All posts by Andrew A. Hooper

April 2017, articles, arts & culture, Community, Humans of Tufts Boston

Humans of Sackler: Patrick Davis, “I’ve been Accused of being a Science Robot”

April 24, 2017 Andrew A. Hooper

Humans of Sackler, 23 March 2017

Patrick Davis, Neuroscience, Fifth-Year M.D./Ph.D. Student: “I’ve been Accused of being a Science Robot”

For this issue of Humans of Sackler, I had the opportunity to sit down with Patrick Davis, an M.D./Ph.D. student in the Neuroscience program. Although I see medical students coming and going around Sackler every day, I confess I haven’t gotten to know many of them – or much at all about the medical school curriculum. So it was a great pleasure to learn more about this from somebody who is as passionate about medicine as he is about science research; Patrick and I had a particularly engrossing conversation about the differences between these two kinds of higher education, and I hope you, dear reader, enjoy and benefit from it as much as I did!

Young Pat with the Chestnut Hill Academy Theoretical Physics Group

AH: How did you become interested in studying science?

PD: I had a physics teacher in 11^th and 12^th grade – Marty Baumberger – who was just the best teacher ever. He got me so into physics that I started a Theoretical Physics group at Chestnut Hill Academy… I went to Brown University as a physics major. I loved the open curriculum, but I was a terrible student. I didn’t do well my first year, so I switched to an economics major for about a year, and that was completely unfulfilling. Eventually I came to my senses and switched to biology… The thing about Brown: it’s chaos. There are no required classes, so you just mix and match and do whatever. There are requirements for your major, but you could theoretically never take a math class if you never wanted to. What happened to me was the best-case scenario: the first year and a half made me a more dedicated student. I learned that if I’m not doing something I really want to do then I’m going to be lazy, and if I don’t work hard then I’m not going to do well.

At a Macklis Lab get-together, chatting with friend and mentor Alex Poulopoulos (left)

AH: What was your first experience with neuroscience research?

PD: When I graduated from Brown, I didn’t know right away that I wanted to do med school or neuroscience. I ended up working at Jeff Macklis’s lab at Mass General Hospital for two years after college, and that was my first real exposure to neuroscience. Jeff made his name with a series of studies on induction of neurogenesis in the neocortex. I met Alex Poulopoulos there, who has been a mentor ever since, and a very good friend. I would credit Alex almost entirely with piquing my interest in neuroscience, but also with my development as a scientist. I love to come up with an idea, test it, go through the whole process myself, interpret my own data, talk to other people about their data – I like the actual scientific process. Alex just started his own lab at University of Maryland School of Medicine; anybody reading this, please apply to his lab! You could not ask for a better person to work for. He’s interested in how neural circuits self-organize, which is extremely interesting to me as well.

AH: Why did you choose the M.D./Ph.D. path and how have your medical and scientific training differed?

PD: I could never be just an M.D. because I love science too much. The fundamental quality of a scientist is curiosity; medicine is more like service and helping people, curiosity about the people themselves, empathy. The preclinical years are a lot of memorization, but once you get into the hospital, it’s more like an apprenticeship. You’re learning how to do the day-to-day things that a doctor does: how to walk through clinical decision-making, interview a patient, present that information to other doctors, how to work with your hands if you’re doing a surgery rotation… Because medicine is an applied science, the goal there is all oriented around the health of the patient; I don’t think that’s really what science is about. For a long time, medicine has been done in a very parochial way: people in this hospital do it this way, people in another hospital do it another way. Evidence-based medicine still gets a lot of pushback. Take stenting for example: doing a coronary artery stent for someone with angina. About half of the stents in this country are done for stable angina – chest pain when you exercise, but not an acute threat to your health – and it’s now been shown over and over again that that is no better, and possibly worse, than just giving them statins and blood pressure reduction medication and telling them to eat their vegetables and exercise a little bit. It’s because doctors think in terms of, ‘I see it happen, it intuitively makes a lot more sense to me, so it must be this.’ Of course the lines are blurred in real life, but a true scientist would say, ‘We have to trust the evidence, why don’t we look at what’s causing the increased risk of doing the stent, or why do statins work?’ The curiosity that is absolutely necessary to be a good scientist is not necessary to be a good doctor… The types of mind that are selected for by these two professions are almost non-overlapping, they’re completely different.

