I was not effective at managing my time was step one and trying out time blocking is step two of a longer journey towards being able to make progress. While this realization was a humbling experience and knowing I have a long way to go on just managing my own time is more humbling, I have the reassurance that this, this managing of a whole project and my own time, is part of what I came to grad school to learn. This skill will make me more effective in my professional future but I think also in my personal life going forward, as the demands of friendships, relationships, and family will continue to build as life goes on.

And of course, there is no one way to effectively manage time. As I have come to see, there is a whole rabbit hole of productivity and time management literature out there. And as I have taken the first couple of tentative steps on this journey, this piece by Adam Grant came out in the Times the other week, striking down time management in favor of attention management. Grant argues that overscheduling ourselves for peak productivity kills the most productive instinct of all, to follow our intellectual whimsy and to pursue the things your brain wants to pursue.

So how does this fit into my path towards being a more effective researcher? Right now, I can’t tell you, I may need to schedule in some time to think about it this week, or maybe it’ll come to me in the shower or on a run.

Boeing and the Ethical Standards of Engineering

As news continues to pour in about the crashes of two Boeing 737 MAX 8 planes, my thinking as engineer turns to how a system of failures resulted in these planes being built and allowed to fly. As with everything, it is more convenient to simplify the situation down to one answer, but this situation has many culprits as many levels: lack of funding to the FAA for proper oversight of the aviation industry, the cut-throat profit-drive of the aircraft duopoly that drove Boeing to avoid full training of the pilots and to make features, including safety features, add-on expenses for the plane, the potential hazards of budget airlines opting for lower configurations of planes, and beyond. Instead, we need to see this as a system of failures at many different levels: technical, economic, and political. However, I want to focus on one level of this system: the lack of rigorous error testing of software.

Ian Bogost of the Atlantic wrote a fantastic piece about this a few years ago in the wake of data security breaches at some of the largest tech companies and about the softening of the term engineer when it comes to software. In his view, engineering as a discipline is inherently to serve the public and engineers must uphold rigorous standards because the entire public depends on their work in building roads and bridges and buildings along with our public utility systems. The field of engineering upholds a strong code of ethics to use the knowledge of engineering for the public good and that the approval of an engineer on a project means that they have ensured their design, be it for a suspension bridge or a water treatment plant, meets the high standards of the code. However, Bogost argues that, when it comes to software, engineers don’t hold up those same standards. Because software can be changed and updated whenever and instantly, the same mindset of ethical standards is harder to apply. If you make a mistake building a bridge, it is extremely difficult and costly to correct it, so you must rigorously ensure correct design on the first time. With software, you can fix a bug instantly and update all systems that use it, so the same pressure does not apply. And the issue with the MAX 8 planes was, after all, a software issue.

As I think about this discussion of the softening of the term engineering in software, I also wonder about the term engineer in the context of biological and biomedical engineering. Like other disciplines of engineering, bioengineers’ designs are technical and complex and the public depends on them for their lives. Think everything from a pacemaker to the newest cell therapies. In healthcare, we have depended on the rigorous clinical trial process overseen by the FDA (which in 2018 licensed more therapies than it had in its history) to ensure that our new therapies hold up to standards of safety and care. In medicine, doctors are guided by the Hippocratic oath and engineers are still guided by the engineering code of ethics. I wonder if the clinical trial process as it stands and these two guiding ethical codes will be sufficient to answer the questions our technology will soon pose: should we embrace germline engineering to eliminate genetic diseases from our population? As therapies get more specific and individualized and more expensive, what right do people have to access these therapies and at what cost?

In my first year of college, we studied the engineering code of ethics. Then, as I entered into my discipline-specific classes, it was never mentioned again. The biomedical engineering department at Purdue required a bioethics course, but not the agricultural and biological engineering department. Many of my friends who are civil engineers are going through the professional engineering licensure process, which includes two rigorous exams and, depending on the state, multiple years of professional experience supervised by a standing professional engineering. As for friends who are not in civil? None are going through the professional licensure process. This seems to me to be a large gap in the training of our next generation of engineers, the ones who will be practicing when we become capable of robustly editing the human genome, of creating increasingly complex AI that we will decreasingly understand the workings of, and face the challenges posed by climate change as our global temperatures tick up degree by degree. If the majority of these engineers will not go through the professional license process, perhaps it is time to rethink or update that process to match where and what people trained as engineers do. And for bioengineering, where we are on the verge of needing to answer a series of complex questions about our direction as a biological species, perhaps we need a code of ethics that combines elements of medicine with elements of engineering, and to make sure that people being trained in the field are also trained to uphold this code.

