The cassava plant is one of the most important food sources in the world. In Africa, it sustains 500 million people and provides a stable income for farmers. The crop is also susceptible to viruses transmitted by the common pest known as the whitefly, which can devastate farms. Biologist Laura Boykin has found a way to stop the spread of these diseases. Boykin founded the Cassava Virus Action Project, where she and other scientists use a pocket-sized device called a MinION to sequence the DNA of cassava strains and help farmers select plants that are resistant to the local pathogens.
On this episode of Gadget Lab, a conversation with Boykin about her work, the power of direct action, and the possibilities afforded by the technology we have today. The show was recorded with a live audience at the recent WIRED25 conference in San Francisco.
Lauren Goode can be found on Twitter @LaurenGoode. Arielle Pardes is @pardesoteric. Michael Calore is @snackfight. Bling the main hotline at @GadgetLab. The show is produced by Boone Ashworth (@booneashworth). Our consulting executive producer is Alex Kapelman (@alexkapelman). Our theme music is by Solar Keys.
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Michael Calore: Hi everyone. I’m Michael Calore, a senior editor at WIRED. Today on Gadget Lab we’re going to bring you a special episode. It’s an interview with the computational biologist, Laura Boykin. She’s the founder of the Cassava Virus Action Project, which does work with farmers in Africa. She’s involved in DNA sequencing and has all sorts of cool science that she does in the field. This is a really fun and wide ranging interview and I think you’re going to enjoy it. I spoke with Laura in front of a live audience at our annual WIRED25 conference and festival in San Francisco. She had fun, the crowd loved it and I’m super happy that you get to hear it now. So without further ado, here’s me in conversation with Laura Boykin.
MC: We are joined today by Laura Boykin. Laura Boykin is a biologist who uses genomics and super computing to help small holder farms in sub-Saharan, Africa, control white flies and the viruses they carry, which have decimated cassava crops. Along with scientists in East Africa she founded the Cassava Virus Action Project. Laura is a TED Senior Fellow and was awarded the Gifted Citizen Prize at the La Cuidad de las Ideas Festival in 2017. Everybody please welcome Laura Boykin.
Laura Boykin: Wow, what a nice intro. What a nice intro.
MC: I read-
LB: Is that good? Am I in there?
MC: I read it from my notes.
MC: I did not memorize it. Let’s start with cassava. Tell us about the plant that you work with. Why is it so important?
LB: Right, so I’m a student of cassava, obviously I grew up in the US. Cassava is a plant that feeds 800 million people globally and 500 million of those people are in sub-Saharan Africa. It’s very high in calories, and the interesting thing about the plant is it’s very low input. A farmer will plant it and they don’t need to … With the changing weather patterns and things like that, the crop is really robust, no fertilizer, no water, it just grows. Usually on a farm … The farms that we’re talking about are about one acre and the farmers will have a mix of beans and potatoes and sweet potatoes. And then there’s always some cassava just in case. It’s the backup when all of those things are done. It’s a super important plant globally. Mainly like, as I said in sub-Saharan Africa, but it’s also found an Eaton in Brazil where it was domesticated and Southeast Asia eats a lot of cassava. The biggest cassava producing country in the world is Nigeria, followed by Thailand.
LB: Those are your random facts for the day. But it’s a really important food security. A lot of the farmers and scientists I work tell me that cassava is a poverty fighter. If a farmer has it, they can feed their families and sell it at the market for important things like school fees and medical expenses and savings. It’s a really important plant.
MC: You describe Yourself as a computational biologist, so I put those two words together in my head and I have a pretty good idea of what that means, but I would like you to tell us what the definition of that role is.
LB: Oh my God. Number one, I hate titles. So I can never figure out what to call myself. Basically, I like computers and I like biology and genomics in particular and putting those things together is computational biology. But when I’m talking to my mom and stuff, she’s like, “Honey, I have no idea what that means.” So I just tell her, “Look, I like computers and I like biology.”
MC: Let’s get into the work that you do specifically. First of all, take us to the places that you work, the farms that you visit and the farmers that you work with. What are these areas like?
LB: Yeah, so first of all, I mean I am one person on a really big team. In 2014 I went to a conference and there was a bunch of East African scientists present and I was talking about super computing as you do and they were like, “Hey, we have a bunch of genomic data, would you like to join our team? We’re working on this cassava problem. And I just was like, “OK, cool. I’m in.” When I talk about the work that we do, it’s not like I just jump on a plane and land in Kenya and just go running out to farmers. I mean there’s this amazing network of scientists and farmers that exist in the region. And like as I said, I’m the computational person on our team and I’m in training on cassava. I’m definitely not the expert.