Even science robots enjoy a night on the town every now and then

AH: What do you like to do when you’re not studying medicine or neuroscience, and how do you find the time and energy to do it all?

PD: I love to teach, I really like being in the didactic role and seeing people learn and discover things for themselves. I tutor for the MCAT, I used to tutor for the SAT, I’ve volunteered for things like middle school science fair mentoring and the Brain Bee. These kids in the Brain Bee were extremely impressive; they knew more facts for this test than I would have! Thomas Papouin and I also started a class trying to teach grad students the basics of the scientific method. There’s a whole rich history of how to think formally and scientifically; and the more aware you are of it and the more you practice it – like by applying these things to your own rotation project or qualifying exam – the better you get at it. The notion that, by just reading papers, this will happen – for some people, maybe it will, but the purpose of the program is to maximize the probability of this happening for everybody… I’ve been accused of being a science robot: the joke between Alex Jones and me is that when I get home, I have a scotch and read PubMed… The M.D./Ph.D.s that I’ve spoken to, the ones that succeed, are recharging one half of their brain while the other one works. Like a shark, like a science shark!

Relaxing by a picturesque mountain lake in the Cordillera Blanca, Peru

AH: Have you had many chances to travel outside of the U.S.?

PD: I’ve traveled through Europe a bit, I’ve been to Peru, Brazil… I was in Berlin at one point, and I decided to just hop on a train and go to Prague. I spent two full days and a night there, and it was awesome. Most of the people spoke English at tourist-type places, but it was fun to walk around, take pictures, be completely by myself… I had a Cormac McCarthy book called “All the Pretty Horses”, and it was nice just being on the train, reading or watching the sites, then walking around the city and going to a café for a coffee or beer. I don’t know much else about Prague, but aesthetically, I can’t imagine a prettier city. Part of why I enjoyed the city so much was because I didn’t expect it to be that way: of course when you go to Rome, you know that one of the greatest civilizations existed here and that every step you take is rich with history, but I didn’t expect this in Prague.

Enthusiastically sharing data at the Society for Neuroscience annual meeting

AH: What topic have you studied for your thesis work?

PD: Under Leon Reijmers’ mentorship, I’m trying to figure out how ‘extinction learning’ happens in the brain: it’s a medically-relevant type of learning that underlies treatment for psychiatric disorders like PTSD. In extinction learning, the patient repeatedly gets exposed to the thing they’re afraid of, you gradually increase the ‘stimulus intensity’, and they learn that it’s safe. So for example, if they’re afraid of spiders, you would show them a picture of a spider at first, then maybe have them in a room where there’s a spider in a corner, then work your way up to having them handle a spider. What I’ve found is that there’s a particular cell type in the amygdala – the parvalbumin interneuron – which acts a critical hub for this kind of learning: if you silence these cells, then you shut down the process of extinction learning. Now I’m using that finding as a jumping-off point to really figure out what’s going on. I’m manipulating parvalbumin interneurons with different frequencies of stimulation and seeing how the amygdala – and the rest of the brain – responds to that. It looks like I can ‘toggle’ the fear state up or down just by controlling this specific type of neuron!

Contemplating the mysteries of the universe

AH: Where do you see the field of neuroscience heading in the near future?

PD: I think that we have tools in neuroscience that 15 years ago, you couldn’t have even fathomed. Not just optogenetics, but recording techniques, chemogenetics, optical electrophysiology, simultaneous local field potentials with single units, closed loop systems… The engineers like Ed Boyden have done us a great favor. But now it’s time for us to step up. I think that in the next 2, 5, 10, 15 years there are going to be many, many discoveries that are really going to blow things open. Once we fall out of love with the mere application of modern tools to hypotheses we already kind of assumed to be true, then we’re going to ask the question: how? You have to record neurons’ endogenous activity, then do experiments that are really informative about what’s going on. In neuroscience, because we have these techniques, we can start asking this kind of question.

