A Scientist’s Quest To See Every Organism On Earth

MANU PRAKASH: We’re ready to go.

FLORA LICHTMAN: Strap on those life vests. We’re going out in a boat.

MANU PRAKASH: Yeah, OK, so I think it’s better to just stabilize yourself. So we’re going to now feel the wind.

FLORA LICHTMAN: We’re with scientist Manu Prakash speeding into Buzzards Bay off of Cape Cod. It’s early in the morning, and Manu is up late in the lab, but it doesn’t seem to get to him.

MANU PRAKASH: That’s it. That’s the coffee. Now, we’re all up. That’s what we needed.

FLORA LICHTMAN: We’re going fishing for the ocean’s tiniest inhabitants–

MANU PRAKASH: All right, nets in, Bill.

FLORA LICHTMAN: –which is something Manu does all over the globe.

MANU PRAKASH: You see the little shine? Those are diatoms. They’re floating diatoms. On this last trip, we saw this really beautiful diatom. It’s nitzschia, and it crawls on another diatom, this [INAUDIBLE] on its whiskers. So it’s like this diatom has mustaches, very long mustaches. And it will just crawl back and forth in it.

Like, I’ve seen both of them in isolation 1,000 times in the field. First time I see what they do together, and the nitzschia is hitching a ride. That’s the joy of this job. You could spend a lifetime on a boat looking at stuff, and you’re still looking at new stuff every single day. You don’t run out of work. You just can’t run out of work. Yeah.

FLORA LICHTMAN: You can’t run out of work when your goal is to see every single creature on Earth. This is The Leap, a new series about scientists who are risking their reputations, their careers, and even their lives to discover something new.

MANU PRAKASH: If I have an intuition, I will follow it no matter what. No matter what people say, no matter what I read, if I have an intuition, I will follow it.

FLORA LICHTMAN: Manu Prakash is not easy to sum up. He’s a MacArthur Genius Award winner and a bioengineering professor at Stanford, but that doesn’t really capture his work. In practice, he’s a physicist, a biologist, an oceanographer, a toolmaker, an explorer, a field researcher, and he’s putting all of these disciplines together in service of one fantastically grand quest, to map the entire tree of life with the help of everyone on Earth.

MANU PRAKASH: The bigger puzzle is really how the life is organized on this planet, and then the quest really becomes, can you see the whole of it. Can in my lifetime, I can see every organism that has ever been described, maybe one millimeter and below.

FLORA LICHTMAN: That’s an insane goal.

MANU PRAKASH: I think it would be awesome to see every single thing and spend time with it. I think it can be done.

FLORA LICHTMAN: How did he get to this big idea? Manu grew up in India, and he loved science ever since he was a kid. And he did well. He got accepted into one of the IITs, the Indian Institute of Technology. It’s super competitive.

MANU PRAKASH: People introduce each other not by their names but the ranking they got in the national score. Like, what the hell?

FLORA LICHTMAN: Wait, give me an example. Play it out.

MANU PRAKASH: I’ll just call a friend [HINDI]. [HINDI] in Hindi means 25. 25 is his rank in the total ranking system of a million people that applied for this exam. So you can see how much pressure there is.

FLORA LICHTMAN: Now, some people thrive in these ultra competitive environments. It lights a fire in them. That was not Manu.

MANU PRAKASH: Like, I won’t say my grades on audio, but I had pretty low grades. The fact that I ever made it to grad school is insane. I’ve never gotten an– other than my first semester. I never got an A. Like, forget about it. Like, it’s B’s, C’s and D’s.

FLORA LICHTMAN: But Manu wasn’t slacking off. It’s just that while his classmates were like jockeying for front row seats, clamoring to get called on, Manu wasn’t even in the room.

MANU PRAKASH: Like, my undergrad, I spent in a children’s school, second and first graders, and I was watching how they draw. And I was writing a computer program from their drawings to be able to draw a child. And–

FLORA LICHTMAN: That’s amazing that you wanted to do that as an undergrad, to create a program that draws like a child.

