The Daily - Is the Future of Medicine Hidden in Ancient DNA?

Episode Date: January 31, 2024

In a major advance in science, DNA from Bronze Age skeletons is providing clues to modern medical mysteries.Carl Zimmer, who covers life sciences for The Times, explains how a new field of study is changing the way we think about treatments for devastating diseases.Guest: Carl Zimmer, a science correspondent who writes the Origins column for The New York Times.Background reading: Ancient Skeletons Give Clues to Modern Medical MysteriesMorning Person? You Might Have Neanderthal Genes to Thank.For more information on today’s episode, visit nytimes.com/thedaily. Transcripts of each episode will be made available by the next workday.

From The New York Times, I'm Sabrina Tavernisi, and this is The Daily. In a major new advance in science, DNA from Bronze Age skeletons is providing new clues to modern-day medical mysteries. Today, my colleague Carl Zimmer explains how a new field of science is changing the way we think about treatments for devastating diseases. It's Wednesday, January 31st. So Carl, you are a science reporter, as our listeners will know, and you write about evolution and the origins of life. And you've recently written a story that really piqued my interest. It was about a major new discovery in our understanding of ancient people.

And it's leading to some big advances, as I understand it, in modern medicine. So tell me about it. Well, scientists have been wondering about two big questions for a long time. One of them is, why do we get sick? The other question is, where do we come from? And they seem like they should have two very different answers. But now scientists are starting to realize maybe the two questions actually have the same answer. The same answer how, Carl?

Well, it's possible that in order to treat the diseases we have to deal with today, diseases often that have no treatment yet, it may be necessary to go back thousands of years and look at how our ancestors lived then. What were the challenges they faced? What was their health like? What kind of genes did they carry? And maybe we can then come back to the present and start to be able to make our own health better. And now researchers have just made some really big discoveries, both about human history and about our diseases at the same time. And this history actually lives inside of us right now in our own genes and has big implications for our health. Okay, so two branches of science coming together, as you say, making some major new discoveries. So tell me about this first field of science, Carl.

What's happening there? Well, you know, once upon a time, if you wanted to study ancient life, you were pretty much limited to fossils. You know, after an animal or person died, their bodies decomposed. And if you're lucky, their bones managed to survive and rock. And then thousands or millions of years later, a paleontologist would come along and dig those fossils out. But now, it is actually possible to dig up those bones and to drill a little sample out of them and find some DNA still surviving in it.

So this actually gives you a glimpse into, you know, the molecular life of these ancient people or ancient animals. And it's amazing enough when scientists can get just a single gene out of a fossil that's thousands and thousands of years old. But actually, the science has come so far in recent years that it's pretty common for scientists to get a whole genome of an extinct species. That is, like like every single gene, every stretch of DNA reconstructed pretty accurately. Once you can look at the whole genome

of some ancient organism, you are really starting to get the big picture of how that thing lived. And looking back at our own past, we can actually use this ancient DNA from fossils to figure out some clues about our ancient relatives going back a couple hundred thousand years, actually. And this includes ancient relatives like Neanderthals, for example. So now we can actually see an entire genome of Neanderthal. But more recently, what's been really spectacular is actually how scientists have been able to focus on the past 10,000 years. And what we're talking about there is that time in history where hunter-gatherers started to domesticate animals and plants and start to farm,

when you started to have the first towns, when you started to have first large-scale societies. And we can actually go now and see what the DNA of these people look like. Actually, we can see thousands of people from this time period. Okay, so we're really getting a clearer picture of how groups of ancient peoples came to be and live their lives many, many years ago. But how specific is that picture? Like, what does it look like? What are some of the things we're learning, Carl? We're learning about all sorts of things about these people's lives by looking at their DNA. I mean, some people today, you know, they can drink milk and be fine with that. And some people are lactose intolerant. Well, we can actually look back at the DNA and say, who was lactose intolerant among ancient farmers 8,000 years ago. We can say that. We can start to actually get clues about the color of the skin of people who lived 10,000 years ago. We can figure out how societies were organized. When

