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Interview with Dr. Jonathan Dushoff

Journalist: Yumnah Jafri

Yumnah Jafri: Welcome to SciSection. My name is Yumnah Jafri and I'm the journalist for the SciSection radio show, broadcasted on CFMU 93.3 FM radio station. We are here today with Dr. Dushoff from the Department of Biology here at McMaster. Thank you so much for taking the time to meet with me today.

Dr. Jonathan Dushoff: Thank you for inviting me.

Yumnah Jafri: Of course. We'll start off our interview today with giving you a moment to introduce yourself to our listeners.

Dr. Dushoff: My name is Jonathan Dushoff. I grew up in the United States and I've been a faculty member in McMaster since 2007, which is a long time. I've also lived in Taiwan, and I was a volunteer with the United States Peace Corps for two years in Swaziland now called Eswatini.

I identify as a theoretical biologist. I like to use a variety of quantitative-oriented tools, whether maths, stats or computation to address problems in biology. My main focus has been on the evolution and spread of infectious diseases.

Yumnah Jafri: I see. That's incredible. How about regarding your undergrad? Just giving a brief history of the work you've done in the past.

Dr. Dushoff: So as an undergrad, I'm a very math-y person and I naturally gravitated towards math. But I grew up with the beginning of the environmental movement and I wanted to find ways to be more helpful, positive...I wound up doing a double major in environmental sciences and math which was a new thing (and not really a thing). There wasn't much to the environmental sciences program at the time, but it sort of foreshadowed…I've spent most of my time since then trying to balance the fact that I sort of have a very math-y brain with the fact that I want to be practical or helpful.

Yumnah Jafri: I would definitely say that is quite a unique combination, one that we haven't heard of before on SciSection. Thank you so much for sharing that. Jumping right into your research then, what made you interested in conducting research on infectious diseases using, as you mentioned, a theoretical approach?

Dr. Dushoff: Well, it's exactly that. I've done math and I've done politics as well. But what I really wanted to do was combine the two and do something that could be quantitative because that's what I'm good at (also practical because that's what I wanted to do). My original idea was more related to my history, the original idea of environmentalism was very much tied with ecology. I did a Ph.D. in an ecology department. But gradually got drawn more towards things that I felt were more directly useful to people.

Interestingly, an infectious disease system is like a mini ecosystem, right? The environment is the people, and the organisms are the pathogens that are trying to make a living in this environment. We can use very similar techniques and concepts from ecosystem ecology that we use for infectious disease modeling at the population level as well. It was very much an attempt to bring together something I'm good at, with something I thought was useful for humanity.

Yumnah Jafri: I, personally, haven't heard of microorganisms, like pathogens being used in a sense of mini ecosystems in our body, but that's a really important aspect of what you're doing currently. How about in terms of modeling patterns of infections in relation to past or present pandemics? I'm sure the COVID pandemic had something to do with this.

Dr. Dushoff: Nothing specific.

It's just the idea of how the infection is spreading in a population, what makes one group more susceptible to infection or to disease or to transmitting disease than another group.

It's part of the whole…same approach of making a dynamical model of a disease. Of trying to link the processes by which the disease spreads within your body and between individuals to the outcomes we see at the level of whole populations or the whole globe.

Yumnah Jafri: Oh, I see! What are some key takeaways from what you have learned at your lab? Which I believe goes by the name of the TheoBio Lab.

Dr. Dushoff: The TheoBio Lab is a group that consists of three core faculty, which is me, Ben Bolker, who's a professor both in biology and mathematics, and David Earn, who came here to McMaster first. It's funny to say “here at McMaster” when I'm 10,000 miles away in Taiwan, but it seems the appropriate way to say it. David Earn is a math professor and he came first, and he recruited me. And then together we recruited Dr. Bolker as an idea of having a core of people who are interested in mathematical ecology and mathematical epidemiology.

It's hard to put one or two key takeaways on 15 years. It's been great working with those two. One of my takeaways is how hard it is for scientists to synthesize work. And part of it is statistics. I've learned about the importance of statistics. I've learned about the importance of communication. I've learned how hard it is for people to think clearly about uncertainty, including scientists, and so, we often talk about how we communicate uncertainty better to the public (which is a huge problem). Everybody in the audience will be aware of that, having lived through COVID. I often worry about how we communicate, as scientists, uncertainty to ourselves (how we understand our own projects), and to other scientists. We have to address all those problems at once. So that is one thing I've learned or observed during my time here.