MANU PRAKASH: Yeah, it’s not that I wasn’t working. I was working hard on all these other things and other ideas that took so much more time. You, kind of, find it funny now once we were opening up. My first patent is a patent in India where I built this robotic kathputli. Kathputli means a puppet.

We have these very traditional puppet shows. It’s a very famous thing in India. We do this in Rajasthan and other places. So basically, a completely automated system that you don’t need a puppet master at the back. You just program the whole damn thing from a computer sitting over. And I did a show for that.

So I mean, it took time, right. So when you do that type of stuff, you’re clearly not attending classes. But I think it was important. It was actually very formative. It taught me that I can create my own boundary around what I think is important, what is successful.

FLORA LICHTMAN: So you created this internal barometer for success. Did you have to develop it?

MANU PRAKASH: I think I would say it is survival. It’s not you develop this because you that there is no other way out. Because I would have died of boredom.

So what I mean by survival was like, oh, I need to find ways to pursue creative things. Otherwise, that other option doesn’t look very good. And then the hope is that others would value it. So when you go down the deep end, you go to the far deep end. I think that’s really maybe what I’m trying to say.

FLORA LICHTMAN: You do.

MANU PRAKASH: Yeah, I mean, I think I’m just saying that you don’t want to do where everybody else is already looking.

FLORA LICHTMAN: This approach worked for Manu. Even though he wasn’t the best student on paper, people at his University saw something in him and vouched for him. He got into MIT for grad school, and again, he paddled away from the crowds. He got to work on a bubble computer, a computer that uses bubbles as bits. And if that’s hard to wrap your mind around, it’s not just you. It was out there even for MIT.

MANU PRAKASH: I arrived, I was in an applied physics lab. All my friends around me, they were all working on quantum computing. It was the most important thing at that time. Our lab had shown that we can divide 15 with, like, $20 million of equipment–

FLORA LICHTMAN: With a quantum computer.

MANU PRAKASH: With a quantum computer.

FLORA LICHTMAN: You got a quantum computer to do, like, a very simple calculation.

MANU PRAKASH: They were doing that, and it was like the biggest thing of that time. And I just was like, nah, it’s– and I was thinking about bubbles at that time, and I was walking in this corridor.

And I had the other friend who’s a good friend of mine, he was in charge of the– Intel at that time at MIT had this amazing, strange germanium, like a $20 million equipment, and he was in charge. And he would tell me all these things about, oh, how important that was. And then he would turn around and was, like, what are you working on. And I was very hesitant to tell him that I’m thinking about bubbles and making a computer out of a bubble, and so I would avoid him whenever we would walk down the corridor.

FLORA LICHTMAN: Like, you were afraid that he was going to look down on it, that he would laugh? It’d be sort of like a quirky thing?

MANU PRAKASH: Yeah, you get laughed out of rooms all the time. I think that’s true. People really have opinions, especially about what others should do.

FLORA LICHTMAN: That bubble computer work, it made it to the journal Science, by the way. So Manu’s an expert now in bubble computers and AI programs that mimic how children draw. How do you get from there to mapping the entire tree of life? Well, it was partly thanks to a roadblock Manu hit after he graduated and landed a job.

In 2011, Manu got offered a professor position at Stanford. And you might think like, oh, Manu has made it. He can relax. But actually the pressure was just ramping up. The tenure clock had started. He had to hire students, get funding, do science, publish, and immediately Manu hits a speed bump.

MANU PRAKASH: I had arrived on campus to learn that my lab won’t be ready in like nine months or a year.

FLORA LICHTMAN: The building was under construction.

MANU PRAKASH: It was a big down moment. It was, like, holy shit. I can’t even start my lab. I can’t recruit anybody.

FLORA LICHTMAN: So Manu decides to go to the field. He wants to apply his physics expertise to real world problems, problems he saw growing up in India.