LB: With that being said, there’s a huge network of people and they’ve spent years building the relationships with the farmers that allows us to do this work. So basically the biggest problem is farmers are typically getting maybe zero to one ton per hectare and they could get 40. So we sat down as a team and tried to figure out what are the steps to get the farmer to 40, that seems like … And the first step was diagnosing what’s killing the cassava.
LB: There are these pathogens, viruses and pests, white flies that are feeding on the plants and killing them basically, reducing the yield to zero. And the time it was taking the scientists to diagnose that problem could be six months because the genomic technologies that exist or existed before this portable stuff, they really weren’t made for the African continent. They are these machines about the size of this table, and they’re $1 million and they require constant power and really specialized skill. This whole genomics revolution was happening, but this large proportion of the population was being left behind. They were really struggling to get their sequences or their DNA data or pathogen data collected. We had heard … I don’t even know if I’m answering the question for crying out loud, but here we are on a tangent.
LB: But anyway, the whole point of this was, it was six months and then we had heard about these little portable devices that were being used to fight Ebola in West Africa. And we were like, why are we not using these in East Africa for farmers? Through this work we really just went out to a farm. Everybody said we couldn’t do it, which is super cool. This woman who was our collaborator, in quotation marks, she bet us two bottles of the best champagne that we would never get this portable technology to work in Africa, let alone in the field. As you know when you question or say that a big population of marginalized people in science can’t do something, oh we’re going to do it. And so we did it. We basically went from six months time to diagnosis, to three hours on the farm.
LB: And that woman, if she’s listening, I’m waiting on the champagne. You know who you are because you’re using the stuff now.
MC: So you brought the actual kit that you use in the field, which is great for audio.
LB: Isn’t that wonderful? There’s lights flashing. It’s compact.
MC: Well, I can describe it as roughly the size of maybe four or five smartphones stacked on top of each other with some cables coming out of it. But why don’t you tell us a little bit about this kit that you use in the field and what’s inside of it and how it works and what you do?
LB: Yeah, because this is Gadget Lab, we need to talk about the gadgets.
MC: It is required, definitely is.
LB: I mean, that’s why brought them, for everyone to hear. They can hear them. All right. Basically on the table is a laptop power bank, which is one of the biggest breakthroughs for us was using this sort of technology without power, because on the farms there’s no power or limited power. We had to get this to work running off of either this laptop power bank or we have another device that we use that runs off of a motorcycle battery. Basically we have on the top here it’s called an Oxford Nanopore MinION. It’s a little portable DNA sequencer. And when you open this thing up, it has what they call a flow cell. And the breakthrough technology or the disruptive part of this is I told you guys that the old technology is $1 million and is huge and this I think costs $1,000. It’s small, it runs off of power bank. And the way the data is generated is different.
LB: On here there’s a membrane and on the membrane there are proteins embedded, 2000 proteins. So DNA as you know, has A, T, G and C, so those are different chemical compounds. They go through this pour and disrupt the current, so there’s electricity running through this device. And as an A goes through it, it disrupts the current in a certain way. And if a T goes through there, it has a different structure, so it will disrupt the current in a different way. You have realtime DNA sequencing happening and the raw data is a frequency, and we use AI to figure out patterns. Quickly, this squiggle is actually an A, and this squiggle is actually a T and a G and all of that is happening on this other device that looks like a little box.
MC: Yeah, it’s about half the size of a jambox.
LB: A jambox. And inside of here, Nvidia has put a GPU processor that does this, what we call base calling. It happens real time. On the farm we’re able to take a sample, extract the DNA, which is another machine that I don’t have here, but we can extract the DNA and then we put it onto here and then we get the data real time. You can visualize what’s happening here on a smartphone or on a computer or on a tablet. Basically it’s all the molecular lab and all the computing needs portable and taken to the farm.
MC: When you’re gathering the data, let’s say you visit a farm, you work with the farmer to isolate certain plants on their farm. You sequence the DNA, you find results that are actionable. What do you do? You just tell the farmer what to do? Do you give them the data?
LB: Yeah. So what we realized is that watching us do molecular biology is really boring. For us it’s, we go around with the farmers and they pick the plants they’re interested in, because farmers know their plants better than we do and they’ll see something weird happening. Or this one they really like and a lot of them aren’t showing symptoms, so a lot of these things look healthy, but maybe the yield was low or whatever. So the farmers go around, we pick the leaves off the plants with them, we extract the DNA and that can take like … That’s probably two hours of the thing. We have pipettes and we’re wearing gloves and the farmers are just like, OK, we have things to do.