you come across a burial with several skeletons in it, when they all have jewelry on it, you can actually show genetically if they're related or not. And that might tell you you're looking at, say, a royal family. And on top of that, look at how these different groups of people with certain genetic markers moved around, how they expanded from one place to another, how two populations might interbreed. So there's an astonishing amount that you can learn now from ancient DNA. So we're basically seeing the stories of different groups of people over time. Yeah, that's right. And there are groups of people that we didn't really know much about before. People who existed thousands of years ago who now we're realizing were actually really important to the course of history. And one of those was actually a group called the Yamnaya.

Okay, Yamnaya. That is not a group I am familiar with, not a household name. Well, archaeologists have known about the Yamnaya to some extent for decades, but they couldn't really say that much about them. What has become clear now is that the Yamnaya were living, you know, maybe 6,000, 5,000 years ago.

They started out as farmers, but they actually gave up farming because they developed this practice of herding cattle and sheep and goats, and they were incredibly successful at this. And they were among the first horse riders. They would use the horses and other livestock to haul wagons, and they would just go across hundreds or thousands of miles of the steppe from the Ukraine all the way over to Central Asia, to places like Kazakhstan. They went from roaming around to exploding across Europe and Asia. And when they showed up, they took over.

And you can see this actually when they arrive in Denmark, for example. Scientists have looked very closely at the DNA in Denmark from skeletons over the past 10,000 years. And you can see that there's a group of farmers there with a certain kind of ancestry. And then, boom, the Yamnaya show up about 5,000 years ago. That's it. It's all Yamnaya. So they showed up in northern Europe from Central Asia and at some point became the dominant population. That's right. We don't know exactly how that happened. There are some very dark possibilities.

This could have been some kind of genocide, or maybe it wasn't such a violent transition. Maybe it was a competition for land that took decades to play out. But in any case, we know that the Yamnaya became the people of the region, and then they became the ancestors of people in Northern Europe today. People today with Northern European ancestry, they come from the Yamnaya. And Carl, why are these people important? I mean, why are we talking about Yamnaya in the context of this genetic stuff? people important? I mean, why are we talking about Yamnaya in the context of this genetic stuff? Well, in addition to being really important to the course of history, they actually matter to us today. Because locked inside of their DNA 5,000 years ago are some really crucial secrets about some of the most devastating diseases we suffer from today. We'll be right back.

So, Carl, you said that this new science was showing us something important about these Yamnaya people, and it had to do with disease, this little code locked inside their DNA. Tell me about that. So this brings us to the second field of science I was talking about, which is the basic question of why we get sick. We get these diseases and they seem to have all sorts of just random symptoms. But if you can understand their history, if you can understand their evolution, maybe they're not as random as they seem. Maybe by understanding their history, we're going not as random as they seem. Maybe by understanding their history, we're going to be able to treat them. Okay, so this is these two fields of science coming together, like a kind of, you know, scientific chocolate, peanut butter, Reese's peanut butter cup. But what's the process once they come together? Like, how do you study disease in ancient people? So on the one hand, you have some scientists who are looking at the DNA of living people

and finding different variations in their genes that put them at risk for certain diseases. There are genes that can raise your risk for heart disease, for cancer, for schizophrenia, for all sorts of conditions. And scientists have actually been able to create pretty long lists of these genes where there's strong evidence that if you have a certain version of a gene, you are at a greater risk of getting these diseases. And so these scientists who are pulling ancient DNA out of bones that are 5,000, 10,000 years old are saying, well, let's see if these people who lived thousands

of years ago had those genes too. When did these mutations arise and how did they spread? Let's trace the whole history of these mutations that today put us at risk of different diseases. So how exactly do they do that? Well, one of these projects is based on a British database called the UK Biobank. What happens there is that half a million volunteers have submitted their DNA and allowed scientists to compare their DNA to their own medical records. And so that they can see links between their genetic variations and the kinds of diseases they're suffering from. So basically these scientists are tracing the diseases people have to mutations in their genes and looking for patterns across populations. That's right.