MANU PRAKASH: Of course, you see pain in the world, and you ask yourself a question, what am I doing about it. And I think when I started the lab, I had already decided that I was going to spend 50% of the time pursuing what I deeply just care about, like, the analogy to how to draw a child. But on the other hand, the other half was about there is a so much inequality in this world. How do we positively contribute?

FLORA LICHTMAN: So Manu decides to focus on malaria. So he rounds up some students, and he takes them to Thailand. d it was a rough trip.

MANU PRAKASH: We’re like, we’re going to go to the most mosquito-infected places. And I took my students. And one of them quit on the trip. So we were in like leech infested rainforest, and I wanted to see them. And like, he’s like leeches are my boundary.

FLORA LICHTMAN: So Manu has no lab. He’s losing students to leech sensitivities, but this important thing happens. Manu visits this remote venom clinic, and it has this fancy fluorescent microscope. It’s really expensive. People are intimidated by it because it costs so much money, and it is locked away.

MANU PRAKASH: It didn’t feel right. It felt this super expensive thing sitting in the middle of nowhere in a rainforest with pouring rain, and nobody’s there.

FLORA LICHTMAN: And this experience, kind of, dovetails in Manu’s mind with another microscope run in he had in India.

MANU PRAKASH: There’s a place in India where there is a Gandhi ashram. This is where Gandhi used to– Mahatma Gandhi used to spend his time. And there’s this photograph that actually stuck there that I hadn’t seen before although I grew up in India. It’s, kind of, funny. It’s Gandhi looking through a microscope. And there was this irony in this photograph. Like, he was not wearing any clothes–

FLORA LICHTMAN: He’s wearing a white cloth around his waist.

MANU PRAKASH: –because this was the non-cooperative movement. So they were burning pants quite literally.

FLORA LICHTMAN: But at the same time, he’s using this European-made microscope.

MANU PRAKASH: It’s just the sense of oh, like, science can truly bridge and can bring a certain– I used to say it was a very iconic kind of a thing that stuck with me for a long time.

FLORA LICHTMAN: So Manu came back with this clarity, this sense of purpose that microscopes were this powerful tool. They could bridge cultures, but they’re constructed to be these precious objects. They’re finely tuned. Lenses and mirrors make them delicate and expensive and, therefore, locked away. So Manu wondered, what if you could change all that.

MANU PRAKASH: I came back, and the first grant I wrote– now, this is laughed out of the room moment. I had visited a matchstick factory before, and I knew that you could make a billion matchsticks in a day. I just saw this massive machinery churning out matchsticks. And I was like, OK, we’re going to take a manufacturing technology that already works, and we’re going to instead of churning matchsticks, why can’t I churn microscopes.

FLORA LICHTMAN: Could he mass produce cheap microscopes? He had a design, and it was unusual. It used a fireworks chemical reaction to illuminate the sample.

MANU PRAKASH: Like, I actually submitted a grant to somebody where there was fire, and there was microscopes.

FLORA LICHTMAN: He didn’t get it, but the seed of the idea was planted. And soon after, Manu met a student who also saw the potential of this project.

JIM CYBULSKI: We had a very clear vision of the type of people that we wanted to serve. This is Jim Cybulski. He was a grad student in Manu’s lab, and he took on this microscope project. Manu and I both started not exactly– I don’t know if I would say poor, but on the poor side, not in rich families. And so it’s just fun to think, oh, if I would have had this, I could have done that.

FLORA LICHTMAN: So they set out to design a low cost microscope.

MANU PRAKASH: And like in three weeks, we actually had what became version one of the Foldscope scope.

FLORA LICHTMAN: The Foldscope was born, a paper microscope that comes together like origami with different pieces of cardboard folding on top of each other. Inside is a single ball lens, which was one of the key innovations. You can hold the fold scope to your eye or snap it onto your cell phone. With it can see single-celled organisms, even bacteria. It’s sturdy enough to survive a drop from a third story building, and it fits in your pocket. And the cost of materials, $1. So they started submitting the design to journals.

