Long-awaited ape genomes give new insights into their evolution — and ours
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The fact that my bed actually listens to my body and adjusts to my needs to keep me sleeping soundly all the way through the night is worth it alone. Not to mention my husband and I never need to argue over firmness because we can each dial in our own sleep number setting. Why choose a Sleep Number Smart Bed? So you can choose your ideal comfort on either side. And now, for a limited time, Sleep Number Smart Beds start at $849. Price?

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Welcome back to The Nature Podcast. This week, the complete sequencing of six ape genomes. And laser plasma particle accelerators get closer to reality. I'm Benjamin Thompson. And I'm Sharmini Bundel. First up on the show this week, reporter Adam Levy has been finding out what sequencing ape genomes tells us about them and also about us.

What makes humans humans? What do we have in common with our closest kin and what sets us apart? Well, to answer that question, we need to look at the group of species that contains our closest relatives, the apes. Apes include chimpanzees, bonobos, gorillas, gibbons. We are also apes. Many people are really confused about this. Yeah. Or don't want to accept this, which is even worse. Yeah. I don't know.

This is biologist Katerina Malkova. To understand the evolution of the apes, including ourselves, we need to understand the genomes, the complete genetic codes of different species. Studying the genomes of non-human apes can provide information about what makes us human,

and provides additional information about parts of our genomes, our DNA sequences that are important for diseases.

Okay, so you can probably see where this is going. Katerina and her colleagues are clearly interested in ape genomes, and this week in Nature, they've published the sequence genomes of six non-human ape species. Chimpanzee, bonobo, gorilla, two species of orangutan, and siamang. But

But given we've sequenced the genomes of so many animal species, why don't we already have them for these apes? Well, it turns out we do, but not in their complete forms. Here's Lucas Kudana, who didn't work on the study. The first ape genome came out actually quite shortly after the initial human genome sequencing was declared finished, let's say.

The genomes for apes that we had until now had substantial portions excluded because they're just very difficult to reconstruct. But that essentially meant that understanding how these portions evolve, we weren't able to say until now. And that's exactly what sets this new study apart. Our goal was quite ambitious. We wanted to assemble the genomes completely without any gaps.

But why is reading the complete genetic code such a challenge in the first place? As a physicist, I've always imagined the process to be fairly straightforward, like reading a book. But it turns out that reading the repetitive regions of a genome, sections of DNA that have a lot of, well, repeating sequences, actually involves piecing together a

puzzle. Previously, to assemble the genomes, we were using short sequencing reads. And these reads were able to read DNA in small chunks. For example, 300 DNA letters at a time. What we can do now is to use long sequencing reads. Hundreds of thousands of letters at a time. This allows us to

to put these larger chunks together easier. The analogy we use for assembling the genome is assembling a jigsaw puzzle. It's very difficult to assemble the repetitive parts of the puzzle, but if the puzzle has a small number of large pieces, then these regions are much easier to

put together. And so, using this approach, the team have now published the complete genomes of six ape species, including the repetitive regions which had previously eluded researchers. Only now we can truly appreciate all the different components of our genomes. So we now know that more than half of the genomes of apes consist of repeats. More than half. Much more common than we thought before.

Uncovering the entire genetic code of these six non-human apes hasn't been easy. The idea was born in the early 2020s, and the team has spanned borders and disciplines. Some collaborators contributed samples, some other collaborators provided sequencing data, and yet others participated in putting these assemblies together computationally and running the analysis.

For Lucas, this work is a milestone, not so much because it provides answers, but because it provides an opportunity for researchers to pose a host of new questions about the evolutionary history of apes.

It's very impressive. I mean, it's clearly the result of an enormous amount of work. Really, it's just a great resource for the community, opening the door to countless new research avenues that could be based on these assemblies. The study already hints at certain research avenues. The paper describes very repetitive genes that are important for immune function in apes, and so could have important medical implications in humans.

The study also outlines plenty of differences between the genomes, potentially paving the way for a better understanding of what makes the different species unique, including what makes us humans.

How that translates to a set of changes that differentiates us really from other apes is, I would say, an open question. But these are very good candidates to understand some of the more unique changes within all the ape lineages, including us humans. So there are plenty of questions researchers can now pose with these complete genomes.

But as far as actually sequencing the genetic code of apes is concerned, is it now case closed, job done? I mean, the job is, I would say, in science never really done. So it's just a next step to the next question. One continuation of the job is to completely sequence the genomes of multiple individuals from each species so that researchers can understand the variation both between and within species.