Guest Post: Homo sapiens goes to grad school

I am beyond excited to introduce Horizons’s first guest post! Ryan Egan and I met when we worked together as Resident Assistants for Shreve Hall during the 2014-2015 school year at Purdue. Immediately, I was struck with Ryan’s even-keeled nature and ability to take the necessary time to think before answering a question. As someone who heavily relies on external processing, I was always intrigued and captivated with the ideas that would come from Ryan’s brain after he had a few minutes to consider an issue. Additionally, Ryan was one of the few people who I was close with at Purdue that went on to pursue a PhD and acted as role model in my mind as I went through my own application process. Currently, he is finishing his PhD in Clinical Psychology at Notre Dame in South Bend, IN and has written a post considering human psychology related to grad school and academia in the context of human evolution. I’ll let him take over now, please enjoy!

 

Homo sapiens goes to grad school

As I entered hour four of reading the same 25-page article, I was beginning to doubt my ability to succeed in academia pretty severely. Irrelevant things seemed to hold my attention better than the seminal paper on life stress and depression recurrence: World Cup scores, the latest imbroglio in Washington, the out-of-place elderly man who always sits at the same desk in the library, and the Wikipedia article about the climate of Russia I had opened in a new browser tab. Was there something wrong with my concentration? Did I have the discipline to conduct a literature search, one of the most basic tasks an academic should be able to do? Was I even interested in clinical psychology? The answers to these questions, I would later decide, were no, probably, and a resounding yes.

I’m convinced that everyone in graduate school, and probably in many other intellectually rigorous settings, experiences similar bouts of self-doubt and concern regularly. And if you don’t, fair reader, I’d love to pick your brain for research purposes. Most of us have some vague ideas about what hardships our friends and colleagues are dealing with, what thoughts are going through their heads as they work desperately on a paper the night before the deadline, but we rarely discuss them with each other. We have too few friends in graduate school, and what if they can’t relate? We mostly assume something is wrong with us, that we really have it worse than all those other people, who seem to be functioning just fine.

This isn’t pure conjecture on my end, nor am I overgeneralizing from my own limited experience. In clinical psychology programs, students complete clinical practica in which they assess and treat clients in a psychotherapy setting for about 14 hours each week (all under the close supervision of a licensed psychologist). My second-year clinical practicum took place at the University Counseling Center at the University of Notre Dame, where I led individual therapy with a caseload of 5-6 undergraduate clients, most of whom had no diagnosable mental disorders but were nonetheless struggling with subclinical anxiety and depression. Sitting with the third client of the day and hearing something like, “everyone else is just doing better than I am,” for the third time really reinforced a peculiar belief in me: we humans are all basically the same. We tend to focus on the differences between people and usually exaggerate them, but the students I saw seemed to share the same basic concerns: I’m a failure, I’m unlovable, and I’m worthless. If not one of these, they may have expressed dismay over the hopelessness of trying to change others or the impossibility of finding lasting happiness in the world. Clearly I have a non-representative sample of mostly white, middle-to-upper-class, Catholic students seeking counseling. Nonetheless, I would be surprised if the general population didn’t share the same self-doubting and occasionally hopeless mindset. For all its administration does to instill campus community and protect its students’ well-being, Notre Dame can still be a pretty academically competitive place for undergraduates and graduate students alike. Yet I have a hard time blaming academia or a particular campus culture for the apparently universal struggles of students. What I have to remind myself is that we’re still just animals, and in our white-collar world, we’re trying to do some things that must seem incredibly silly to the geese, dogs, and squirrels around campus.