MANU PRAKASH: And like you have this moment when you share your thing with someone and say, how are they going to react. It’s like your baby is ugly, kind of, a moment. And I remember that across with many people even when it was fully functional, it had the same kind of specs that it exists now, just people couldn’t fathom the idea that we’re going to make something that’s supposedly so delicate and so precious out of something that’s like art and craft.

JIM CYBULSKI: There was this underlying tone of people questioning the approach that we were taking. If people spent a lot of time in their career doing microscopy and then you claim, oh, we get comparable performance for $1, that is bound to raise eyebrows.

FLORA LICHTMAN: Because it somehow challenges the idea that to do good science, you have to do it on fancy microscopes at a fancy institution.

JIM CYBULSKI: Our goal is to break the model. A lot of people don’t want to break the model.

FLORA LICHTMAN: Despite the skepticism Foldscope got through the peer review gauntlet, and Manu and Jim published the paper in 2014. And at this point, Manu, a young professor at a very competitive institution racing against the tenure clock, could have very easily just taken the publication win and moved on. He’d proved the idea was possible. Leave it to someone else to get it into people’s hands. After all, public outreach is not the kind of work that typically gets you tenure or advances your scientific career. But Manu wasn’t calculating that way. He had an intuition, and again, he followed it.

MANU PRAKASH: I walked into a lab and really, almost on a whim, I just declared to Jim, we’re going to ship 10,000 Foldscopes. And he, kind of, looked at me, and he knows me. And so he, sort of, smiled to a certain– he was confused. And we had no money.

FLORA LICHTMAN: Foldscope is cheap, but international shipping is not.

MANU PRAKASH: I think I had at that time around 100, 150k left in my bank for the lab. And I did a little back of the envelope calculation, and it was telling me it was going to cost around two $50,000 to just ship microscopes around the world. When I say world, I meant everybody. It didn’t matter which country. If we were going to get a request from Congo, we’re going to ship to Congo. But I just was adamant.

JIM CYBULSKI: I think it’s one of these scenarios where you have to believe you can do it, and you have to start on the path and then hope that something will present itself that will enable you to proceed.

MANU PRAKASH: It was insane, like this room that was filled with scissors and supplies.

JIM CYBULSKI: And so a lot of cutting, a lot of cutting.

FLORA LICHTMAN: All done in the lab.

JIM CYBULSKI: Oh, yeah. Oh, yeah. Graduate students, yeah.

FLORA LICHTMAN: Manu is out on a limb, and it’s not just because he was sinking his startup money. Distributing microscopes to any kid or adult who wants one anywhere in the world, that’s not a traditional research project. It wasn’t about making a discovery that was going to land him in a big journal. And so some colleagues were skeptical.

MANU PRAKASH: As a young professor, you’re always told, oh, no, you need to do what fits in the framework of a profession. And I just I absolutely hate that. I know somebody from the grapevine heard about what I was doing, and senior mentors around me, they reached out. It’s like, oh, so what is your plan, what are you trying to do.

And I just– all I said is I just want to see what people do with this in the world, no questions asked, nothing in return. Let them figure out what’s best for them, not for us. We don’t need anything other than just people to play and explore.

And the risk there was just trusting others, and I built that very deeply in a lot of things that we do. I start with a position of trust.

SPEAKER 1: You guys.

SPEAKER 2: Oh my God, look at that. Oh, there’s all kinds of silliness.

SPEAKER 3: I cannot believe how we–

SPEAKER 4: We can barely get our microscope to see those.

MANU PRAKASH: Human mind is so curious. Once you share sets of capabilities, they will explore.

FLORA LICHTMAN: Manu and Jim started a company for Foldscope. Jim’s the president. They’ve distributed almost 2 million Foldscopes to people in over 160 countries.

[NON-ENGLISH SPEECH]

They created a website where people can upload videos they took with their Foldscope attached to their phone.

[NON-ENGLISH SPEECH]

And you can hear and see people all over the globe scooping out teaspoons of pond scum, grabbing the hairs of their dogs, taking droplets of their own blood, and making discoveries.