Yumnah Jafri: I believe that's a really important point that you just made regarding science literacy as a whole and science knowledge/communication. I guess at SciSection, that's exactly what we're trying to do and educate the public about research. Maybe stepping back a little bit, what do you think you did differently compared to your peers when you were an undergraduate student, that helped you become who you are today, or have the same interests that you have today?

Dr. Dushoff: That's an interesting question. I am not somebody who's been good at planning or looking at the big picture. It's worked out for me, but it's not a course that I advise to people. I think the way I wound up where I am is by following my interests. I went from ecology and then I went to Eswatini where I taught for some years. I did politics for a few years in D.C. Following my interest was very important, but having a talent is the thing that saved me from not being good at planning. I'm unusually good at quantitation and logic and so forth. So, I was able to follow my interests but also wind up being able to be competitive for a faculty position without doing a really good job of career planning. Not sure that's a path I advise people, but that’s the truth of it.

That said, not being good at career planning is not good advice and having a talent is not really advice either.

But if you are hoping to wind up in research, I think following your interests or respecting what you're interested in, and what you like to a certain extent probably would be good advice.

Yumnah Jafri: So, a mixture of doing what you like and also doing something that you're good at. Somewhere between that, right? .

Dr. Dushoff: Somewhere between what you like and what you're good at, I think is right.

Yumnah Jafri: I think that's great advice. Maybe in terms of students listening to the show right now (you briefly went over this), who are interested in pursuing research, in terms of getting opportunities or knowing if research is the correct path for them…

Dr. Dushoff: I would say (this is also probably jumping ahead) but I would say thinking about your own research questions. Not just, ‘how do I impress the professors’, but what kind of questions do I want to answer?

If you can read some papers and think about...’Okay. Is there something there that I have a question about? Is there something there that I could imagine myself being interested in?’ Obviously, it's good to work hard and it's good to try to focus on conceptual learning. It's very easy in university to get caught up on both sides as profs, we need to give you grades and tastings, and as students, you're often trying to cram and get the grades that you're supposed to be getting. I guess some of that is necessary, and I guess some of that is good for your brain. But to the extent that you have the time and energy to step back and think conceptually, that's what's building for your future. Those are the tools that are going to help you be a better researcher.

Yumnah Jafri: The importance of just allowing yourself to think about what you find so cool in the world, and maybe things that you hope to gain more knowledge on and kind of going from there.

Dr. Dushoff: Yeah, biology is super cool. If you ever have the chance to just step back and just…any time I go to a biological conference, I just hear something that I find literally unbelievable.

Yumnah Jafri: I have to wholly agree with you as a biology student myself, so definitely on the same page as you. And maybe in an overall sense, you mentioned in terms of scientific conferences…What do you personally think our scientific community as a whole needs the most right now? This could be in terms of whatever you think.

Dr. Dushoff: I've talked already a little bit about statistical philosophy and the fact that even a lot of scientists aren't really clear on that score. And I think better statistical philosophy and more integration of a statistical approach into a lot of research projects would be helpful.

More broadly, I think we need better ways of collaborating and synthesizing information. We have so many peer-reviewed articles, and I'm guilty of this too…We build our careers and our reputations by publishing journal articles. But I think we need to figure out what are better ways to move forward more collaboratively and with more synthesis of information.

I don't want to oversell this, but I was thinking about this interview and thinking that some of the same problems that we see in political society, about people having their own interests and being competitive, and just how difficult it is to draw people together. It doesn't seem to be working in society and in science in some sense, it's harder because the concepts are more difficult and there's this technical layer on it as well.

I do wish for science to have better quantitative and statistical controls and better ways of having work build more directly on other work. Sort of less spinning in all directions and more progress. That said, you can't go too far in that direction either, right? Because then you wind up trapped in a single paradigm where everybody's agreeing on something which some proportion of the time is going to turn out to be wrong or just too limiting.

Yumnah Jafri: I see what you mean. I'm sure our listeners as well, in terms of not boxing yourself in as scientists, but our information is just so spread out. Maybe our research isn't as in depth in one circle or one field. I have no idea. Is that what you're going for?

Dr. Dushoff: There's a lot of controversy in a lot of fields about the whole state of the peer-reviewed literature. There are many articles and maybe disagreeing with each other. The control that the journals exert often for profit versus the whole world of preprints where you have even less validation of what's the highest quality science. I don't know. I guess I'm not really answering you as much as expressing my own uncertainty about how best science can go forward. We've seen that with the COVID, even scientists haven't really reached clear consensus on a lot of important issues.

