The First-Person Project

John Gibbons ’05

Northampton, MA

Assistant Professor, Biology, Clark University, Worcester, MA

Major: Biology, Minor: Sociology

I grew up in southern Connecticut, in a suburb of New Haven called Bethany. In high school, I really loved filmmaking. When I was applying to colleges, I didn’t know what I wanted to major in, but I thought it might be nice to have exposure to a film department.

Keene State was one of the only public schools around that had a filmmaking department. That was a big draw for me. Also, I played soccer in high school and I wanted to keep playing – I played for a year at Keene. So just having that liberal arts feel, I could bounce around and take classes in different departments the first couple of years. I think I declared three majors, psychology, sociology, and biology. I really liked film, but I didn’t want it to be my major. I liked psychology, and I really liked sociology. So I ended up minoring in sociology. And then I took a couple of non-major bio courses that I loved. One was a human evolution course, and the other was a speciation course. Speciation is basically how populations will diverge into two completely separate species. That got me hooked. The human evolution course got me interested, and then the professor who taught the speciation course put a note on one of my exams that said, “Have you considered majoring in biology?” I liked biology, but had been intimidated by it. That note from the professor was the turning point, and I just went for it.

One thing that drew me to biology was just having all these little pieces of data and putting them together to tell this bigger story. That’s something I still try to do now. How can we interpret natural phenomena, and how can we interpret fossil records and the geological record and genetics, and how can we put all this stuff together to now tell a story? Good biologists are good storytellers, too. I tell my students, when they’re presenting their own research, to pick a really good story from the research to get people excited about it.

My Keene State soccer career was cut short when I injured my ankle. I think maybe it was a blessing in disguise, because I probably wouldn’t have majored in biology if I’d stayed with the team. It’s a big commitment. I declared my major at the end of my sophomore year, and took an extra semester to graduate in order to jam in all the courses I needed. Professor Kristin Porter Utley played a really big role in my future. I did research with her, and she encouraged me to apply for an undergraduate research grant from Keene State. We got 500 bucks and I was so excited. We were trying to identify the insect that was pollinating a certain wildflower that was native to New Hampshire. So I got to take historical records from the Keene State herbarium of where these plants occurred, and go up and down New Hampshire and Massachusetts in my car to try to find them. It was amazing, and, as most projects do, it shifted – from pollination to population genetics. The whole research process of starting with one question, and noticing something really interesting, and going in another direction – that’s a lot of what I do now, to be honest.

I graduated in December 2005, and then I took some time off from schooling. I really liked population genetics; I didn’t know what I wanted to go back to school for, though. I moved to Boston and worked for four months at a pharmaceutical company. And then I found the perfect job in Cambridge at the Broad Institute, which at the time was an MIT- and Harvard-affiliated institution; it is now independent. The Broad is the leader in genome sequencing.

I was part of a big group working on human genetic studies. What you do is take two groups of people, one with a certain disease, and other closely matched with their demographics but without the disease. Then you analyze about 1 million segments of DNA and you look for differences between the two groups. My role was to generate the data so that people could look at these million segments of DNA. We worked on type 2 diabetes, lupus, and some psychiatric disorders. It’s an academic institution, and they would bring in the best people to talk about really interesting stuff. So I started applying to graduate programs, including one at Vanderbilt University in Nashville. When I went to my interview, they said Wow, we just hired a faculty member from the Broad Institute. He’s starting in the fall.

So I went back to Broad and met him, and I ended up joining his lab in the Vanderbilt PhD program. My degree is in biological sciences. I specialized in genomics and evolutionary biology. My dissertation is called “The Function and Evolution of the Aspergillus Genome.”

After grad school I did a post doc for two years at the Harvard School of Public Health. That was a good experience, one you can’t really beat as a biologist. Then Clark University in Worcester, Massachusetts, advertised for this faculty position in the Biology Department. It’s the type of job I wanted because it’s a small liberal arts school, kind of like Keene State, and it also grants PhDs so you can build a strong research program. There really aren’t many schools like this. I was really fortunate to get an interview and then a job offer.