Just as any others species, humans have been shaped by evolution. This includes our brains and hence our mental processes and behaviors. The genus Homo emerged almost 3 million years ago, and Homo sapiens have been around for about the last 10% of that span, 300,000 years. In contrast, civilization dawned around 12,000 years ago, meaning for the vast majority of our evolution, we were hunter-gatherers without much in the way of culture or language. The consequence of this is that we’ve had a relatively miniscule amount of time to adapt to the civilized world. Consider how unnatural it is to sit in one place and focus on the same task for more than 20 minutes. When our hunter-gatherer ancestors foraged, they walked from place to place, constantly interacting with their surroundings, shifting their attention from tree to bush to stream, and receiving rewards, mostly food. The main reward in academia is publishing a paper, and we’re lucky if this comes every few months after dozens of hours of meticulous thought about fine abstract points. By the time we finish writing our introduction sections, our ancestors would have assumed sustenance was not forthcoming and moved on to greener pastures. Add to this that early humans probably didn’t participate in very much analytical thought. The human brain was designed by evolution to do many things efficiently (e.g., trigger flight in response to a saber-toothed tiger, remember the location of the good water source, and even estimate the chances that a potential mate will bear children or invest in parenting); reading, writing, and lecturing are not among these things. It is tremendously difficult, and may even literally burn calories, to focus sustained attention on unnatural tasks for 8 hours every day. Although we don’t fully understand the functions of sleep, evidence has shown that our ability to accomplish these sorts of difficult analytical tasks is diminished without it. Modern hunter-gatherers appear not to sleep for more than about 5 hours a night (who can relate?), but they may not need the 7-9 hours experts recommend for the rest of us.

As I look around at the paradise my species has created ⸺ an air-conditioned, artificially illuminated computer lab free from disease-carrying insects and stocked with a vast supply of fresh, clean water available upon the press of a button ⸺ I shrink at the notion of living as our ancestors did, constantly facing death by starvation, infection, predation, or homicide (which I was surprised to learn was much more common back then). The fact remains, however, that none of us is well-suited to the work of an academic; we force ourselves to overcome our nature and gradually train ourselves to sit at a desk for hours on end. The optimistic psychologist or neuroscientist’s view is that the brain is highly plastic, molding to the environments we place ourselves in. No, we shouldn’t automatically be able to write a manuscript or conduct a literature review, but we can often make slight beneficial changes in our work environments, reward ourselves for effort even when the end product is imperfect, and allow ourselves a break multiple times per day. As a graduate student, I often have to remind myself that I’m still learning, not only about psychology, but also about myself and my human roots. I try to maintain confidence that good habits and faith in myself will translate into success in science despite my very human limitations. Thus, in the immortal words of fun., “It gets better.”

monkeys

If you would like to contact Ryan directly, you can reach him at regan1@nd.edu.

Qualifying Exam

One of the things about graduate school that continues to amuse me is the blend of the modern and classic. The facilities and research ideas are all cutting edge and yet there is so much about a PhD program that echoes the long traditions and history of academia. Nothing in my graduate school experience so far harkens back to old academia than the three major milestones in the program: the qualifying exam, the prospectus defense, and the thesis defense. The qualifying exam is, as the name suggests, an exam in which the faculty of the department determine whether you are deemed qualified to continue the pursuit of the doctorate degree. Here at BU BME, this is done after the first year. The prospectus defense is where you show what you have done in the lab to date and propose your path forward for the next few years, which is typically done after the third year. And finally, your thesis defense is when you defend your total body of work to the faculty and they decide whether that body of work is sufficient to be worthy of a degree being awarded. I took my qualifying exam this past week and wanted to write a post about the experience along with some advice for anyone who will have to take a similar exam in the future.

The first thing to note is that the format and difficulty of the qualifying exam varies greatly from program to program. Here at BU BME, our exam was an oral, paper-based exam, in which we chose two research themes of the eight our department covers, were assigned three papers per theme, and then questioned on the papers by a panel of three faculty: one specializing in the first research theme, one in the second, and a third chair that oversaw the whole exam.

I don’t think I did anything particularly unique in my approach to studying for the exams and because each program’s exams are different, I feel like any advice I could give here would not be applicable. Instead, I’ll share some thoughts on my approach and attitude the day of the exam, both leading up to it and in the room.