We also need to expand this complete genome sequencing to other apes and to other primates to be able to understand what makes apes apes at the level of DNA.

So, of course, science never sleeps. There's plenty of work to be done to truly uncover the secrets within these ape genomes, as well as to expand the set of complete genomes so that we can pose even more questions. But for now, both Lucas and Katerina are celebrating this milestone in understanding our closest relatives and us.

Obviously, it's a monumental manuscript. There's tons of information and there's tons of details. For me, I mean, it's fantastic to see the quality of non-human primate genomes being elevated to the same level that we have gotten used to in human, which will really enable a full comparison of all the parts of the genome. I think it's very exciting. I honestly thought that this would never be possible in my lifetime.

we finally can come up to some conclusions about the evolution of these genomes because we have the final data for these individuals.

That was Katerina Markova from Penn State University in the US. You also heard from Lucas Koderner from the biotechnology company Illumina, also in the US. To read Katerina's paper and a News & Views article Lucas has written to accompany the research, check out the show notes for some links. Coming up, how to make a new kind of particle accelerator compete with more conventional kinds. Right now though, it's time for the Research Highlights with Dan Fox.

An enormous, many-limbed creature called a sunflower star has found a place to hide itself and escape a mysterious epidemic.

Sunflower stars can reach one meter in diameter and have as many as 24 arms. But the star has no defense when exposed to star-wasting disease, which causes it to disintegrate in just a few days. The cause of star-wasting disease is unknown, but since 2013, it's claimed 90% of sunflower stars worldwide, leading the species to be declared critically endangered.

Researchers compared sunflower stars near islands off the coast of British Columbia in Canada with those living in coastal fjords. They found that populations at the islands had declined significantly. However, in the fjord's deeper, colder reaches, where the stars ventured to avoid glacial runoff at the surface, populations remained stable, showing signs of disease but without high mortality.

The scientists think that high temperatures might accelerate the disease's progression and that fjords might provide a safe haven from the epidemic, making protection of these areas crucial for the animal's survival. You can find that research in Proceedings of the Royal Society B. Solar panels made of moon dust could be a low-cost solution to powering a future lunar base.

To survive in the harsh environment on the Moon, solar cells need to be encapsulated in glass, which tends to make them heavy and expensive to launch into space. To tackle this, a team of researchers made moon glass by melting simulated lunar soil in a furnace. On the Moon, this could be done using concentrated sunlight.

The team then added a layer of perovskites, which are highly efficient at turning sunlight into electricity. These and other materials in the cells made up just 0.6% of the device's weight. The rest was moon glass.

The device could convert 12% of incoming sunlight into energy and remain deficient after exposure to radiation equivalent to eight years on the moon. The researchers say that when combined with moon glass, just one kilogram of perovskites brought from Earth could be used to create 400 square meters of solar panels, roughly the size of a basketball court.

If you're over the moon hearing about that research, you can read the full paper in Device. Next up on the show, researchers have shown that, in principle, they can make a long-sought kind of particle accelerator work as well as the alternatives currently in use.

Right now, many particle accelerators are known as radio frequency, or RF accelerators, which are part of some famous experiments you've probably heard of, such as the Large Hadron Collider.

And while such accelerators have led to some huge discoveries, they have their limits. So researchers have been working on alternatives, like accelerating particles using the powerful electric field made by a plasma. But despite being successfully demonstrated more than 20 years ago, it's been hard to get this type of accelerator off the ground.

Now, though, a team writing in Nature demonstrates a proof of principle of a laser plasma accelerator that produces a beam stable enough to compete with the performance of a radio frequency accelerator. Reporter Nick Petrichow spoke with one of the authors, Andy Meyer, and asked him a bit more about how current radio frequency accelerators work.

So you have two metal plates, put some voltage in between, and if you have a charged particle passing through it, it requires some energy and thereby gets accelerated. And you can repeat this many, many times and thereby get to high and high energies. There's a limit to it. If you put the voltage to 11, then boom, you know, the forces between the plates will break down, so it doesn't work anymore. So there's a natural limit to it, which in the end limits the energy.

the size of the accelerator. And does that size limit them in any other way? Yeah, not necessarily. I wouldn't say limit. It's just that this technology has been around for, I don't know, 100 years, probably, give or take, and it's basically maxed out. So people have built all the applications using this technology that are possible or economically sensible.