articles, arts & culture, Community, February 2017, Humans of Tufts Boston

Humans of Sackler: Nafis Hasan, “I Refused Determinism”

February 9, 2017 Andrew A. Hooper 2 Comments

Humans of Sackler, 30 January 2017

Nafis Hasan, Cell, Molecular & Developmental Biology, Fourth-Year Student: “I Refused Determinism”

This month I present, for your reading pleasure, excerpts from my interview with Nafis Hasan from CMDB. Nafis and I had a remarkably wide-ranging conversation covering existential philosophy, cultural differences between Bangladesh and the US, the exquisite symmetry between ecology and cell biology, and current controversies in carcinogenesis research. I can only hope to capture in the space below a mere whisper of his deeply-considered intellectual convictions and passion for social justice. Fortunately, Nafis has also authored an editorial on Science Activism in this very issue, and I strongly urge you, dear reader, to check that out next!

AH: Where did you grow up?

NH: I grew up in the house that my father and his brothers built in Dhaka, Bangladesh, and moved to the U.S. when I was 18. Most of my dad’s siblings and their families lived with us in Dhaka. As kids, we didn’t really have the notion of “privacy” for the longest time: the elders would each get a room and the kids would sleep in the living room on a big mattress. My cousins and I would all get into trouble at the same time… it was fun!

AH: Have you had any opportunities to travel around the States?

NH: For F1 visa (student visa) holders, you have a 3-month window where you have to find a job or get into school. After graduating from Lafayette College [in Easton, Pennsylvania], I thought, “If I have to leave the country, I might as well see it.” So when one of my friends said, “Let’s do a road trip,” I said “Let’s do it!” We started from Pennsylvania, went down to Virginia, our first stop was Shenandoah – I had actually never been camping before that, it was all a very new experience. We had two American kids, a Colombian kid, and a kid from South Africa… It was very liberating, and I started to see the country as it really is. At the same time, on the road, I was interviewing for jobs. I remember doing a job interview [by video phone] at a McDonalds in Idaho. I borrowed a shirt from one of my friends who dresses nicer than I do, since the interviewer could only see the top half of me… Over the course of two months, I think I applied to 200 jobs. Finally, I ended up getting a research tech job at Thomas Jefferson University in Philly.

Basking in the beauty of nature at Yellowstone

AH: What was it like adjusting to American culture?

NH: When I came to America, I had no idea what to expect, I had only heard things from my cousins who came here for college and what was on TV. One thing that I had in my mind was that I was going to try and meet as many people of different nationalities as I can. But there was a big cultural divide, how they grew up versus how I grew up. I think the road trip really helped me to understand the diversity of American people and especially during these times when people are so polarized, I reach out to that experience. We grew up seeing this version of America as the land of opportunity, the land of freedom, but America is not the government, is not their foreign policy, is not the consumerism that has taken over the world… America is more about the people that you meet here, and that’s how I see the country. America encapsulates the dichotomy of homogeneity versus heterogeneity, and I think that’s so beautiful.

AH: When did you begin to discover your interest in biology research?

NH: In Bangladesh I went to a private school that taught everything in English. The division of sciences starts in 7^th grade, and biology was definitely the most interesting to me. At the same time, I was caught up in the process of deconstructing my religious identity, because I was reading biology which has hard facts about how your body works, which calls into question how life was created… I found that more fascinating than having a set answer imposed by some superior being.

AH: How did you choose your field of study for grad school, and why is it so interesting?

NH: I started reading a lot of scientific nonfiction, presenting cancer as a very complex biological phenomenon, which was fascinating to me. I also had a solid foundation in breast cancer by the time I applied for grad school and I wanted to pursue that… I had seen lots of tumors, but no mammary glands. The more I learn about the mammary gland, the more I am fascinated by it. It develops throughout life: initially it’s just a branched structure that looks like sticks; when you get pregnant, it almost flowers, with grape-like clusters that come up through alveologenesis and these alveoli then revert back to the branched structure after weaning. It’s comparable to how trees shed leaves in the Fall, except in reverse: this course of nature – the seasons that you see – the same dynamic is there in animal tissue. And all of this is happening through the lifetime, after the majority of the organs are already fully developed!

