In The Club, We All ... Archaea?

Thor. Loki. Heimdall. They're not just Norse gods or Marvel characters. They're also the names of various Asgard archaea. These microscopic organisms are found all over the world, from marine sediment to mud volcanoes to hydrothermal vents. A growing body of research suggests we owe them an evolutionary debt. This episode, Emily and guest host Jon Hamilton explore the wild world of archaea: Where are they from? What do they do? And what can they tell us about the origins of life on earth? Interested in more stories about life's origins? Email us at [email protected] mailto:[email protected]. We'd love to hear from you! See pcm.adswizz.com https://pcm.adswizz.com for information about our collection and use of personal data for sponsorship and to manage your podcast sponsorship preferences. NPR Privacy Policy https://www.npr.org/about-npr/179878450/privacy-policy

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• 0:00Speaker 00

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• 0:18Emily Kwong?

  You're listening to Short Wave from NPR.

• 0:23Emily Kwong?

  Hey, Short Wavers, it's Emily Kwong here.

• 0:25Speaker 02

  And John Hamilton.

• 0:26Emily Kwong?

  With a story that kind of picks up where Regina and I left off in November. So, John, do you remember the episode we did about hydrothermal vents and the origins of life?

• 0:35Speaker 02

  Oh, how could I forget? The two of you were getting at this idea that maybe the building blocks for life, you know, nucleotides, amino acids, were created around those super hot vents on the ocean floor.

• 0:47Emily Kwong?

  DNA and RNA, for example, are extremely vulnerable to, like, UV light. So maybe they first form deep in the ocean where they'd be protected from those rays. That's amazing.

• 0:56Speaker 02

  I mean, it sounds plausible to me.

• 0:57Emily Kwong?

  Right? And it left me with so many questions. Like, where did life go from there? You know, what's the next chapter, the moment where that molecular bath gave rise to discrete life forms, to single-celled organisms, prokaryotes, and eventually to complex multicellular organisms like you and me, eukaryotes? And there's this one type of life form that I think is key to telling that story, John. Have you heard of archaea?

• 1:23Speaker 02

  Or archaea, as some say.

• 1:25Emily Kwong?

  Tomatoes, tomatoes. Both pronunciations are fine, but do you know what they are?

• 1:29Speaker 02

  I do, but only because years ago, I happened to run into a biologist who studies them. I have never seen archaea in the wild.

• 1:36Emily Kwong?

  It's not your fault. They are tiny. Even under a high-powered microscope, the largest archaeans look like tiny dots. But if you zoom in closer, you'll see they possess all kinds of shapes. They're spheres, they're rods, they're spirals. They look like bacteria, but they're not. And despite having no nucleus, no organelles, I think these overlooked microbes have main character: energy.

• 2:02Speaker 02

  So today on the show, we're going to give archaea their due.

• 2:06Emily Kwong?

  How our microbial ancestors gave us our mighty immune system, are at the center of one of the biggest ideological battles in biology, and are connected to the legend of Thor.

• 2:16Speaker 02

  Bring it on, Kwong. You're listening to Short Wave, the science podcast from NPR.

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• 3:44Emily Kwong?

  Hey, Shorewaders. Emily Kwong here. Before we get back to the show, I have an update about Planet Earth. It's almost completed. It's 365 days, six hours, and nine-minute orbit around the sun. Those six hours add up to an extra day every fourth year, and that's why we have leap years. And 2024 was a leap year, which means we had one more day this year to bring you stories about astronomy, scuba diving lizards, social media algorithms, the COVID endemic, yes, not pandemic, how Rubik's cubes work, what happens to your brain when you sleep, extreme rainfall, all of that. Skincare trends on TikTok, noise pollution is possible because space blindness, invasive spiders. Of you, honestly, your monetary support of our work, geomagnetic storms, either through a classic donation or by joining programs like NPR Plus.

• 4:29Emily Kwong?

  With NPR Plus, you know this. You donate a small amount each month and get special perks for more than 25 NPR podcasts. You're gonna get sponsor-free listening, bonus episodes, and even exclusive and discounted items from the NPR shop. NPR Plus members, you help us continue to bring you stories about, gosh, lead water pipes, needle phobia, whale menopause, nuclear fission. Like, if you've been sitting on this all year, maybe head into 2025 with NPR Plus in your back pocket. With your help, we can keep this going. Every week, bringing you stories you're curious about, stories you didn't know you were curious about, stories that are fun to tell your friends, stories that make you think about your place in the universe. Join today.

• 5:12Emily Kwong?

  Go to plus.npr.org, plus.npr.org. That link is in our episode notes. Thanks for listening. Back to the show.

• 5:22Speaker 02

  Emily, so it seems like archaea has sort of come into their own in the scientific world in the past few decades. So walk me through that.