My exam was at 9am on a Monday morning so from the moment I woke up I was only thinking about being in that room, trying desperately to show that I understood the assigned papers to a full extent. What struck me the morning of was the feeling of nervousness I had was not akin to the nervousness I experienced in undergrad before a final or big exam, it went back further to high school, and was much more like the feeling before a track meet or a band audition. I realized that this exam, getting up to a board and answering questions, was much more like a performance than a test, and so I shifted my attitude and approach. I got up early and went for a short run, not too long to be exhausting but long enough to get my heart rate up and have some post-workout endorphins flood the body. I went through the same morning routine before heading to campus with plenty of time to make a cup of tea and relax before heading to the exam itself. As I stood outside the room waiting for my committee to show up, I did a lot of deep breathing, which slowed my racing heart rate and at least made me physically calm if not mentally calm (because my brain was certainly still freaking out).

When I walked into the room, the words of my high school track coach came into my mind: “trust your training.” I knew in that moment that I was not going to have any brilliant revelations or new ideas during the exam, my job was to simply execute on the studying I had done for the weeks leading up to the exam. With that attitude, when there was a question asked I didn’t know the answer to, I gave it some thought, either admitting I didn’t know the answer but could think out loud of some of the steps, or I would simply recognize I was not going to come up with the answer on the spot and moved on. This way, I did not get stuck on something I was not going to get the answer to and build up excessive negative energy in the middle of the exam. With this approach, I was able to demonstrate what I knew, wasn’t thrown off by what I didn’t, and finished the exam feeling mostly positive. I will also add here that I was lucky to have been assigned a committee that was true to the format of the exam and did not venture too far off track from the content of the papers.

One last piece of advice in terms of mentality when approaching the exam is, the night before, similar to the morning of, doing anything to take your mind off of the exam. No cramming you do the night before will pay off so instead I watched the penultimate and season finale episodes of Westworld with my roommate, the perfect distraction to get my mind off of quals and to allow me to get plenty (read: enough) sleep the night before.

A few days later, I received an email from my department that I had passed the exam and had met the requirements for PhD candidate status. My last piece of advice is that now, in graduate school, there are few preset ways to celebrate the milestones and so you have to go out and make your own. In the months leading up to the exams, I led an effort among my friends in my program to rent a beach house down on Cape Cod for the weekend immediately following the exams. So, after weeks of constant stress levels leading up to the first major milestone in our grad school journey, we were able to escape the city and sit out in the sun for a few days. So while the first few days as a PhD Candidate were relaxing and carefree, the email from my committee did not hesitate to remind me that my Prospectus is now just two years away so now it’s back to the bench.

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-Mark, PhD Candidate (!)

Water Music

We walk, pace moderate but with intent, along the river with a vague notion of expectation. Yes we both indicated we were going on the Facebook event and there were multiple posts from the performance organizers on what exactly was happening but I did not read them in detail. Did I choose not to? Was I too busy? Was I just not interested enough? Regardless, there was a nice contrast in walking to something without a fully-fleshed out picture of what was happening; there is so little in our world left to mystery.

We hear the instruments before we see anything, a murmuring of low brass and percussion floating over the esplanade, over the lagoons, over the groups of runners and walkers, over the evening picnickers and the dog walkers, floating over us as well, carrying on from what was in front of us to what was behind us. The music wasn’t for us, it didn’t stop once it hit our ear drums, we were there for it. Perhaps we can try to have fewer things be there for us and have us be there for more things.

We arrive. Fifty musicians spread out along the Esplanade, spaced out to allow the audience to move among and about them. We are wary at first, so we walk along the sidewalk where the majority of the audience is standing static, listening to only the musicians that were close to the spot where they chose to stand. As we near the end of the length of the field, we walk around the edge to the back corner of the performance. We gather up the courage and begin to work our way back, not along the sidewalk with the rest of the audience, but among the musicians, experiencing the performance as it was designed to be experienced.

And it is stunning.

Walking behind some of the performers I see that each is running a synchronized clock while the sheet music is divided into repeating motifs marked to be played for a certain amount of time. For a given section of the piece, time is still as the performers repeat a simple motif, but for us, as we wander and weave our way through, it is the moving through space that provides the dimension of time: as we near a trombonist, their low notes crescendo as the soprano saxophonist we move away from diminuendos. Dynamics and layers of the piece become not decisions of the performers but our decisions, our movement as much a part of the composition as their playing.