100 miles?! — First Century – Repping Sackler at 2015 Tufts Century Ride

AH: What is one of the big challenges or controversies in your field at the moment?

NH: Traditionally, cell culture is done in two dimensions, on plates that are usually plastic – and plastic is not a natural substrate for cells to grow on, so you can’t recapitulate the same 3D environment where the cells are growing inside an organism. You can either try to mimic the natural environment as much as possible, or try to make a scaffold that is biocompatible… Cells need to be able to manipulate their environment, just as the environment should be able to provide them with physical or chemical cues to make them grow or organize in certain ways. Our lab has a very organic approach to it: we do 3D cultures in type 1 collagen, the predominant structural protein found in the mammary gland stroma. We believe that “organicism is greater than reductionism.” This is where we’re at odds with a lot of others in the cancer field, where reductionism is still the predominant philosophy. And we’re not saying it’s bad! It’s just insufficient to explain carcinogenesis.

Community, December 2016, Events for Students, Humans of Tufts Boston

Humans of Sackler: Stacie Clark, “Full of Surprises”

December 9, 2016 Andrew A. Hooper

Humans of Sackler, 1 December 2016

Stacie Clark, Molecular Microbiology, Third-Year Student: “Full of Surprises”

For this issue of Humans of Sackler, I had the chance to chat with Stacie Clark from the Microbiology program. As someone who mostly socializes within Neuroscience, it’s a real privilege for me to meet students from other programs and learn about some of the incredible, borderline-science-fiction work that’s going on right under my nose here at Sackler! Equally striking, I’ve found, is the treasure trove of unique passions and fascinating life experiences that lie just below the surface of our fellow students when we really get to talking. I’m grateful to Stacie for sharing a few of hers, and hope that you, dear reader, enjoy our conversation!

001 — Hiking through Glacier National Park, Montana

AH: When did you realize that you wanted to pursue a career in science?

SC: My parents told me they always knew I’d end up in science. From the moment I could walk, I was outside digging for beetles and worms and building terrariums. I was in the honors science program in high school, and I did a year-long project on hand sanitizer and bacterial survival. I was working in a lab as a high school student, and realized I really liked doing that. I think I was born for science, and my parents were super-supportive. When I was growing up, we went hiking all the time, they took us to the EcoTarium in Worcester, and we were members at the Museum of Science and Aquarium. So I was always exposed to all sorts of science.

002 — Swimming at a waterfall in El Yunque rainforest, Puerto Rico

AH: What places have you traveled to outside of Massachusetts?

SC: I studied abroad in Puerto Rico. Worcester Polytechnic Institute does this differently: they call it the IQP, Interactive Qualifying Project. The point of this project is to teach you how to work effectively in groups and communicate with people outside the university. I worked in the rainforest in Puerto Rico, and we did a project evaluating stream crossings. We wanted to look at how their bridges were affecting stream flow and water quality, so we got to hike all through the [El Yunque] rainforest and evaluate all these different stream crossings. We got to see parts of the rainforest that no one gets to see!

003 — With Pablo the capuchin monkey in Costa Rica

AH: What did you do between graduating from WPI and starting your Ph.D. at Sackler?

SC: Before I started grad school, I had always wanted to work with exotic animals. So I literally just Googled ‘volunteer experience in Costa Rica’ and this small remote place in Costa Rica popped up. I booked a two-week trip, went by myself back-packing in Costa Rica, and volunteered at an animal rehabilitation center. It was quite an adjustment: I was on a mountainside in southern Costa Rica, and it got pitch-black at 6 o’clock at night. I would go into the rehabilitation center, clean the cages, prep all the food, and then feed and play with the animals. The monkeys were my favorite, and there was also an anteater. His name was Gomer; if you went into his cage and just yelled out ‘Hey Gomer!’ he’d come crawling out, and he loved being held. We’d do enrichment activities for some of them too – so with the anteater, I would walk with him out in the jungle and let him go searching for termites and ants on his own, and then I’d go bring him back to his cage. I think everyone should go on at least one trip by themselves, because you learn a lot about yourself and it’s just a good experience!

