Greg Bowman, PhD, Computational Biophysicist at Washington University School of Medicine and an associate professor at Washington University, talks about the Folding at Home Project.
What is Folding at Home?
BOWMAN: Folding at Home is a massive, distributed computing project that tackles some of biology’s hardest problems by harnessing the computational power of hundreds of thousands of citizen scientists around the world to volunteer their computers to run simulations of proteins and other key components of biology.
Why do you need them to do this? Why can’t you just do it?
BOWMAN: Oh, my goodness. These calculations are insanely intensive. Our easy problems could take 100 years on a powerful desktop computer and our hard problems easily get into, you know, millions of years or the age of the universe. And so, what we’ve done is devised ways to break these essentially intractable problems up into completely independent pieces that we can send out to many thousands of people to run in parallel.
If a person says, I want to do this at home and they download the Folding at Home, is there any requirements? How long does it take for them to run each step that you’re asking them to do?
BOWMAN: One of the great things about Folding at Home is that anybody with a computer and an internet connection can participate and add value. So, the more powerful your computer, the better. But anyone can help.
So how long does it take? Like, you said it would normally take 1,000 years…
BOWMAN: Oh, yeah.
By getting these little pieces parts, what are you breaking it down to?
BOWMAN: One of the great things about Folding at Home is that anybody can participate. So, the more powerful your computer and the more computers you contribute, the better. But anyone can help accelerate the simulations that we’re performing. And so, we can take these things that would take, you know, hundreds or millions of years and actually complete them in a matter of months. And so, this is a huge boom to science and is providing tremendous insight into things like the SARSCOV-2 virus that’s responsible for COVID-19 disease, we’ve got projects on multiple forms of cancer and Alzheimer’s disease and other pathogens. And so, this is a really general platform that your computer can help out with.
And you’re focused primarily on proteins, right?
BOWMAN: That’s right. My lab is focused on proteins, which is very broad because these are the molecular machines that perform most of the active processes associated with life from, you know, muscle contraction to sensing light in the eye and sound in the ear and digesting food and building more pieces of cells. They are busy little machines.
And did your interest in proteins kind of start on a personal level?
BOWMAN: My interest in proteins really stems from childhood experience of losing most of my vision to a juvenile form of macular degeneration. When I was in middle school, so a couple of years after losing most of my vision, I started hearing in the news about the Human Genome Project and the cloning of Dolly the sheep. And so, this got me really excited about becoming part of the biomedical research force and contributing to our understanding of biology and ability to treat diseases like my own and many, many others.
Now, with your macular degeneration, what can you see right now?
BOWMAN: So, with my vision, I essentially see it very low resolution. The center of my retina – the back of the eye that detects light is gone, and that’s where you have the highest density of light-detecting cells. And so, I see with my peripheral vision, which just has a far lower density of these cells. So, everything is basically grainy and it’s hard for me to read signs or recognize faces and I can’t drive, for example, but I can walk around and not bump into things.
Now, have you worked with this Folding at Home with your specific problem?
BOWMAN: I haven’t done too much specifically with Folding at Home and my vision. It’s only within the last two years that I actually found out through sequencing exactly what mutations are responsible for my vision, and so I think we’re just getting to the point where we know enough about what’s wrong in my particular case and the methods and computational power that we have with Folding at Home. But I’m actually really excited to explore that now. It’s gotten put a bit on hold with the pandemic, unfortunately, and the attention that we’ve been devoting to that, but I’m super excited about that direction.
Now, with the pandemic, how are you working with the citizen scientists?
BOWMAN: The pandemic has been, you know, a really fascinating scientific journey because we know so little about this virus and obviously there’s a very pressing need to fill that gap in our knowledge to expand our ability to fight back against this pandemic. And so, what we’ve been doing is working with our community of citizen scientists to simulate every possible protein from the virus to understand how it contributes to the virus’s ability to evade our immune systems and affect new hosts and build new copies of itself and how we could potentially break these proteins with small molecules or mimic them with vaccines. And so, this has been amazing because pre-pandemic we had about 30,000 volunteers helping with our calculations, which was already an amazing resource, and at peak we had over a million devices helping run our simulations of components of the SARSCOV2 virus. So enormous potential to do a lot in parallel.
It sounds like, to do anything with any disease or virus, you’ve got to know, you’ve got to be able to break these proteins down to, like, really have a tremendous impact and stop it.
BOWMAN: Yeah. With any infectious disease, you want to find parts of the pathogen that are unique to the pathogen that you can target and break to kill them off without negatively impacting, you know, the human being that you’re trying to save. And then there’s many related problems with human diseases like inherited diseases like mine where you actually want to do the opposite. You want to take something that’s broken and try to fix it, which is an even harder problem and one that we’re excited to be conceptually making advances on.
Now, before COVID, did the Folding at Home project have a major impact in any type of disease yet or is it still kind of unfolding?
BOWMAN: Folding at Home has been around for over 20 years now and contributed to lots of problems. Initially, very basic research problems like how do proteins fold or build themselves into their functional structures. But in recent years, we’ve contributed to a lot of biomedical research as well. So, for example, just before the pandemic, we found some really cool new ways to potentially combat Ebola infections. And with a collaborator of mine, we were actually able to repurpose a new flu drug to combat a virus called SFTS that fortunately many of you probably haven’t heard of because it impacts other parts of the globe but, with climate change, you know, it’s more likely to impact parts of the United States as they become more prime habitats.
Where do you see the future of Folding at Home?
BOWMAN: The thing I’m most excited about with Folding at Home is just how general of a platform this is and how quickly we can turn our attention to new problems. And so, as we’ve, you know, gotten some momentum up with our work on SARSCOV2, it’s been really gratifying to turn some of the computational power loose on our ongoing projects with Alzheimer’s disease and antibiotic resistance and other massive global health crises that we all need to be working together on to deal with before they really cripple society.
How many states or even countries do you think it’s in?
BOWMAN: We’re almost everywhere, it feels like, that human beings habitat. So, we have volunteers contributing to Folding at Home from almost everywhere that human beings live. We actually will periodically generate maps that show a little pinprick of light everywhere where one of our volunteers is contributing from, and it’s really fun to zoom around and see the little pinpricks on Madagascar and other exotic-seeming areas from my perspective just all over the globe.
Anyone can participate?
BOWMAN: Anyone can participate. And so, we really do have people all over the globe.
Perfect. OK. I think that’s it. Anything I’m missing?
BOWMAN: No, think we hit on things.
Interview conducted by Ivanhoe Broadcast News.
END OF INTERVIEW
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