The balance of teaching and research is what brought me to Clark. I’m continuing with my PhD work in my lab here – I’ve taken two of my favorite projects and am expanding them. I’ve recruited students from my Human Genome class to join me in the lab. The class is basically looking at human genetic data and trying to understand how it’s allowed us to track historical routes that humans followed when they migrated. As a species we evolved in eastern Africa, and were there for 150,000 years, and then we left. You can actually use genetic data from current human populations to track how we migrated across the earth. We do that in the course: we study how populations have adapted to certain environments, so, for example, there are genetic changes in populations that live in really high altitudes that allow them to make use of limited oxygen.

Students in that course create popular science podcasts as their final project. It’s really fun. You can grasp the concepts better when you can explain them to a general audience. I’m interested in hosting a podcast myself. I was featured on the Gastropod podcast, which is a food podcast, because one of the fungi that we study, Aspergillus oryzae, has been domesticated. It’s known as koji, and it’s used to make sake, rice wine, soy sauce, miso – all these fermented foods – in Korea, Japan, and China. Fermented foods are really hot right now. So I got to talk about it on the podcast. The episode is called “Meet Koji, Your New Favorite Fungus.”

I had an undergrad who started with me his first year, then did a master’s with me, and now he’s at Vanderbilt in the same lab I was in, with my advisor, Antonis Rokas. He’s doing really well. And then there are some students who are interested in med school; they are interested in the human health aspect of our research program. And there are students who are interested in genetic counseling and grad school. So it’s a whole gamut. I teach a course called Introduction to Bioinformatics. It’s basically computational biology – How can we use computers to analyze DNA sequencing data? About 10 years ago a burst in different technologies allowed us to sequence DNA is in different ways. It produced tons of data. When the human genome was originally published, sequencing one human genome cost about $100 million. Now you can do it for about $1,000. And this has happened over 15 or 16 years.

We have to use supercomputers to analyze our data, because there’s so much of it. So this course is taking DNA sequence data that’s represented on a computer, and we analyze it in a bunch of different ways. The students have to learn command-line computing, a little bit of programming, but more importantly, How do you take these huge data sets and get something meaningful out of it – how can you answer a biological question with these big data sets? I really love teaching that course. With the work that we do now, we are trying to use genetics to tell a story. Different biological processes leave distinct signatures on the genome. We use computational tools to hunt for those signatures.

In our research, we study this food mold, and we also study a different species of mold, an opportunistic human pathogen called Aspergillus fumigatus that causes about 100,000 deaths a year. In the US it’s rare, but it can cause infection in people who are severely immunocompromised. If you’re going through chemotherapy or organ transplantation surgery, or have HIV/AIDS, it’s really hard to treat. We’re trying to understand the genetics of what makes it such a prominent human pathogen. It’s in the soil. I have a student who has been isolating it from Clark all around campus. It’s all around; it’s in the air. If you’re walking around outside you’re probably inhaling hundreds of spores every day. 

It’s a problem in sub-Saharan Africa, and in the US and Europe it’s becoming an issue because we use a lot of immune-suppressing drugs for different procedures now, and that’s increased the frequency of these kinds of infections. Right now we’re working with different model systems to understand how they are causing infections, and if different natural variants can infect at higher rates. We’re sequencing a lot of genomes and we’re collecting phenotypic data. Our goal is to conduct genome association studies and pinpoint different variants in genes that might be involved in making certain isolates really pathogenic, really virulent. If we know certain isolates cause infection, there are ways to knock out the genes.

My wife, Ali, and I live in Northampton because we just really like it. It’s affordable, it’s beautiful, it’s a good community. We have a two-year-old; his name is Jack. Jack’s been a lot of fun – a lot of work, but a lot of fun. My wife is a psychologist with a practice in Boston. We do a lot of gardening, so we have a big garden, and Jack’s been helping out with that. I play in a couple of indoor soccer leagues, too.

I’m not teaching introductory biology courses right now, but when I do, I hope that I’ll have a chance to return a student’s exam with a note suggesting that says “You should be a biology major,” because that was so encouraging for me. Regardless of what field of biology you going into, you are learning how life works at the fundamental level. There’s something so important and gratifying about that. So every little piece of information you’re adding helps you understand life a little better. For me that’s the big picture.

After college I took a year off and then enrolled in an MA/PhD combo program in history at the University of Maryland. I did my master’s work on early Atlantic history, taking that same interdisciplinary attitude that I’ve always had. I worked with my advisor and one of my classmates to develop a reading list for works that were Colonial in nature, but saw the touching of different empires throughout the Atlantic World. Not just the English coming to America, but the interplay of the English and the French and Native Americans going back to Europe and being treated as other and commodities and exotic.