LB: So we got to work out … I think we need to do a better job of, I don’t know, entertaining or explaining or whatever when we’re with the farmers. Well first of all we weren’t sure it was going to work, so our whole strategy is getting better. But at the end we tell them, look, these seven plants that we tested, some of them are virus free, some of them are infected with these particular viruses and that’s great, good, yeah, whatever. But the actionable parts are what we tell them to do. Depending on what strain of virus they have in their field, there is … Cassava breeders have many varieties that they know are tolerant to different viruses, so we’re tapped into the national … In each country, the cassava breeder.
LB: So we’ll tell them, “Look, you have these three viruses, the cassava breeders say this is your prescription, so you’re going to have to burn this field…” They have to trust … “You have to burn this field and plant this variety,” And they can get the virus free material from a number of different places. Some people sell it, the government will also deploy it to them. And there’s a lot of people that, not a lot, but there’s people developing apps for farmers to know where to go to get clean material based on what is in their field. So that is what we do. Give them the results, give them either the material or where to get the material. And then they plant it and see.
MC: I see. So I know that all of the data that is collected and collated by your team is owned by the communities that you work in. You release it basically as open source data.
MC: Tell us why that’s important.
LB: Yeah, so it has to be done that way. We just have to do it that way because this colonization of STEM has to stop. We have to stop going in, taking samples, going away and publishing papers behind paywalls where number one, the scientists in the community can’t read it. And number two, the data is somewhere that’s … The farmer needs to know where the data is, they just do, they need a local contact of … I mean, OK, yes, farmers are not sitting around with supercomputers, but if they know that this extension worker has access to their data, then that’s what matters. The communities that we work in half to have the data first. And for us generating, we thought, let’s just move the data closer to the problem and then you can make a decision faster.
LB: Immediately, real time we get the data and this little device can store up to a terabyte of data and then this is transferred locally onto their machines. Because another thing, we just can’t rely on the internet, it’s just not there. It’s just not. As much as we’re living in a fantasy world that we’re going to fly balloons around, I’ve given lat longs, I’ve given lat longs to this gentleman who I can provide those. We need data, we need data at these lat longs, let’s stop talking about it, here you go. Get it there, we have science to do.
LB: But anyway, we can’t rely on, it at all. And there’s only so many coffees and teas that we can buy in the hotel to use their free Wi-Fi, they’re not a big fan of us uploading a terabyte of data, I’m just saying. It doesn’t go down well. We try, but it doesn’t go down well. For us, having the data locally is empowerment, but it’s also logistically the only way it can happen, you know?
LB: Anyway, the data does not belong to me or anyone else. It’s protecting a bunch of people who need food. So we need to make it available real time. So smart people, besides ourselves can help look for patterns and help us figure it out.
MC: Right. And who are the smart people? Are there organizations in East Africa? Are there just farmers with smartphones and hotspots that want to use it and engage with it?
LB: Yeah. So for me, I mean, I have to say that there are some amazing scientists like Dr. Joseph Ndunguru who’s at the Tanzanian Agricultural Research Institute in Uganda. There’s Dr. Titus Alichi in Kenya, there’s Professor Elijah Ateka at Jomo Kenyatta University. There are amazing scientists that work at the governmental level at these national agricultural research centers that drive all the change. It’s a privilege for me to be on this team that I’m on because they just allow me to do computer stuff. I’m in charge of two C’s, communication and computers because I’m on a team with introverts, so I get stuck through in this stuff, but … God, I hope they don’t listen to this.
LB: But anyway, I have to say we have a website, the Cassava Virus Action Project and you can look at it and you can totally see this team of people that is driving the change from the ground up. I think that’s what’s really different about us is we’re out there doing it. We’re on the ground trying it. We’re sitting under a farmer’s tree doing the stuff nobody told us we could do. And we did that because we’re a really diverse inclusive team that just works like a well oiled machine to get stuff done because we care about this overall mission of farmers should not be hungry. We have all this tech in this stuff. Let’s just stop talking about it and start doing it. So anyway, it’s a big network of people that we work with.
MC: Let’s take a quick break and then we’ll come back and hear the rest of my conversation with Laura Boykin.
MC: I watched one of your TED Talks. I think it was your most recent TED Talk …
LB: Oh dear.
MC: It was great, you’re a star. But I think it was the one from Edinburgh, Scotland, if anybody wants to look it up. But you said something that struck me in a way that I felt as though I should write it down. Here’s the quote, “We have all the technology we need, but the knowledge and resources are not equally distributed around the globe.”
LB: Mm-hmm (affirmative).
MC: Can you tell us why you feel that way? What makes you feel that way?
