How AI can unlock the mysteries of our health, with Kevin Slavin

0:00Starting a business comes with its share of ups and downs, which is why staying true to your vision is essential. a non-negotiable for Romeo and Milka Bregali, Capital One business customers and co-owners of Ra's plant-based restaurant in New York. Romeo and Milka took a leap of faith when starting their own restaurant, gutting an empty space and building it from the ground up. Every pipe, every wall, every detail. But building from scratch came with a heavy financial burden, which is when they turned to their Capital One business card. With the flexibility of the card's no preset spending limit, they were able to spend more and earn more rewards while bringing their vision to life.

0:36Today, Raz's success is proof that with passion and the right support, it's possible to make your dreams a reality. Learn more at CapitalOne.com slash business cards. Pioneers of AI is made possible with support from Inflection AI. It's not just enterprise AI. It's your enterprise AI. There are these major shifts in consciousness over time. for a long time we believed that the earth was the center of the universe and you know and then the bunch of science gets done and that goes away and then we think that our species is the center of all life and then a bunch of research gets done and that's obviously false there's this third one that i think is still in progress which is the notion that each one of us is an individual organism i'm trying to help get us past that fallacy as quickly as possible.

1:31Because we're not, because we're filled with tens of thousands different organisms in our gut. Those have profound effects on our outcomes and who we are. That's Kevin Slavin. He's a dynamic thinker in the field of metagenomics, which is how we learn about microscopic organisms like bacteria. These microbes live around us, on us, and inside of us. We generally consider, you know, air and the environment in general as a white space, right? Like it's just sort of kind of empty. And of course, you know, that's absurd the minute you start poking at it. It's incredibly rich in genuinely millions of species that have direct outcomes for all of us, not just pathogens.

2:19Also lots of stuff that just straight up keeps us alive and in many cases helps us thrive. and all of which are invisible to the eye. Each of these tiny microbes have their own characteristics and figuring out what is what takes a lot of compute. Here is where AI comes in. AI can detect patterns in the DNA of these microbes far quicker and more efficiently than we have ever been able to before. This is a big deal because, like Kevin said, these tiny species that we never see have real impacts on our bodies and our world. Which is why, on this episode, we are digging into the significance of metagenomics, our gut biome, as well as our environmental biome.

3:09Once you understand how microbes shape us, you'll understand why it's so groundbreaking that AI can help decode them. I'm Rana El-Khalyubi, and this is Pioneers of AI, a podcast taking you behind the scenes of the AI revolution.

3:36Hi, Kevin. Welcome to the show. Thank you. So there are a bazillion directions we can take our conversation today, but I wanted us to particularly focus on this idea. A lot of your work, especially recently, has been focused on understanding and managing the microorganisms and the microbes both around us and inside us. So for some of our listeners who are not familiar with this space, can you give us a sense of the complexity and the vastness of both the number of microorganisms that are within our body, but also around us? So these are estimates, right? But we understand there to be about six and a half million species of life on land and maybe like another two million in the sea.

4:19So call it eight and a half million species on earth. We have names and at least a crude understanding of about two million of those. So the space of everything that's left is enormous. You know, the part of what was interesting to me when I first started this is how vast this world is and how little we know about it and that how would we even begin to interact with it in order to understand it. And that's on and off what I've been working on for about 10 years. So how do you do that? So now you've, you know, we've got 2 million of these that we can at least name. What did your work do? So what I was interested in and initially, and what has become a very urgent and widespread field is, can we find out what's around us?

5:08All these organisms that we can't see that we might not even be able to name? How would we even detect them? There are different aspects of this kind of investigation. The first thing is that you need to be able to collect the DNA that you're going to be looking at. So you have to be able to gather all the genomic material, but then you need to be able to figure out what you've got. Part of what was making all of this possible right around that time was kind of the advent and lowering costs of what's called metagenomics. And here, I will pause and explain what metagenomics is because it's just not part of most people's breakfast.