As we walk with just a handful of other audience members who are experiencing the piece as it was meant to be experienced, I look to the shore of the river, to the sidewalk where the majority of the audience stands static, unmoving. I can only think of how limited, how narrow their experience is because they have chosen to stand. Not only can they only hear the eight or nine parts closest to them, but they are also missing out on the dynamics of moving closer to and further from different performers. I look at the mass of people and their limited perspectives, their bubble, and think about how I spend the majority of my time surrounded by people who are also pursuing graduate degrees in bioengineering.

As we are walking among the performers, among the ethereal and ritualistic composition, the sun sets over MIT and the music intensifies. Right next to us, a kettle drum starts beating out an aggressive rhythm. We jump. The vocal part ahead of us starts to decay into dissonance as the trumpets blare ominously. We are in the middle of so much change, so much is happening all around, it is overwhelming, disorienting, but we keep walking. As we move, the music decays back into ethereal tones and the piece ends harmoniously. When the percussion suddenly entered on the next piece, we were at the edge of the field and could only hear a few parts, we were not in the middle of it all, but we turn and walk towards it.

As the last piece nears its conclusion, the percussionists pick up rocks and start to click them together. The low brass holds out a few notes as the performers begin methodically walking towards the river, all staring at the horizon. The piece ends as the percussionists toss their rocks in the river, letting the Charles have the last say of the night.

I went to this performance last week, just a few days before my qualifying exam. Could I have spent the night continuing to frantically study and stress? Absolutely. But balance can be hard to come by in graduate school. And that’s okay. I am beginning to see the some of the beauty and joy in removing many distractions from your life and focusing solely on a captivating research problem, and there will be plenty of times like that in the coming years. But I also have a strong belief in balance of time and balance of ways of thinking and thinking artistically is something I certainly don’t do enough of, so I like to jump on the opportunities when I can. There’s a world inside the lab but there is also a world outside the lab; one thing I am continuing to figure out is strategically choosing when and for how long to live in each.

Pros and Cons of Life in the Hub

One day last week I started the day by quickly running into my lab at BU before I hopped over to Harvard for day one of the Boston Bacterial Meeting and ended the day by taking the red line down to Kendall Square to attend the Swissnex biotech pitch contest. I joked with my friends that this was “just another average day in the life of a Boston life science grad student” (when of course in reality my life is a constant trek down Comm Ave between my apartment and lab), but under that joke was real recognition and appreciation of living in a city where it is possible to work, go to a conference, and attend a startup event all centered around my industry and all within just a few miles of each other.

One of the main reasons I committed to BU for grad school was the fact it would place me in the middle of the biotech hub that is Boston. This is something I also would tell the program recruits when they were here earlier in the spring as one of the selling points of BU. Interestingly, one of them asked me “well, how often do you actually take advantage of the high density of other grad students, academics, and industry connections in the city?” This question made me pause because I certainly do not take advantage on a daily basis but every now and again there is a day like the one where I went to three events near three universities all about biotech and all in one day.

And then there is the matter of the conference I was at: the Boston Bacterial Meeting. What other city could host a conference that is focused on a subfield, albeit a large subfield, of a scientific discipline and have over 600 people register and attend? Over the two days, I saw presentations and posters from Harvard, MIT, Northeastern, Tufts, and BC, along with some (arguably) less Boston schools like UMass Medical, Dartmouth Medical, and one poster from UW Madison (?). I hold that Boston is truly special in its density and quality of life science and medical research and I don’t see this reputation going away anytime soon (despite threats from New York or Silicon Valley).

So yeah, here I am, just another bioengineering grad student infatuated with Boston and not being able to shut up about it because of how great the research is, how many biotech companies there are, the strength of the professional network, and the availability of venture funding.

To avoid the total cliché, I do sometimes think about the potential downsides of being in the biotech hub. From limited observation of my first year in grad school, I have seen a certain bias within the Boston academic community. BU interviewed a number of new faculty members this spring and the majority of them were currently post-docs in Boston-area labs. If this is a general pattern, it would mean that the Boston academic community is slightly “inbred” and we are not getting the full range of intellectual diversity aspiring faculty from around the country and around the world have to offer. Of course, this was one year of recruitment in one department at one university, but it was something I noticed nonetheless.