LB: I mean, what makes me feel that way is that I ground truth that statement. When I do science, I’m not doing science at the five star hotel. I’m not really interested in your meetings where we’re going to talk about what butcher paper, markers and stuff. That’s edited because I wanted to say another word, but I’m editing myself. No, for me it’s like I’m ground truthiness. I want to do science with scientists. I don’t want the smoke and mirror, I’ve seen what happens, it’s not. I do science in Australia and I go to Tanzania and we don’t have power and we don’t have internet and we don’t have any lab equipment. These are facts. We have no computers. And I am so grateful to the team that accepts me and shows me the reality. I don’t want smoke and mirrors. I don’t want you to turn on the generator when I’m there. Let’s see how it is to do science here.
MC: Mm-hmm (affirmative).
LB: And it is ridiculous that it is this way. I mean, this portable stuff is great for the farm, but it’s also what we need in the labs. There’s no power.
MC: Yesterday you were here on stage at WIRED25.
LB: Oh dear.
MC: What? It was a great talk. You spoke a lot about fighting for equity and inclusion in science and fighting against the systematic racism and sexism in science. How can small handheld devices like these improve the equity in science?
LB: Yeah. For me, the genomics game has been run by white people, mainly white men outside of the lower resourced places on the planet. When you democratize DNA sequencing, you completely change the game for everyone, because it is about the data that’s being generated. But the thing that we … Everything about our project from the bottom up is wrapped in social justice. The imagery, the BBC, who’s where, we make sure every single thing you will see about us is wrapped in social justice from the beginning. The work is great, but also you are never going to see me pipetting or doing something because it is our team in East Africa that runs the game. I am the computer person. And when we go meet ministers, it’s powerful to have a white person just sit there and be quiet.
LB: So when I go, I sit and I just am there as moral support. When we’re showing … Because a part of this is we have to get the governments in the region to uptake this technology. We spend a lot of time doing calls to ministers and two weeks, three weeks ago I met with the president of Sierra Leone. But when you democratize DNA sequencing, it shifts the power in the science game, and the thing that I love so much about this project is the bleeding edge of genomic technology is being run by East African scientists. And that’s a paradigm shift. It’s a huge paradigm shift, because now it’s like, oh well no, they’re not getting your leftovers. They’re doing it.
MC: That’s great. Is some of the outreach that you’re doing when you go and talk to governments and you’re encouraging them to pay attention and invest, is that working? Are they investing in labs? Are they hiring scientists to collect and maintain this data that’s being gathered in the field?
LB: Yeah, so we’re trying really, really hard. There’s an organization called the East African Community, which is kind of like the UN that over sits all of the six countries in East Africa. And they’ve asked us for a proposal to do capacity building and to empower their trade regulators. Because if you can certify with genomic technology that your stuff is virus free, then you can open trade up to a lot of different places. They have been really receptive and they also know that this can put them on the map in leading in regulatory things. So yeah, it’s slow but steady. And one thing that we see is important is sustainability of this.
LB: We don’t have big foundations funding us because we feel like if the governments invest then it’s a sustainable solution. So we’re trying to hustle as hard as we can to get governments to make this sort of technology part of their core science and technology agendas. Because it is about cassava, but it’s more about empowerment of scientists to be able to handle outbreaks of stuff and biodiversity, and wildlife and all of that. We started with cassava because that’s what we know, but we just have a vision that everybody’s going to be able to do it and it helps everyone.
MC: I want to back up a minute and talk about the plants.
MC: You mentioned before that what you provide to the farmer is sort of a prescription for what they can plant that is resistant to the viruses that are local to their area. And what you’re asking them to plant are plants that have been genetically modified to be there … No? You’re shaking your head no, they’re not?
MC: OK. Tell us about how those plants are … Are they just purely bred to be resistant to these viruses?
LB: Yeah, so there are people that are working on GMOs solutions to these particular viruses that are circulating in the region. But the governments have laws that prevent GMO solutions being given to farmers. There’s a lot of people that are working on regulatory issues and a lot of people developing solutions. But for us it’s how long are we going to wait? We have things that we can use that have been conventionally bred. Right?
MC: Mm-hmm (affirmative).
LB: So all of the things that we have access to give farmers freely is all conventionally bred stuff and breeders have documented what they’re resistant to. That’s what they’re being given as improved varieties from local plants.
MC: Right. And is that resistance to genetically modified plants? Is that a purely regulatory thing? Like if they grow it, they may not be able to sell it at the market? Or is it more of a cultural distrust of the few organisms?