But if you now can change one of these properties often of the accelerator, then you probably can rethink

what you can do with hot accelerators. And so that brings physicists like yourself to the idea of laser plasma accelerators. What's the idea behind these? How do they work? A plasma as we use it is a hydrogen gas where we completely remove the electrons from the ions. So what we have is a static ion background and then sort of an electron gas that floats before the static ion background.

And now if you shoot in a very, very, very powerful laser pulse, this laser pulse, you know, a little bit like a snow plow. It pushes electrons to the left and to the right, and it trails a cavity that is void of electrons. But in essence, you have the laser that trails this plasma wave. And in this plasma wave, there's very, very high electric fields.

that you can use to accelerate an electron, for example. And so, in principle, this is working in a very similar way to the radio frequency accelerators. There's differences in charges, and that allows a charged particle, like an electron, to basically be shot very quickly. Exactly. So you need electric fields that are super strong, and the radio frequency accelerators can go up to a certain point before things break down, and then afterwards you can use plasmas that support

Fields even stronger than that and then continue to accelerate. And what would be the advantage of these kind of laser plasma accelerators versus the more conventional radio frequency ones? The fields are a thousand times stronger roundabout. So to get to the same energy, you can build the accelerator a thousand times shorter, which is huge. Like if you do the numbers, you can go from kilometers to meters.

to like big accelerators are easily like one, two, three, four kilometers long. And if in principle you could shrink that down to a couple of meters and put it in your lab in a basement, that's pretty cool. Now, this is a type of accelerator that people have been working on for about 20 years at this point. What have been the main challenges to actually getting this to be a viable technology? So our biggest advantage is our biggest weakness, if I can say that. So

Radio frequency accelerator structure is like on the order of a meter or two. You can think about a finely manufactured metal tube and it's polished and it's with high accuracy build and so on. And then you build it and connect it to your radio frequency electric fields and then you can use it for accelerating over and over and over again, billions and billions of times.

So what we do with laser plasma acceleration is super stupid because we build a new accelerator with every shot. So every laser pulse that we shoot into the plasma creates a new plasma cavity that we then use to accelerate particles. So the big challenge is to make the acceleration reproducible from shot to shot because the structures now instead of meters are micrometer scale, so much, much smaller.

And to make these structures reproducible and therefore the properties of the electron beams reproducible is much, much more challenging. And so in your new paper, you've taken a different approach with this, or maybe it's better to say you've combined a few different approaches. What have you done exactly to try and resolve this issue? So I'm at the EASY, which is the National Accelerator Lab. And obviously the majority of people here are working on radiofrequency accelerators.

But we try to learn from them as much as possible and try to adopt their proven techniques to our field. And I think this is really where the fun starts, this interface of modern accelerator technology and plasma technology. And so we rediscovered an old trick. And so we came up with a technique that uses actually RF accelerator cavities.

to improve the energy stability of our electron beam from the plasma quite dramatically so that in combination it's now comparable in performance to radio frequency based accelerators. So we basically get the best of both worlds. We keep the compactness of

of the plasma acceleration but with a little bit of extra radio frequency accelerators we can get their stability. And so what precisely is it that you were taking from the radio frequency world to try and get that extra stability here? What's the key thing? Our

electron beam has a certain energy spread so the electrons sometimes have a little bit more and a little bit less energy and then what we do is we use a specific setup that we call a magnetic chicane and stretch the electron bunch in time when it's energy sorted we then send it to the RF cavity and the RF cavity gives it a position dependent kick so the electrons that have too much energy they get a little bit decelerated electrons that have too little energy get a little extra kick and overall

Basically, we cancel out the energy deviation. And this is something actually that has been used with RF accelerators, I think back in the 50s, when radio frequency accelerators had not yet the performance as they had today. The guys back then used a similar trick.

Basically, we rediscovered this technique and now apply it to plasma accelerators. So you're basically evening out the spread of energy and bringing everything back together at the end to make a more stable beam. And so is this now mission accomplished? Like, there we go, plasma accelerators fixed. They totally work now. Is there more to do? Actually, so we made the first step.

So before that, the typical performance of a plasma accelerator was on the order of a few percent energy spread and energy jeta. I think with our proof of concept experiment, we demonstrated that in principle, these beams do exist. And a project that we actually started earlier this year is to build a prototype. So we build up on the experiments that we describe in the paper and now build, if you want, the real thing. That was Andy Meyer from DayZ in Germany.