I also wonder about the effects of supply and demand of so many qualified researchers and entrepreneurs in biotech. Interestingly, Boston physicians have some of the lowest salaries in the country. On the other hand, Boston biotech job demand is scheduled to outpace supply within the coming years. This means that Boston needs to continue to draw in talent from outside the city and the population will continue to grow and shift towards the biotech industry. This potential shift makes me think about the shift in Silicon Valley during the dotcom boom and continued growth of the tech industry in the region and of course, how the infrastructure of the region did not grow to meet the demand, leaving swaths of suburbia as some of the most expensive real estate in the country and San Francisco with one of the highest costs of living in the country. Of course, Boston already has one of the highest costs of living in the country and I’m sure that the continued influx of highly-trained technical specialists will only continue to drive that up. Silicon Valley continues to struggle with how to maintain reasonable costs of living for its residents outside of the high-paying tech industry and I think Boston will continue down a similar trend in future years.

All things considered, I am sure that the biotech boom in Boston has done more to benefit the city, its economy, and its culture than harm, but I do wonder what lessons we can learn from other stories of rapid expansion in history to better manage the city and all of its inhabitants as we go forward. I wouldn’t trade living in the hub for anything but I am curious to see ideas and plans for how to effectively manage the growth of the city going forward.

Committing to a Lab

The Biomedical Engineering PhD program at BU uses a rotation program for students to find a lab to do their thesis research in. This means that we spend our first year spending six to eight weeks in a number of different labs to find the best fit. Now, at the end of my first year of grad school, I am going to use this post to reflect on my experience in our rotation program and some thoughts and pieces of advice for future grad students in rotation programs. And, of course, I will end with officially announcing where I have committed to complete my PhD.

 

Step 1: Picking Rotations

Rotation programs are great because it breaks down the grad school decision of picking a school and picking a mentor into two decisions separated by about a year and gives you options. The bad news is that it gives you options. Picking your rotation PIs is as critical as picking your list of grad schools to apply to because, ultimately, this is the person who you will end up working under for five or six years and whose name you will be tied to professionally in the scientific community in perpetuity. No pressure.

Most of my fellow students in my cohort came in knowing at least one PI they wanted to rotate with because they connected well during our visit weekend. If you are an incoming grad student, there is probably at least one PI you picked the program you did for and so you will probably end up rotating with them first. From there, programs usually have some sort of seminar class in which PIs who are recruiting grad students share their research to generate interest in their groups. Most of the people in my cohort found their other rotation PIs either through our seminar class, by taking their classes, or through word of mouth and found them organically throughout the year.

I, on the other hand, was a bit more directed. I acknowledge the oddity of this approach and chalk it up to my type A, future-focused personality and do not condone it as the best way to go about setting up rotations, but, leaving my interview weekend last spring, I had three great meetings with PIs and knew they were the ones I wanted to rotate with. I contacted them over the summer and came into my first year with my rotations set up.

 

Step 2: Doing Rotations

When I started my first rotation, I was instructed to look for three things in a lab: fit with the research, fit with the PI, and fit with the lab (i.e. the other people in the lab). This is the framework that I carried with me through each of my rotations.

If your graduate program is structured like most and you are taking classes while also doing your rotations, one thing I would stress is that the goal of your first year is to find a lab home. This applies in that classes, while important, are not the main focus of grad school. Spending as much time in and around your rotation lab will benefit you more in the long run than perfecting that problem set or rereading that paper for the third time. On the other hand, the goal of a rotation is not to do groundbreaking research. When you are spending time with your rotation lab, along with trying out the kind of work you would be doing if you joined that lab, you should also be trying to engage with and integrate into the lab culture as much as possible to really get a sense of what it would be like to join that lab.

Other pieces of advice that I have heard but did not necessarily take advantage of is to go to lab meetings of labs that you will rotate with in the future or have already completed a rotation with. This way, you can keep up to date and in the know on what is going in the lab or feel out part of a lab dynamic before you start working. This will smooth the process of starting a rotation and ultimately joining a lab, especially if it was one you rotated with early in your first year.

I will leave this section with those pieces of advice. I had a wonderful time in all of my rotations here at BU so I’ll just move on to the decision section.