SPEAKER 5: That is amazing.

SPEAKER 6: Oh, look at that.

MANU PRAKASH: Literally anybody walking around can make profound discoveries on this planet just by observing, putting those pieces together. And you have to enable that. You have to enable that by making sure that scientific tools are just part and parcel of our life and our culture.

JIM CYBULSKI: Manu has enabled that joy of discovery for millions of people. That is a profound contribution. But for Manu, this isn’t just about lighting up people’s curiosity or letting them in on this secret, invisible world.

This is also about real science, about Manu’s grand quest to map the tree of life. If we truly want to understand this ship that we are on, we must take an approach that is driven by millions of people walking around and observing. When we do that at a planet scale, like the rate of discovery would be astronomical.

And it does require sometimes to meet these characters, you have to go to their homes. They don’t come to you. And that’s just– that does require you to be dangling off of trees or going out at sea. And it just I think I feel like at least if I have a good true personal acquaintance with a significant portion of the tree of life, that would make me happy, yeah, real, true personal acquaintance.

FLORA LICHTMAN: Why do you think that getting acquainted with the tree of life? Why is that your thing?

MANU PRAKASH: I think the why is very simple. Every organism is an idea, and every one of them is a new idea. It’s not just about the classical way people have thought about evolution. Oh, there was a niche. This must be the optimal way. No, some organisms are just absolutely, profoundly, for the lack of a better word, strangely dumb. Just It’s like, what the hell. That’s not how you should do it, and that’s still an idea.

FLORA LICHTMAN: There are a lot of dumb ideas.

MANU PRAKASH: Right. Exactly. That’s what I’m trying to say. I don’t want to put every one of them on a pedestal of just this, oh, what a beautiful puzzle it’s solved. It’s like and then you see, once in a while, just this brilliant thing that an organism does that we’ve never just thought about it like, oh, I’m going to steal photosynthetic organelles from another animal and don’t have to eat ever again. So, I mean–

JIM CYBULSKI: Or I’m going to ride your whiskers.

MANU PRAKASH: I’m going to ride your whiskers. That’s correct. Yeah like, what the hell. That’s a brilliant idea.

FLORA LICHTMAN: With every new idea, we understand our world a little better. There are now over 1,400 scientific papers referencing Foldscope, discoveries in diagnostics and public health and agriculture. People have even discovered new species using Foldscope, adding new twigs to the tree of life, just as Manu trusted they would.

Oh, wow. Oh, this is an incredible one. Hold it. Hold it. And so–

Oh my God.

MANU PRAKASH: Do you see your hair? You see the big line? So you have to pass this one around to everybody.

SPEAKER 7: I have black hair.

MANU PRAKASH: I’m not saying this is easy. I’m not saying I’m good at it or something, but it’s just you have to strip science away from what other people think. It really is what you think. Sometimes I think about people that I want to reach, that I haven’t reached, and that’s like, I judge myself on that. Or like sometimes some place in the tree of life is taunting me. Like, you’ll never understand me. I’ll judge myself on that.

But I think these are all internal. Like having an internal parameter, using that as an anchor to say whether you’re successful, that’s far more interesting.

[MUSIC PLAYING]

FLORA LICHTMAN: The Leap is a production of the Hypothesis Fund. Manu has been recognized by the Hypothesis Fund as a scout for his bold science and enabling others to pursue their big ideas. You can learn more about this recognition and volunteer role on the website.

This show is hosted by me, Flora Lichtman, and produced by Annette Heist, editing by Devon Taylor, Pajau Vangay, and David Sanford, fact checking by Nicole Pasulka, additional production help from Ruth Lichtman, mixing and scoring by Emma Munger, music by Joshua Budo Karp. Special thanks to Christine Kurihara, the Marine Biological Laboratory in Woods Hole, and to all the Foldscope users all over the world who shared their observations online. And thanks to you for listening.

[MUSIC PLAYING]

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