5:43So if we were to talk about genomics, I would say, okay, well, you spit into a jar and I know that you're a human. And I look that up against the fully characterized human genome. And I can make a bunch of conclusions based on the specific variations within your genome. Okay. But if I give you a bowl of soup, what do you look it up against? Do you look it up against the tomato genome? Do you look it up against the cow genome? Do you look it up against pepper genomes? Where would you even begin? And you can't. You have no idea where to begin, especially if you really want to find out everything that's in the soup.

6:22So you have to do what's called metagenomics. And metagenomics is basically saying, okay, look, we have no idea what's in the soup. So we're just going to break up all the DNA of everything in there, and we're going to look that up against the entire tree of life, which, you know, from a computational perspective, is ambitious. And so that's quite a task. Back when we were first doing it in 2014, it took many days and was really displacing a lot of computational resources. These days, it's a lot better and a lot easier. Probably because there's a lot of harnessing machine learning. Exactly. So part of it is just computational strength, right?

7:04There's GPUs that specialize in this kind of thing and so on and so forth. But really, it's the ability to use machine learning and AI to start to do some baseline predictive aspects. Kevin is talking about what to do with the genomic information once you collect it. But there's still the question of how to even collect this data. If you're analyzing, say, someone's gut biome, you analyze their fecal matter. Basically, their poop. But what if you want to measure the environmental biome of, say, Boston? How do you collect data on that scale? Back in 2014, Kevin found an inventive way to do just that.

7:45I arrived at using honeybees to gather the DNA for us. It's what honeybees do. You don't have to pay them, although they do need help to survive. And they are optimized by millions of years to basically gather every microbe that they come across. Pollen is the most obvious one, but also everything else that they fly through or touch adheres to their skin. They're basically little swabs that are broadly sentient and can go and gather. And so we built hives that would give them something to wipe their feet on when they got home. and then we would send whatever the bees had found to the Weill Cornell Center for Computational Genomics and they would sequence whatever we had gathered.

8:28And that sequencing is the second step. But here I should say that back in 2014, I was using honeybees. But through that work, I also met and ultimately became friends with and collaborators with folks who were using other techniques. So one was Jessica Green. She was using HVAC filters. So if you think about the filter in your air conditioner or your heating system, it's purifying your air. But from a microbial perspective, that's like a fishing net and it catches everything. So she would collect things through the HVAC. And there was Chris Mason, who at the Weill Cornell Center for Computational Genomics in New York, who was using grad students.

9:08And at that time, they went into every subway station in New York City and physically swabbed every single subway station to find out what was in the subway station. So you can use bees and you can use HVAC filters and you can use grad students. And then there was a grad student named Mariana Mattis, who was in the Eric Alm lab. And she built back then the very first robot to go into the sewers and collect essentially wastewater to find out what was in there. I'm a huge fan of Mariana, by the way. Shout out, Mariana, you listen to this. Truly, you know, a genuine pioneer. But, you know, I think with all of us, we were all fascinated by this capability to gather genetic material and genomic material from the environment.

9:56And really, at that time, everyone just sort of thought that was a bit of a folly. A folly because back in 2014, the world didn't know why we would even need to collect and analyze the genomic material of a city. That, of course, changed by 2020, when COVID upended our lives. The need to understand which invisible microbes were in our environments suddenly became critical. We'll get to that in a minute after a short break. Stay with us.

10:59Transcription by CastingWords in Loom, and now AI agents in Rovo, which connects the dots across your work so nothing gets lost. It's one AI-powered teamwork platform designed for how modern teams actually build. Learn more at Atlassian.com slash TeamChanger. That's A-T-L-A-S-S-I-A-N dot com slash TeamChanger. Take us to like January or February 2020 and how this ability to both collect and then understand what's in the air around us. How did that become really important? I would say that March of 2020, there still weren't diagnostic tests available. And yet, here I was talking to scientists that I've been talking to for years saying, I don't know how to find it in somebody's body because we didn't have rapid antigen tests yet or even PCR.