And so then what you can do is you can compare their DNA of these living people in Britain to all of this ancient DNA from across Europe and Asia. And you can try to figure out, well, where is their DNA coming from? Who did they inherit their DNA from? And did they actually inherit some of these disease genes from those ancient people? So it's kind of like a 23andMe to figure out who you were related to in the Bronze Age, right? And whether they passed down anything to you that might make you sick now. That's right. And what they found were mutations that today we know increase people's risks for a whole bunch of different diseases. But with a

twist. Some of these mutations were beneficial to those people thousands of years ago. Okay, that is kind of mind-blowing. Okay, so explain that to me, Carl. What's an example? So we can go back to the Yamnaya for a really powerful example of this. So the Yamnaya were herding animals. They were with their animals all the time. They were just going back and forth along the steppe, always with the animals.

And that was great because that gave them a source of meat. It gave them a source of milk, of leather, wool, like this incredible resource to have right on hand. But animals have something else. They have diseases. And so if you're going to be living with animals, you are actually at risk of picking up some of the diseases that they're carrying. So, Carl, were the Yamnaya the first people to actually live with animals and then therefore get sick from them? to actually live with animals and then therefore get sick from them?

Well, the Yamnaya were getting diseases from animals at a rate that was really different than people had before because they were living with these animals so much of the time. And we actually know that because we can see it for ourselves in their bones. When you drill into the bones of the Yamnaya or other ancient people, you can get out the DNA of the people themselves, and sometimes you can also get the DNA out of the germs that killed them. Hmm. Amazing. It is amazing, and we know for a fact that they were dealing with a lot of diseases,

and it turns out that they were actually evolving a resistance to them. Evolving a resistance to them how exactly? So if you had a mutation that ramped up your immune system so that you were better able to fight off these germs that were spilling over from these animals all around you, that would mean you're more likely to live long enough to have kids and pass down that gene to them. So if you look across the DNA of Yamnaya, they have a lot of mutations for the first time that are associated with a really strong immune response. But there's something else that's really important about these genes in the Yamnaya.

These are some of the same genes that today can put people at risk for certain diseases. One of those diseases is multiple sclerosis. Multiple sclerosis, like very debilitating disease. That's right, yes. When people develop multiple sclerosis. Multiple sclerosis, like very debilitating disease. That's right, yes. When people develop multiple sclerosis, their immune cells look at their own nerves as the enemy. They actually will attack the nerves in the body.

And this is incredibly debilitating. It can progress to the point where people can't walk, have trouble talking. You know, to the point where people can't walk, have trouble talking. It affects millions of people today. And yet we're seeing some of the genes that put people at risk of MS today actually being beneficial in the Yamnaya. Okay, so explain that, Carl. How was it protective to the Yamnaya, but obviously very debilitating and problematic today? Like, how did that happen? So if we go back to the Yamnaya,

four or five thousand years ago, they are being exposed to a lot of diseases, a lot of bacteria, maybe a lot of viruses. Now, recently, like in the past century, a lot of those pathogens have gone away. So you have pasteurized milk, you have clean water, you have all these innovations that make these pathogens much less of a threat to people's health. But they still have this aggressive immune system. They

still have an immune system that evolved for this tug of war with the pathogens. And now if the immune system is not being continually challenged by these pathogens, it looks like sometimes the immune system makes mistakes. In its aggressiveness, it misfires so that there are opportunities to get confused and to start to look at a person's own body as the enemy. Okay, that's pretty interesting that like something that was so protective through the ages suddenly becomes a real hindrance because everything changed really in the past 100 years or so. But how exactly does knowing this actually help people who have MS today, Carl? What are the practical implications here? Well, it helps us to understand why it is that some people get MS and other people don't. Recent research has pointed to a virus called Epstein-Barr as the trigger for MS. In other words, you probably don't get MS unless you get infected with Epstein-Barr. But the fact is that most people get infected with Epstein-Barr,