AH: What do you like to do when you’re not working in the lab?

SC: I volunteer at the animal shelter in Quincy; I’ve been doing that every Monday for four years. I take the dogs out for walks, play with them, cuddle with them if they want to… They only get to go outside twice a day, that’s the only time they get to really play with people. I understand that work-life balance is really important to your mental health, so volunteering on Mondays is the one thing that I won’t let grad school take away from me. It’s something that I do for me that I enjoy – and I’m also a big dog person.

005 — Group photo with the Leong Lab (middle row, second from right)

AH: There are so many disciplines within biology – what got you interested in studying bacteria specifically?

SC: I’ve always been fascinated that an organism so small can have such a large impact on humans – that still blows my mind! They’re incredible organisms that can mimic the proteins we have, which I find pretty amazing. We’re full of bacteria, they do a lot for us – and the microbiota is a huge field now. Everyone is fascinated in studying microbiota and the impact they have on our health in general.

AH: What particular species of bacteria do you study, and what makes it so interesting?

SC: Yersinia pseudotuberculosis is a model pathogen that we use to study community behavior of bacteria within its host. Yersinia can establish a distinct niche within the spleen of a mouse, and once it forms a microcolony, it can replicate to high numbers despite the presence of the immune system. You get a recruitment of innate immune cells to the site of infection, triggering a response in the bacteria to create specialized populations within that distinct cluster; I always thought that was cool, the response between the bacteria and the host cells.

arts & culture, Community, Events for Students, September 2016

Feature: Humans of Sackler

September 12, 2016 Andrew A. Hooper

Do you have fun and interesting hobbies? Have you traveled to fascinating places? Held unusual and challenging jobs? Do you use cutting-edge technology to conduct biomedical research of earth-shattering importance? Are you a human? If you answered “yes” to any of these, you could be the next Human of Sackler!

Humans of Sackler is a monthly blog featuring individual Sackler students’ firsthand accounts of their path to the Graduate Biomedical program. Inspired by Brandon Stanton’s “Humans of New York” blog, the aims of this project are to highlight the Sackler School’s rich diversity of backgrounds, interests, and personalities, and to engage with the public by revealing the human side of scientists.

If you are interested in contributing to or nominating someone for the Humans of Sackler blog, contact Andrew Hooper (andrew.hooper@tufts.edu, Subject: Humans of Sackler) to set up a brief interview at your convenience. We look forward to hearing your story!

Read the first issue here: Humans of Sackler, 25 July 2016

articles, arts & culture, Community, Events for Students, Summer 2016

Humans of Sackler: Jaclyn Dunphy, “Good Things Come to Those Who Waitress”

July 25, 2016 Andrew A. Hooper

I’m Andrew Hooper, a fourth-year student in Dr. Jamie Maguire’s lab in the Neuroscience program. For as long as I can remember, I’ve been fascinated by the stories of how scientists came to be scientists. Where are they from? When did they recognize their passion for science? How did they get their foot in the door? What is it about their topic of interest that so captivated them? And what breakthroughs just over the horizon would most excite them? There are as many compelling, eye-opening answers to these questions as there are scientists, and I decided to highlight the diversity of backgrounds and perspectives at the Sackler School by gathering and sharing some of these stories. Inspired by the format of Brandon Stanton’s wonderful “Humans of New York” blog, I called this project “Humans of Sackler”.

Recently I had the opportunity to sit down with Jaclyn Dunphy, a fourth-year Neuroscience student in Dr. Phil Haydon’s lab. We discussed the questions above and many more, and I’m very happy to share with you a small sample of our conversation in this, the first issue of “Humans of Sackler”. Enjoy, and please look me up if you’d like to share your story and be the next Human of Sackler!

Humans of Sackler, 15 June 2016

Jaclyn Dunphy, Neuroscience, Fourth-Year Student: “Good Things Come to Those Who Waitress”

Humans_Image1 — Graduating from the Masters program at Kent State NEOMED

AH: Did you come into college with a biology major, knowing that that’s what you wanted to study?