11:56But I think that we all know how to figure out if it's in the room. We could do that, couldn't we? And so for a while, the very first instantiation of this, which is like I would say by March of 2020, was what's called surface testing, which is basically using the same swabs that go up your nose, but swabbing your coffee cup, the doorknobs, the elevator buttons in your building and so on and so forth. And looking those up against what was now a fully characterized SARS-CoV-2 genome, we put together a program for the World Trade Center in New York mid-2020 so that they could get a handle on when COVID was present.

12:36This is a complicated way to do things. It's fraught. You're not detecting it really in the environment. You're really detecting it on, you know, Lisa's coffee cup. So that was not destined for long-term success. And I moved on to working with some folks at another company that had figured out how to do airborne detection of COVID. And that was using electrostatics, and it would basically pull air through a fan, effectively, and then bind microbial material to a metal plate. And then we could take the plate and then sequence whatever we found on the plate. And like that, you could find out not whether somebody in particular had it, but whether it was present in the room, was somebody exhaling it.

13:23And so there was a moment, a few months, where detecting COVID in an office or a hospital or whatnot was a useful signal. But then with the advent of Omicron, once that happened, it was a little bit like saying, I'm going to sell smoke detectors right outside a forest fire. And it was a piece of information that nobody needed. Is SARS-CoV-2 present in the Starbucks? Yes. Is it on this bus? Yes. What about this school? Yeah. So that was also not really a viable business. So I migrated over to Ginkgo Bioworks, which is a biotech company out of Cambridge. and they had a division now known as Ginkgo Biosecurity that was sort of taking the same questions and sort of scaling them up.

14:06And the ways that they were scaling them up was to say, okay, it's not useful to know that it's on somebody's coffee cup and it may not be useful to know that it's in the school. But from a national security, as well as a public health perspective, it may be useful to know what just entered the country. It may be useful to know what just entered a secure space of some kind. And in particular, if you can get full genomic information about what you're capturing. So in other words, not just saying SARS-CoV-2, what leads to COVID is present, but also what particular, right? Like which particular variant is present.

14:49So really being able to capture the full genomic profile of the things that you capture is half the problem, right? But also, what do you collect to give you the significant signal? And in the case of Ginkgo Biosecurity, they entered into a program with the CDC called Traveler Genomic Surveillance, TGS, which in, I believe the number is 10 airports. In those airports, when airplanes land, the 250 passengers get off the flight, and then the little truck comes up to drain the wastewater from the plane. And instead of just sending that more or less to a landfill, a sample of that is extracted and brought to our lab.

15:33And that could tell the folks at Ginkgo Biosecurity not just who landed, but also what landed with them. And to take it one step further, it's not just who landed and not just what they brought with them, but also where did they bring it from? And that's where you get into a kind of data and information that is especially interesting if you work in the intelligence community or national security because you're learning what is happening in other countries. So it's a way to gather a genomic landscape at a global level without having to deploy specific genomic surveillance in every location. So this is really powerful because it enables you to determine whether a virus or a biological agent is kind of originating from nature or it's created in a lab.

16:31because this distinction is important, right? Because it has obviously national security and biosecurity implications. Absolutely. There are three general threats from a biological perspective to let's just call it civilization or national security. Those three threats are things that are natural. It used to be that we would say that there was a 1 % chance every year of something that was kind of COVID scale. And I would say that most epidemiologists and other folks in the space would agree that it's generally around 3 % risk every year due to things like climate change and human encroachment on animal habitats, things like that.

17:09And, you know, 3 % every year, you know, adds up quickly. You do that over 20 years and it's a coin flip of whether we have another consequential flu or COVID-like event. So that's one type of threat. Another threat is a lab leak, which may also be natural. but were not intended to be consumed outside of a lab. And then the third risk is something that is genetically engineered and adversarial. And that is a thing that keeps the folks who know a lot about it up at night. And then the question is, if and when somebody uses something like that, how would we know? So not Ginkgo Biosecurity, but Ginkgo Bioworks developed a tool called Endar, which is basically a means by which you can look at a sequence of DNA and evaluate whether this was made by nature or by humans.