For more on that story, check out the show notes for a link to the paper. Finally on the show, it's time for the briefing chat where we discuss a couple of articles that have been highlighted in the Nature Briefing. And I've got a story for you this week that I've been reading about on Science Alert from a paper in Science Translational Medicine.

And it's basically about poisoning mosquitoes with human blood. Right. I have many questions about this. Let's start at the start then. Well, human blood, not usually, I will say, poisonous to mosquitoes. In fact, they rather like it. And, you know, you may have heard of the fact that mosquitoes are the animal responsible for the most deaths

in the world because of course of all the diseases they spread malaria being a particular big one right and there's lots of ways that people are trying to get rid of mosquitoes really to try and thus reduce malaria transmission and one idea that's been around is okay well what if

Right, so mosquito control obviously is a big part of trying to reduce malaria transmission. That often involves spraying pesticides, this sort of thing. But this is

I guess, seemingly coming about it from rather a different angle then. How does it work? So this particular paper has basically looked at a drug called netizanone.

And the good thing about this is it's a drug that's already being used by some people. It's approved for treating certain rare inherited diseases. So there are people already taking this drug. So one of the things that the researchers did was looked at people who are taking this drug, got mosquitoes to feed on them to drink their blood.

And they found that the mosquitoes died within 12 hours. So this is a substance that mosquitoes will die if they drink blood with it in. Right. So rather than being toxic to humans, it's toxic to the female mosquitoes that are biting them. Yes. And they looked at which mosquitoes were killed because apparently the older mosquitoes are more likely to be carrying malaria. So they made sure that the drug was effective there.

killing mosquitoes of all ages. They did some mathematical modelling to find out if you had different doses, how long it might last in people, what would you need to actually have these effects on the mosquitoes. And they were comparing it to an existing drug, ivermectin, which you might have heard of. Now, ivermectin can do the same thing. It can potentially kill off the mosquitoes and

as they're feeding on you if you're taking ivermectin. So they wanted to compare netizanone to this already existing drug and see if it was any better. And they found that you needed higher concentrations of netizanone in order to kill the mosquitoes, but netizanone will act more quickly. So often within a day, the mosquitoes will die. And it also sticks around in the human blood for longer. So it's more likely then that a mosquito is going to be exposed to it. Well, that sounds like a positive thing.

outcome. Shalmini, obviously this is presumably quite an early trial. What happens now? Well, it's proof of concept stage. And, you know, there are other things that need to be looked into. So in previous examples of people looking for these kind of drugs, using these drugs to kill mosquitoes, they've had problems with the drugs themselves.

killing other insects in the ecosystem so maybe like vital pollinators they don't think that's happening here but that's a potential worry you've also got to look at in the real world will something like this actually reduce malaria rates and another worry is what about insecticide resistance what if the mosquitoes over time start becoming resistant to this so yeah a lot more steps

needed to actually see whether this could have a significant impact. Well, combating mosquitoes and malaria is something we've covered a lot on the podcast. You and I have covered it a lot, everything from potential vaccines through to a rather potentially unusual way of doing it, as you've described here. So one for us to keep an eye on. But for the time being, let's move on to our next topic.

story today and it's a story that I read about in nature based on a nature paper and it's all about Minecraft. Minecraft is of course a video game, a cultural phenomenon. I don't think it's unfair to describe it. There's a movie that's out right now which is apparently super popular. I see I've not played

Minecraft, I'm not a big video games person, but I've seen sort of, you know, like younger nibblings playing it, Little Nephew. It seems very popular. Oh, it is hugely popular. In fact, I bet there are people playing Minecraft while they're listening to us talking right now. But for listeners who maybe aren't as familiar with it then, so Minecraft, it's kind of a sandbox game, right, where you're dropped into this sort of blocky world, all sorts of different terrains. You can build things, you can craft items, you can go on adventures, you can just sort of

chill out and create stuff if you want. And this story is about an AI system, right? And it's about how an AI system has, for the first time, figured out how to collect diamonds in Minecraft without being shown how to play. Ah.