I focused my work on culture and on religion. I’ve always been interested in witchcraft and the cultural questions around it. Where does the Enlightenment actually start in England, and how much does that influence what’s happening? So I started there with witches and then spun into vampires, werewolves, and mermaids – and my dissertation looks at how Enlightenment ideology both challenged and fueled discussions about each of those. For instance, there were reports that Columbus had encountered mermaids, and that John Smith had similar encounters. This all led to a cultural discussion that permeates pop culture and that, by the early 20th century, becomes American folklore. I’m trying to put this story together in a different way. It’s a work in progress.

While I was a full-time grad student, I needed a summer job. A professor who is an archivist helped me get part-time work in the National Archives in Washington, DC. I was still taking classes and working as an instructor at the university, but as my school commitments lessened, I began working more at the archives – and asking questions about the people I worked with: what did they do, did they like it, and was it a career? Eventually, I landed a full-time position in the National Archives facility in College Park, Maryland.

I like working with people and I also like working with records. I started as an archive technician and have worked my way up to an archivist job. It’s a career that I love. It’s rewarding and I’m supper happy to be here. We have a lot of people with library science degrees, but we also have a lot of people with history degrees – it helps to put things into context. People come in, they say, “I’m doing a research project on this topic; this is what I’ve already researched; how can you help me?” So I have to be able to understand what they’re talking about and put that into the broader context of how the federal government intersects with their project. That’s really what I do every day.

People come in with great projects. A lot of our researchers come from overseas, and they’re working on big projects on American foreign policy. It’s really exciting to see them work through their project until they find that we have exactly what they want. We also help them through the disappointment of learning that we only keep about one to three percent of federal government records that are designated as permanent. Sometimes what people are looking for just is not going to be here.

Finding what people are looking for is sometimes surprisingly easy. Some of it is just learning where things are and learning how to use our database effectively. Sometimes people do come in with really obscure requests, and sometimes I find the obscure things and it just blows my mind that we kept them and that someone created this document that I’m holding from 250 years ago. That’s really, really fun to do. A lot of people visit our downtown facility for military service and pension records from the Revolutionary War on. And a lot of it has been digitized – we have the muster roll from the Revolutionary War and all of the service records and pension records from the pension office from the Civil War – mothers and wives writing in that their sons and husbands have died in the war and they need payment.

Some of those files are really extensive – hundreds and hundreds of pages of correspondence plus original marriage certificates and birth certificates. One woman’s husband had sent home a dead critter that he caught in his tent, and she sent it back to the pension office as proof of her husband’s service. We still had it in the records!

Researchers have to go through security and an orientation, and then they drop their stuff in a locker before they are allowed to come upstairs to our research complex. We have hundreds of visitors every day, so we’re a well-oiled machine. They come and talk to me and my colleague in our consultation room, and then we have staff who go and get the records the visitors want. Most of our records are open and available, but we do keep some records and artifacts in a treasure vault – really old maps, really old documents, treaties, and important documents with presidential signatures. Not all the presidential signatures are in a special vault, though. I find FDR signatures all the time – all of the correspondence, everything that went across his desk, he’d initial or sign.

I think I’ve found my life’s work. What’s the career trajectory for someone at the National Archives? It varies, depending on what you do. It’s nice to know that I have opportunities and it’s also nice to know that I enjoy what I do every day. It is challenging. Sometimes people ask very hard questions, but trying to figure out how to help them is really great. Sometimes people will ask something really obscure, like “I’ve heard that on this particular date, someone from the Department of Treasury turned a document over to someone at the Department of State, and I want to know why that happened.” That’s where I would go to the finding aids that we’ve got to try and track down correspondence retired by the agencies.

Outside of work, I like to explore. My boyfriend and I are both history nerds, so we benefit from living in the DC area where there are always museums and historical sites to visit. We like setting out and finding new hiking trails, too. We both spend our work days inside, so it’s fun to get out and try something new.

One cool thing I did last year was serve as a judge in the national finals of National History Day, which the University of Maryland hosts. Middle and high school kids have a competition to put together a history project, and they compete at school, county, and state levels. I got to judge exhibits for middle school and high school, and they did such fantastic work. I was blown away. It was another one of those moments where I was really glad I do what I do. I’m going back for the 2017 round too!