JD: I wanted to be a teacher when I started college because I had a really great biology teacher in high school. I went to Xavier, a private Catholic college, so I also thought I might want to be a religion teacher. For the first couple years I took biology, education classes, and theology classes. But I had a ‘coming to terms moment’ with what my major was going to be around sophomore year, and so I just went through the bulletin of all the courses that were offered and picked the ones I liked the best – and they tended to be related to biology, so I figured that’s what I should be doing. I didn’t know what I could do with the degree. I had never heard of graduate school until after I graduated!

AH: Were your parents interested in science, or did your interest develop totally independently from family?

JD: I think my interest in science definitely goes back to roots that I have with my dad. He has a workbench in the basement, and some of my earliest memories of us spending time together were us building rockets in the basement. He was very into space and stuff, so we would build rockets down there. Also, I was in this program for gifted students when I was in fourth and fifth grade, and we were assigned weird projects – like if you’ve heard of the ‘egg drop’ project, where you have to drop an egg off of a roof and get it not to crack? I would get assignments like this and take them home. I was really excited about them, but my dad was even more excited! So we would work on those things together, and I would go back to school with something that was, like, 80% his idea and 20% mine. So in those couple of years we had five or six things we worked on together in the workshop downstairs, and that was really fun… We built a bridge with Popsicle sticks, and I could stand on it. I could stand on it to this day! We made I-beams – not my idea. I’d never heard of that, but he was like ‘We need to build I-beams!’ We even sanded them – it was intense.

Humans_Image3 — After a day of kayaking on the Charles

AH: After you finished undergrad, what did you do for work and how did you transition eventually to grad school?

JD: I was working at an upscale restaurant called Bistro on Main, close to Kent State’s campus, where Kent State professors take their seminar speakers out for dinner. So I had seen a couple groups of them come through, but one night I was waitressing for a table of four people: three people from NEOMED/Kent State and their invited speaker, Wendy Macklin. When I came to the table they were talking about prion disease, and I said, ‘Oh, that’s odd dinner conversation’. And they asked ‘How do you know what that is?’ in a very accusatory but jovial tone, and I said ‘Well, I just graduated with a degree in biology’ and they were like ‘Then what are you doing here?’ and I said ‘Waiting on you, what does it look like?’ So after that, all four of them took turns harassing me, they asked ‘Do you need a job?’ and I said ‘No, I have a great job, I’m making a lot of money doing this, I’m just trying to figure out what I want to do.’ And they said ‘Well, if you figure it out, then here’s my card.’ They put the card in the bill and they said, ‘Give us a call if you want to work as a technician.’ And I didn’t even know what that meant. At that point, I thought I was going to be cleaning rat cages. So I interviewed with one of the professors at the dinner, Bill Lynch, a few weeks later. It was the worst interview I’ve ever had, it was terrible! He’s a virologist: he asked me whether viruses are living or not. I didn’t know it at the time, but that’s a controversy among virologists. So I just picked a side, and then he argued me all around in circles until I switched sides, and then he asked me why I switched sides..! I left feeling so defeated; it was the first experience I’d had of someone who really, really questioned my thought process. I felt terrible, I felt like I had done such a bad job. But he ended up offering me the job because he liked that I didn’t give up, he liked my enthusiasm.

Humans_Image4 — Demonstrating the Blind Spot at the Museum of Science, with Alex Jones (right)

AH: What was it about glial cells that made them so interesting to you?

JD: I fell for astrocytes – I liked that they were so abundant but they were so under-studied. There was so much to learn. What are they doing? There has to be more to the story. Later on, when I met Phil Haydon, he said that in the field of glia, there’s a lot of low-hanging fruit, and I felt like that was very much the case. Glia are… I hate the word ‘support’ cells, but they are support cells for neurons. Neurons are like actors in the big play that is the brain, so the glia are stagehands, directors, producers, writers – they’re the ones that actually control the show. But the ones that you see and you care about are the neurons.