18:12Now, if you think about the computational task there, you're looking at something that has never existed before. And then the question is, does this look like something nature did or something that humans did? And that is the kind of thing that AI is really necessary for and really good at, because what it needs to be able to do is to look at the entire space of all nature in the world, all genomic information in the world, as well as the history of all genomic information in the world. I am fascinated by this idea of building micro-friendly kind of architectures and urban design. Tell us more about that and how do we bring that kind of thinking to our schools and homes and hospitals?

19:00I grew up in New York City in the 70s. Most of the buildings on the Lower East Side were all empty. Why were they empty? They were empty because in the 20s, there was a series of epidemics in New York, including tuberculosis, that were so serious and so prevalent that the city just said, okay, you know, the pathogen is definitely a problem. But the other problem is that people are living in such cramped conditions in environments that don't have circulating air, that don't have sunlight. And so they made a law that said every room in any place that you live in New York City needs to have sunlight and air.

19:36And at that time, the landlords, who were not wealthy people themselves, couldn't afford to make those changes to the buildings. And so they just kind of walked away. But it was illegal for anyone to live in them because they were so dangerous from a pathogen's prevalence perspective. We designed our water systems around cholera. We have always designed and redesigned the ways that we live around the biological threats that we have faced until COVID, where we mostly just shrugged our shoulders. It's a horrifying missed opportunity. There's so much that the microbes around us can say about our health and safety.

20:22And while there has been a missed opportunity since COVID to redesign our indoor spaces, I'm still hopeful. AI will accelerate our understanding of the pathogens and all other kinds of microbes in our environments. But there's a whole other microbe world living inside of us. We get information about them through the waste our body produces. and there's a lot we can learn by understanding them. AI could help. That's after a short break.

21:04Meet Nicole Nicholas, Capital One business customer and co-owner of Ansett Uncles, a plant-based restaurant and community space in Brooklyn, New York, that got its start from a need for unity. The inspiration, it was born from the desire to create a space that felt like home, where we can connect community culture, good food, and come together with family and friends. That's how we birthed aunts and uncles. Nicole and her husband, Mike, were fulfilling their dream of bringing people together out of their home kitchen. But they soon learned that the demand for community was greater than they knew.

21:35It became overwhelming and we were like, we need home, but not in our actual home. So we realized that there was also a need in our community for something bigger in our neighborhood. So we had to find a place. Moving from a home operation into a storefront was a huge next step. But Nicole and Mike were able to take it on with the help of Capital One Business. It's not for the weak. As a small business, finding resources is super important because that's the way you'll be able to manage and scale. We would have never done that without having Capital One to be able to help us along the way. The cashback rewards are very helpful.

22:10You know, it just gave us that runway to be able to breathe a little bit. Then you get to focus on the cooking of the food and making the experience great. To learn more, go to CapitalOne.com slash business cards. All right, let's switch to the microbes within us and how important these, because these microorganisms aren't just hanging out in our gut. They're actually really key to our energy production, nutrient production, our health and wellness. So tell us more. We're at the phase of knowledge production where we know that they are deeply consequential, and we know a little bit about some specific ones that matter.

22:51But we are still really untangling what does what. We need to pay more attention to it. the state of the human microbiome, which is very different than it was 100 years ago, is consequential to our outcomes and that that could be everything from our immune system to autoimmune diseases to who knows what. The first one I came across that felt very sort of concrete was there's a specific microbe Toxoplasma Gandhi that is in one out of three Americans. And if you have it in you, you don't know that you have it. It doesn't announce itself, but it will change your risk profile. You are far more likely to crash your car or become an entrepreneur or all the other things that involve poor assessments of risk.