 

Part 3: Committing to a Lab

In my short experience on this planet, I have found that large life decisions which, to me, seem that they should stem from rigorous and objective criteria, often stem from a gut feeling or subjective nature. This applied to when it came time for me to commit to a lab. There were a few objective criteria like that the lab was actively growing and recruiting, which means there was available funding, that the PI had a fairly hands-on style and was willing to mentor directly at the bench if necessary, and the size of the lab was in the medium range so I would have a community around me while also not being lost in the shuffle. But, at the end of the day, I think I just had a gut feeling that I would work well with the PI of my third rotation. Luckily, when I asked to join, she immediately said yes, and thus I am now I Ph.D. student in the Sgro Lab at BU.

 

Overall Reflection

I think one benefit of a rotation program is that you get the opportunity to build relationships with the grad students and faculty member not only of the lab that you ultimately commit to but of other labs in the department or on the campus. At a practical level, this could spur some potential future collaborations but also simply lets you build up your professional support network at a new school faster. Life transitions are made more difficult because your support network is pulled out beneath you and having the opportunity to work with and interact with multiple labs on a new campus definitely eased the transition process for me.

Sometimes in a rotation program you may feel a bit listless because you do not have a home or a boss keeping you accountable on a day to day basis, but I think the benefits of connecting with more people throughout the department make up for that. Now that I am committed to a lab, it’s time to strap down and get some work done. Speaking of which, gotta pop over to the bench (i.e. my own bench in my lab!).

Building with Biology: Editing our Evolution Reflection

Last night, I attended a public engagement forum at the Boston Museum of Science that was part of their Building with Biology series entitled “Editing our Evolution.” The event was designed as a pilot and part of the audience was composed of people who work at science museums around the country who came to participate and then take the workshop and do it in their own communities. The workshop was focused on addressing societal and ethical questions around gene editing and germline engineering. The opportunity to play the role of the “synthetic biologist” was presented through the Biological Design Center at Boston University. I’ll first talk about the format and logistics of the forum and then write a reflective piece on what I thought of the experience.

 

What Happened

The forum opened with a small panel discussion moderated by one of the Museum of Science employees and featured George Church, the renowned geneticist and bioengineer, and Sheila Jasanoff, the director of the Science and Technology Studies program at the Kennedy School at Harvard University. While George offered expertise in the technical and scientific details of gene editing, Sheila offered a perspective on the intersection of science and culture. Their discussion was fascinating and echoed many of the ideas and questions I personally have about the implications of gene editing and germline engineering, albeit in much more articulate and knowledgeable words. Their discussion lasted about forty minutes before we moved on to the table discussion portion of the program.

Our table discussions started off with a round of introductions. At my table, we had two people coming from other science museums, a retired M.D. and his daughter, a local couple, one who was a research methods professional and the other a laser engineer, an electrical engineering graduate student, and a computer scientist who was in town for work for the week. We then dove in to discussing three scenarios related to gene editing: one was if we would choose to use a gene edited cure for DMD (Duchene muscular dystrophy) on a hypothetical child, another was the use of an individualized gene therapy for sickle cell and the questions around accessibility, and the last was about using germline engineering modify BRCA mutations (a mutation in the body that raises the risk of breast cancer). For each scenario, we first considered questions if money was not a factor like would we choose to do the therapy, how would we explain our decision to our children, and what would the implications be of not doing the therapy. We then moved on to consider cost and who and how such therapies could and should be paid for. Finally, at the end, each table shared one interesting point or thought that was brought up to round out the discussion.

 

My Thoughts

I want to open by saying I thoroughly enjoyed the experience of participating in the workshop and I think the Museum of Science did a fantastic job in organizing and structuring the event. As someone who has a natural tendency to talk more than they listen (maybe you could tell because I write a blog), I challenged myself to focus on listening first and then speaking later. My first observation that surprised me was the immediate reaction to the panel with Dr. Church and Dr. Jasanoff, where one of the volunteers from another science museum made a comment that they spoke very politically and did not address the question of the ethics of genome engineering. This comment caught me off guard because I felt both of them spoke thoughtfully and with heavy nuance about the subject, inherently acknowledging there are no easy answers to give for any of these questions and so they didn’t. I found it interesting that this came off as being “political” and “not answering the question” to someone from the public, even someone who works at a science museum. This makes me wonder about when people complain that politicians are always avoiding the answers to questions and being political in their answers. As a layperson when it comes to politics, I had always assumed that was true and that it was their job not to give a straight-forward answer as to not offend any of their constituents or donors. Now, I wonder if they really are giving the best answers they could in situations with no easy answers, as Dr. Church and Dr. Jasanoff were, but unless you are as knowledgeable about the subject as they are it comes across as avoiding the question.