Oh, I have no context for collecting diamonds. Is that something that's hard to do in Minecraft? Yeah, it is hard to do. Now, diamonds are super useful in Minecraft, but getting them requires multiple steps. And a team from Google DeepMind has developed this AI system called Dreamer, which has accomplished this. Now, I think what's important to know here is that

No two Minecraft experiences, no two Minecraft games are the same, right? You can start a new game and it will be totally different from the last one, right? It's essentially a randomly generated world. Now, this is useful because it challenges AI systems...

that researchers want to make that are able to sort of generalise solutions to problems. It's not just they can solve a solution to a problem and then flounder everywhere else. So the world changes so much that it's helped them test this AI system. Yeah, so I mean, you know, I imagine that the scientists behind this aren't purely aiming to end up with an AI that can play Minecraft. There's a sort of general principle here. Presumably, it's not just science.

them telling the AI what to do. I'll follow these steps. Then at the end, you get diamonds. Absolutely right, Sharmini. So previous AI systems that have been designed to collect these diamonds have relied on watching videos of humans playing or being led through each step by researchers. And it is a multi-step process. Like, for example, to start off with, you have to break down trees to get wood, use the wood to make

a crafting bench, use some more wood to make a wooden pickaxe, collect some different things, blah, blah, blah, blah, blah. So multiple steps to assemble the correct tools to collect a diamond. And these are buried deep underground in the Minecraft.

And this system, Dreamer, explores the game on its own using a trial and error technique called reinforcement learning. So it identifies the actions most likely to get rewards and discards those that don't. Now, reinforcement learning has been used quite a lot in AI research, but it tends to end up with systems that are quite specialist and can't transfer their knowledge to new things.

Now, the key to this system is that Dreamer imagines, in heavy inverted commas, imagines the world and the future scenarios. And this helps guide its decision making. So like if I chop down a tree, I might get some wood. Right. That's sort of the imagination it's using there. And this allows it to try things out and predict the potential rewards of different actions. But using less computational power, there would be needed to actually do them all right to figure it out.

And in addition to that, the team behind the work give the AI a plus one, like a little bonus every time it completes one of the steps involved in diamond collection, right? Everything from creating planks to making a furnace, mining iron. And this helps prompt Dreamer to select actions more likely to lead to a diamond. Okay, now...

It's not that straightforward, though. The team reset the game every 30 minutes so that it doesn't become accustomed to this one situation and has to kind of think on its feet. And in testing, it took about nine days for Dreamer to find at least one diamond, while an expert human player can do it in about 20 minutes or so. But the expert already knows how to find the diamonds, I guess, that this AI is learning how to play Minecraft, learning how to...

do all these steps sort of reinforced as it goes by the researchers giving it these little points. And as you alluded to earlier on, really, the aim of this isn't to make an AI that's really good at Minecraft.

In the article, it says that the diamond challenge really was an afterthought. But they realized that this was a good way of testing out their algorithm because things are never quite the same. And it seems like other researchers are quite positive about this development and what it represents. And it's hoped that results like this could eventually be used, for example, to help robots teach themselves how to achieve a goal in the real world with kind of minimal assistance from humans.

It's always fun when the researchers are using computer games to help develop their science. Computer games are just designed for fun and entertainment and challenging the mind and being used to usefully challenge the AIs as well, which is great. So thanks, Ben, for that. And

We'll put some links in the show notes to those stories and also where you can actually sign up for the Nature Briefing, where you get more stories just like those, but directly in your email inbox. And that's it for this week. But before we go, a little bit of good news. A few of our podcasts got shortlisted for Webby Awards. Ooh.

Yeah, I know, right? Very, very pleasing indeed. Award nominated. Yeah, absolutely right. And as well as the judges' awards, these shows are also up for what's known as a People's Voice Award. And what we need is the help of listeners, listeners like you listening right now, to vote for us. It'll only take a couple of minutes, and we'll put links on where to do so in the show notes.

Brilliant. And as always, if you want to keep up to date with what we're up to, you can follow us on X or Blue Sky, or you can get in touch. You can send an email to podcast at nature.com. I'm Shamini Bundel. And I'm Benjamin Thompson. See you next time.

I don't know about you, but the number one thing I look forward to when I return from traveling is a good night's sleep in my own bed. That has never been more true than it is now that I have a Sleep Number smart bed. I get so sore after traveling on planes, but after literally one night in my Sleep Number smart bed, my body feels restored, rested, and relaxed.

The fact that my bed actually listens to my body and adjusts to my needs to keep me sleeping soundly all the way through the night is worth it alone. Not to mention my husband and I never need to argue over firmness because we can each dial in our own sleep number setting. Why choose a Sleep Number Smart Bed? So you can choose your ideal comfort on either side. And now, for a limited time, Sleep Number Smart Beds start at $849.

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