23:40And so is that you or is that Toxoplasma Gandhi? You know, it's basically the interaction between you and something that you can't see. Each one of us is teeming with life and it's not neutral. It has very profound effects. And there's something called C. diff, C. difficile. You can pick it up in particular when you're in hospital and your immune system is suppressed. And C. diff doesn't necessarily kill you, but it's a very aggressive disease and it's wholly resistant to antibiotics. And the most effective treatment for it is a fecal matter transplant. There was a case about 10 years ago. These were some of the earliest fecal matter transplants for C.

24:19diff, right? So they used, in quotes, healthy poop to repopulate his gut. Having nothing to do with the C. diff, he also had alopecia. He had lost all of his hair. And there are lots of people who have alopecia and it's just a thing that happens. It's just a mystery. So here's a person who had alopecia and C. diff and they used healthy poop to address the C. diff and all of a sudden their hair started growing back. So we still don't really know what alopecia is, but now we know something about how it is produced. It has something to do with something in your gut. To me, this is where AI can play a really huge transformative role, right?

25:02Because the relationships between these microorganisms and the things we ingest and our biologies, It's so complex, and this is where AI can hopefully help map it out. I agree. The computational space is so vast, and I think that where AI can help is that it's in essentially being able to just notice patterns that would be otherwise invisible. And those patterns allow you to engage these data sets with a little bit better predictive power or far better predictive power. One of the areas that I'm really interested in is once you're able to really understand a person's microbiome and also like, you know, skin bio, right, oral biome, can you then use that to create personalized medicine, right?

25:53And maybe that's for me, like personalized probiotics. This is exactly the mix of things that I need to take. What needs to happen for us to get there? I think at a systemic level, it feels a bit far at the moment to me. Because we don't know enough. Yeah, we don't know enough. And because our interaction with the world, which changes our microbiome to some degree, is it is broadly stable in many respects, but it's not fully stabilized ever. And so then the question is, like, is the thing that you're taking this month relevant to what you should take next month? Will it be relevant if you move to a different part of the state or if you travel to another country?

26:35Probably not. I think the idea of personalized medicine is still built around the idea of a discrete individual. And here we're talking about a kind of collection of organisms that's in flux and will remain in flux. So that is a vexing problem. Yeah. And to me, it also comes back to, I mean, absolutely, yes. And what kind of sensing technology, like how are we collecting that data, right? Because if you are getting a, I don't know, a stool test every three months or a blood test every six months, to me, it's not dynamic enough. Like we're not getting enough sample points. Yeah. Yeah. And really, stool is, you know, poop is really the only single best way to find that out.

27:22And, you know, yes, there are smart toilets that all, you know, those exist. They will continue to exist. They will get smarter. And that is not the Japanese type of smart toilet that can change temperature and stuff. This is actually a toilet that can analyze your. Yeah. Yeah. I would call those those other ones kind of wise toilets. Those are toilets that can help your mood. But smart toilets basically can do the kinds of essentially genomic surveillance on your own stool. It's certainly possible to do that for things that are targeted, like if you're looking for specific things, which include cancer.

27:59But the idea of being able to pick up things that you weren't looking for, it's still a serious computational task. and the types of extraction that need to happen for that won't be built into your toilet this year. Well, if any of our listeners are working on these smart toilets, please do reach out. We'd love to learn more. I mean, actually, to one of your earlier questions about how pathogens have shaped the environment, it's a fundamental dynamic that the overall efforts, in particular in the United States, but globally, to just reduce the number of microbes to which we are exposed has done what they wanted it to do.

28:41But it also did a bunch of things that we didn't want it to do, which is basically reduce the diversity of the microbes in our guts and our skin and our mouth. We need better tools to be able to evaluate why that matters. It may well be that if we've eliminated our exposure to n number of microbes, maybe that's okay, except for the following seven. But we don't know yet. And that is really the edge of the edge. And if we are ever able to answer that question, it will be because AI has become powerful enough to do so. Yeah, amazing. Okay, last question. If you could have AI do anything in the world for you, what would you have it do?