We can look also at climate change where there is really a strong scientific consensus. But if you scratch the surface, there's also a lot of problems there. Right? There is a scientific consensus, but there are scientists who don't follow it and who are publishing peer-reviewed articles that go in other directions. There's also been a certain amount of defensiveness among establishment scientists, which I think is entirely understandable. There are really bad faith attacks on science, but some of the defensive responses haven't been productive either, and I don't know what the solution to all of that is. But I do think that we as scientists, need to find a way to do our science while at the same time thinking about ways that we can improve the way our field operates. That's a hard thing to do.

That's a hard thing to ask as a scientist, and most of us don't want to think about it. I'm sitting here talking to you and I'm kind of wishing I could just go back and do science instead of worrying about the structure of science.

Yumnah Jafri: You mentioned like not really being sure of a solution. Honestly, I don't know if there's a solution, but talking about it, I feel like is a step in the right direction.

Dr. Dushoff: And there are a lot of smart people working on different models for peer review and different models for how we should be communicating about and building on scientific results.

There's been a big movement towards openness in a lot of fields, and I think that has the possibility to be very helpful. When I publish a paper, I try to share as much as possible about how I did it. I don't generate my own field data. I don't generate my own data from the real world, and so it's easier for me to do that. I don't have as much investing. I haven't spent decades chasing flies around the landscape or interviewing patients. I don't generate data that has its own confidentiality concerns. So, it's easier for me than for others to share data, but to the extent possible, it's good to share data and we should absolutely be sharing code. When you publish a paper, you should publish the pipeline that you use to get from your data to the answers. There's been a big change during my lifetime as an active scientist towards openness in things like genetic and genomic data. So, we now have huge amounts of publicly available data in a lot of fields, and I feel like that could be a step towards this idea of a more collaborative way of doing science.

Yumnah Jafri: Thank you so much for the in-depth answers. For our final question, for fun, what do you think is the most interesting infectious disease? And this could be in terms of pattern, structure, methodology…whatever you think.

Dr. Dushoff: Interesting. I had an answer to this and during our talk I was thinking it's probably not enough fun because there are a lot of really cool processes going on in biology. The answer I had, and then maybe I'll try to say something a little weirder after, but the answer I had in terms of what I'm interested in now is how complicated immune responses are. We're seeing this with COVID. We're seeing this with the re-emergence of the flu. The thing that really interests me is, how we can span between what your immune memory cells (and so on) are doing, and all the crazy things that viruses and other pathogens do to try to hide from them. How do we understand the link between that, and the immune system is probably the most complicated thing we study other than the brain. How do we understand the link between that and the population level outcomes? What's going on with our T-cells and our antibodies, that's going to explain the future burden of flu or COVID at the level of a whole population? So, that's a thing that I'm finding very interesting right now. It's less weird and fun, maybe.

A story that I had heard from when I was an undergraduate that really fascinated me was about diseases or parasites that affect host behavior in ways that benefit themselves, so that there are diseases of caterpillars that change the caterpillar's brain. Instead of hiding in the grass, from birds…it will climb up to the top of a grass stalk and act weird so that a bird will eat it. That spreads the virus. Or the one I learned as an undergraduate was bot flies. If they infect male mice preferentially; lay their eggs near the testicles so that the larvae can push the testicles in, which reduces the testosterone of the mouse, which makes it less aggressive and less brave, and increases the probability that it's going to survive long enough for the bot flies to hatch. Stuff like that is really cool and there's a surprising amount of it. Rabies, which is a disease I study, is less fun because it's so nasty for people. But that's basically what rabies does too. It drives animals crazy so that they bite other animals to spread rabies.

Yumnah Jafri: That was definitely weird! Weirder for the second one, the bot flies. Just thinking about that from an evolutionary lens, it's crazy how things just happened and now “suddenly”, there's no aggression in the mice. They're very susceptible to the infection. It's wild.

Dr. Dushoff: There must have been some heritable variation in how female bot flies chose where to lay their eggs that worked out for them.

Yumnah Jafri: With rabies as well, I'm sure many people are already aware of how scary that disease is. It's great that you're studying that.

And that's it for this week of SciSection. Make sure you check out our podcasts available on global platforms for our latest interviews.


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