LB: I think the first stopping point is the regulation, right? The governments have laws that prevent … I think they use the term biotechnology, they prevent those things from going to farmers. But there’s also a lot of of scientists that I’m working with, including Dr. Ndunguru In Tanzania who spend a lot of time with farmers discussing genetically modified plants. And my view on the topic is we’re given a choice, you go to the supermarket and you get to choose whether you buy that or you buy that. And farmers in East Africa deserve that choice as well, right?
MC: Mm-hmm (affirmative).
LB: And some are going to take it and some are not. But I guarantee you that some of the farmers I’ve met in Northern Uganda where their kids don’t have enough food. I mean seriously not enough food. They’re going to consider the options to feed their families, I mean I would. But the biggest stop is the governments and the regulations.
MC: I want to get back to the handheld devices.
MC: What you have now is a stack of sort of three small devices, each of them handheld, each of them with a specific purpose. What do you think the future of this kit that you carry looks like?
LB: Yeah. I’m hoping … These things that I have now, this company has already made them all put together. It’s like a smart phone, a supercomputer and a sequencer. They’re already shipping what that looks like. But we still need to use pipettes and we need tubes and we need gloves. It has to be easier, it has to be one machine that I just drop a leaf into and out pops the answer. Because now we’re having to do a DNA extraction and then we’re having to prepare a library and then we’re … I think it will just be, hopefully the things that TV is making up on CSI.
LB: I mean I’ve bet someone, because I like to bet, and then move forward towards it, that a farmer will be able to do this without an extension officer in the next three years. And I bet my friend Monica [inaudible], Monica you’re going to pay up, because I think a farmer is going to be able to do it. I think they’re going to. All of us are going to have complete control over our data, you can do this with your own genome. I mean we get contamination in sequence ourselves all the time. Or dog urine from them peeing on the cassava. I mean I know you wanted to know that.
LB: I mean because you sequence everything when you’re out there.
MC: Right, right. What does it look like for a farmer who wants to do that? Are they walking around? They put on the gloves and they-
LB: No, no gloves. I think the algorithms have to get good enough to just filter out the human parts of it, and just … I mean obviously the advancements are happening in the hardware. I think the software and the algorithms will get even better to detect what we’re looking for. This is great, but the software to analyze this type of data, it sucks. There is a wide open space in this field to develop software that can live off of GitHub and might have a GUI for us.
MC: That’d be perfect?
LB: That would be amazing. And maybe written in Swahili and stuff too.
MC: Yeah. Every localized language.
LB: Just saying you.
MC: So you’re also taking advantage of massive compute infrastructure in Australia. Can you tell us about that?
LB: Yeah. So I moved to Australia because there’s a lot of people doing supercomputing there, radio astronomers. So there’s a square kilometer array … There’s not much happening in Western Australia, so they can do their quiet zones and things. But at the time, seven years ago, it was kind of like this genomics thing and the super computing were all kind of happening. We use this gigantic Cray supercomputer to basically … Once we generate all the data, it becomes unknown, and then you have to match it to knowns. And there’s this database called GenBank that houses all of the genetic data that exists on the planet and that matching is computationally intense. It’s just billions of iterations of trying to figure … It’s a needle in a haystack, and that is a huge computational challenge. Even when we’re in East Africa, we can log into the supercomputer in Australia and use the compute resources.
MC: So when you’re uploading the terabyte of data, that’s what you’re uploading into?
LB: Yeah. I mean we really need these tech companies to think about solutions of bringing big data to big data.
MC: What do you mean?
LB: Work that out people. I mean, I don’t even know. I mean we have a bunch of data that’s unknowns and the knowns live over there and we’re stuck with no internet. I mean this is the reality of what we’re doing.
MC: Send in more balloons.
LB: I’m telling you now, I’ve sent them the lat long. I’ll send it again. Bring us the internet.
MC: Well thank you so much for joining us today and thanks for coming to WIRED25.
LB: I know, Oh my God, I can’t believe I’m here, but OK.
MC: It’s really amazing to have you here …
MC: … and hear you tell your story and give us things to think about.
MC: People can find you on Twitter by going to @Laura_Boykin and they can send you pictures of their cassava plants.
LB: I mean send me all the things. Selfies, our team is really good at taking selfies too, so you should check that out on our page. That’s a secret to our success is taking selfies as a team.
MC: Well, thank you so much, Laura.
LB: Thank you.
MC: All right. That was my interview with Laura Boykin recorded live at this years WIRED25 Conference. Thank you for listening. If you have any feedback you can find me and my co-hosts on Twitter, just check the show notes. We will be back next week with a regular episode, our last episode of the year, in fact, so come back for that, it’s definitely going to be something special. This show is produced by Boone Ashworth and our consulting executive producer is Alex Kapelman. Until next week.
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