and maybe a couple million people have MS. So clearly, there's something special about these people. And what's special is that they have inherited these genes. And if you can understand how those genes first evolved, what their functions were for 5,000 years ago, that can actually help you to understand how they're going wrong now. So, you know, right now there are some, you know, fairly effective treatments for MS. They're okay for some people. They're not great for others, but they're crude. They're kind of like a sledgehammer. Basically for others, but they're crude. They're kind of like a sledgehammer. Basically, they just sort of take the immune system and just dial it all down. That's good in some ways because then your immune system is not going to be attacking

yourself so readily. But you do need your immune system. You actually do need it to avoid getting really sick from infections. So really what we need to do is find a better balance. We need to understand that what's happening is that the immune system just has lost this partner in this dance of survival. And so how can we mimic that? Are there drugs that could actually, like, give the immune system that balance again without us having to get really sick and things like that? Okay, so understanding the origins means we go from treating MS with this big sledgehammer to a little scalpel, right? We can really fine-tune the treatment.

That's right. fine-tune the treatment. That's right. And we start to understand, you know, why different people are at greater risk of getting MS. You know, why are the rates highest in Northern Europe? You know, people came up with all sorts of stories for a long time, but we actually know why. We know because the yumnaya showed up. So it takes some of the randomness out of it, right? This research has really helped us understand something incredibly important about this very debilitating disease. It has. And this is really just a trial run for this whole approach. This research was based just on the UK biopank, just on people in Britain. But when we look forward, it's not just going to be British people whose history scientists are going to be unpacking.

It's going to be people all over the world. We're going to be learning not just about multiple sclerosis, but we're going to be learning about diseases like heart disease, diabetes, conditions like schizophrenia. And it may be possible to understand how it is that actually maybe the genes that put us at risk of these diseases today were giving us other benefits thousands of years ago. So in effect, we could be sitting on a whole new cache of future cures, right, in all of our archaeological sites. Like, is the future of medical research paleontology? It could be. It could be. This is what scientists sometimes call evolutionary medicine.

But really, up till now, it's been more of an idea than a reality. But the experts I talk to say that with ancient DNA research like this, evolutionary medicine is now finally coming of age. Carl, thank you. Thanks so much. We'll be right back. against Homeland Security Secretary Alejandro Mayorkas. Republicans are poised to charge Mayorkas with refusing to uphold the law and with breaching the public trust in his handling of a surge of migrants across the U.S. border with Mexico. Democrats and many legal scholars say the committee has not produced any evidence that the secretary has committed an impeachable offense. Even if the House votes to impeach Mayorkas,

he is not likely to be convicted or removed by the Democratic-controlled Senate. But the action could force an election-year trial on the politically charged issue of immigration and the southern border. And Hamas said it was considering a proposal to pause the fighting in Gaza and exchange Israeli hostages for Palestinian prisoners. The deal's terms were finalized in Paris over the weekend by the United States, Qatar, Egypt and Israel, and involves a six-week ceasefire in exchange for the release of more hostages.

release of more hostages. In a statement, Hamas's political chief, Ismail Haniyeh, suggested that the group was open to the deal, but also reiterated its longstanding demand for a total withdrawal of Israeli forces from Gaza, one that Israel has repeatedly rejected. Today's episode was produced by Alex Stern and Jessica Chung, with help from Shannon Lin and Carlos Prieto. It was edited by M.J. Davis-Lynn, with help from Mark George. Contains original music by Chelsea Daniel and Dan Powell, and was engineered by Alyssa Moxley. Our theme music is by Jim Brunberg and Ben Landsberg of Wonderly. That's it for The Daily. I'm Sabrina Tavernisi.

See you tomorrow.