My next observation from the discussion was that most of the table was very up for what I would consider controversial treatments. Even when it came to genome engineering to remove the BRCA gene, the table was mostly in favor. It was at this point I had to realize this audience was a self-selection of people who were interested in science and lived in and around Boston, which is a strong bias when compared to the average American. Still, I was surprised how open people were to these technologies. If you had asked me similar questions early in my undergraduate career I would have also probably been all in but my years of training in the field since then have made more skeptical of the field and I find myself wanting for more evidence of safety and assuredness of control before rolling out such technologies. This makes me optimistic that, as my time in the field increases, my skepticism and caution also increases. If this is true not only for me but for synthetic biologists and bioengineers around the country and around the world, then this increases my confidence in their ability to consider stakeholders and implications of their work and not fall into the stereotype of the results above everything mentality we see in popular culture.

The last note I will add is that the time for this discussion absolutely flew by. We always had more to discuss about each case study than we had time for and the ideas people were bringing to the table were interesting and forced me to really think about the best way to respond, given I was the “expert in the room.” I hope to participate in any future iterations of the Building with Biology series at the Museum of Science and to consider how I can continue these conversations both with the people in my program and with the general public. This kind of engagement is essential and I hope that I can continue to develop as an expert and an advocate in the coming years.

Sexism is Alive and Well at BU BME

The BU Biomedical Engineering department hosts four to six department seminars each semester. PhD students are required to attend at least four and many faculty also attend, making them one of the few times during the semester in which a large number of students and faculty in the department are gathered in one place. It is these seminars in which we present the face of the BU Biomedical Engineering department to the larger academic world.

With this context, it frustrates and angers me to be writing about an incident that occurred at our last department seminar. The speaker was Dr. Danielle Bassett from the University of Pennsylvania’s Bioengineering department. Our department scheduled this talk two years in advance because she is in such high demand. Her work lies in the developing field of network neuroscience, a fascinating blend of neuroscience, graph theory, and network dynamics. She has been awarded a MacArthur Genius Grant, an NSF CAREER Award, and named one of Popular Science’s top 10 brilliant scientists in 2016. The talk was fascinating and Dr. Bassett did an excellent job of walking a bunch of engineers through this interdisciplinary and cutting edge approach to studying the brain. It was when we hit the question and answer session that things went downhill fast.

A few questions in, Dr. Bassett called on a faculty member from the BU BME department, my department. His “question” was a thinly veiled accusation that the field Dr. Bassett described as network neuroscience is not as novel as she had made it seem and that the techniques she described had been used for decades. To be more specific, he referred to her calling the field new and developing as “amusing.” It is also worth noting this faculty member is more on the senior side of the faculty. While I was sitting stunned in my seat that a faculty member made such a disrespectful comment, one that he probably would not have said to a younger male professor in the field, Dr. Bassett took the insult in stride and went on to explain the fields that network neuroscience is newly synthesizing and why this approach is different from the approach of system neuroscientists from the past few decades.

I don’t have to get in to the statistics on female underrepresentation in science. I don’t need to remind you that women drop out of the sciences because they see fewer and fewer women the higher up the academic hierarchy they look and because this lack creates a toxic environment for the few women that are in those upper levels. The “question” was embarrassing for everyone in the room and stained the reputation of our department as a whole. The fact that Dr. Bassett took the question in practiced stride reveals how much she has had to deal with people constantly questioning her ability and intelligence. And this is coming from someone who is literally a MacArthur GENIUS.

As a male in a male-dominated field, I can never know the full extent of discrimination my female colleagues experience, I can only do my best to listen to their experiences, be aware of my own behavior, and work with others to improve our environments to free them of such discrimination. It is worth noting that, so far, I have found the BU BME department to be a welcoming and inclusive environment, which is why this situation stands out so starkly. That being said, last week’s seminar was a disappointing reminder that such sexism is alive and well in the field, including right here at BU. Today, I recommit myself to work to ensure that one day, one of these reminders will be the last.