• 5:28Emily Kwong?

  Yes, we're living in the archaeasance.

• 5:32Emily Kwong?

  There's been this big debate in science. Like, I remember it from high school biology. For a long time, microbiologists divided the world into two domains.

• 5:42Speaker 02

  Okay.

• 5:42Emily Kwong?

  Eukaryotes, animals, plants, fungi. And prokaryotes, bacteria, which are single-celled organisms. And archaea went undetected for a long time until Carl Woese came along.

• 5:54Speaker 02

  Okay, so who is he?

• 5:55Emily Kwong?

  Okay, so Carl Woese was a microbiologist, most recently based at University of Illinois Urbana-Champaign. He passed away in 2012. But I spoke with someone who's become a torchbearer of his legacy, someone who knew him. Microbiologist Rachel Whitaker, also at Urbana-Champaign, remembers Woese as someone with a big-picture brain, someone willing to take on a question as intimidating as the origin of life.

• 6:20Speaker 04

  The way evolutionary biology had been done. In the organismal side of this world was to look at traits that change over time, you know, butterfly wings and plant leaves and seed colors and the beaks of the Darwin's finches and things like that. And that's really hard to study when you're looking at microbes because there's no traits. I mean, they do have different shapes and they do have different surface structures and stuff, but back in the day, when we were just discovering, you know, microbes, that was really hard to even say how they were related to each other.

• 7:01Emily Kwong?

  And Woos said that physical properties are not a reliable way to tell those relationships. He really pushed for a molecular approach. This was back in the 1970s.

• 7:10Speaker 04

  People were starting to use molecules, amino acids and RNA. They were starting to use those as signatures of evolution.

• 7:20Emily Kwong?

  For him, one molecule that was found all over the map was the ribosome. That's the machine that turns RNA into proteins. He began to study RNA sequences using these giant films of gel and cataloging their differences, tracing how they evolved over time.

• 7:35Speaker 04

  He had these notebooks and notebooks and notebooks, and I've seen these notebooks. There's like shelves of them, which are basically saying the size of each of these little bands in these two dimensional gels. And based on that, he was finding relationships.

• 7:51Emily Kwong?

  And then, right down the hall, his colleague Ralph Wolf found these weird microbes at the bottom of the food web, responsible for the greenhouse gases in cows. These microbes, they were a single cell, they kind of looked like bacteria, but also kind of not.

• 8:04Speaker 04

  Until he walked down the hall and said to Carl, "Woos, you should really look at these guys, they're very different. I don't know what they are."

• 8:11Emily Kwong?

  And because Woos had developed this molecular tool for comparing RNA sequences, he could use it on these mystery microbes. And he determined they were not bacteria. They had different cell walls, their RNA was more similar to eukaryotic RNA.

• 8:25Speaker 02

  Weird. So, I mean, what were they?

• 8:27Emily Kwong?

  Something new, something never before seen by science. And he gave them a name, archaea, which means... Ancient things.

• 8:34Speaker 02

  Oh, I get it. Archaea, archaeologist.

• 8:36Emily Kwong?

  And he made this argument that there were actually three domains of life: bacteria, eukaryotes, and archaea. Now, in the decades since, more types of archaea have been found in the soil, in the ocean, and notably in some of the most extreme environments on Earth, like hydrothermal vents.

• 8:56Speaker 02

  I was waiting for that.

• 8:57Emily Kwong?

  And the story doesn't end there because, John, in the last decade or so, at these vents, scientists have discovered a special type of archaea, which really complicate the story of life. They're called Asgard's.

• 9:09Speaker 05

  The first one was found in this hydrothermal vent in the North Atlantic called Loki's Castle.

• 9:18Emily Kwong?

  This is Brett Baker, a marine biologist at the University of Texas at Austin, someone who studies these Asgard archaea.

• 9:25Speaker 02

  All right, I'm getting the theme here. Asgard's Loki, Norse mythology.

• 9:29Emily Kwong?

  Correct, yes. And after the discovery of these Loki archaeota in 2015, Brett says.

• 9:35Speaker 05

  Then we found this other group that was related to it. So we called it Thor. We collaborated and found a bunch more groups, and Odin, and Heimdall.

• 9:44Emily Kwong?

  Ever since, Brett's team and others have been sequencing the genes of these Asgard archaea, found in hot springs, aquifers, freshwater, saltwater environments around the world. And what they've found has challenged the work of Carl Woz and the story of how life began.

• 10:00Speaker 02

  How so?

• 10:02Emily Kwong?

  OK, so these Asgard archaea, their genes are actually really similar to eukaryotes. And then Brett told me.

• 10:10Speaker 05

  They started finding all these proteins in the Asgard's that are like, they've only been seeing eukaryotes before.

• 10:18Emily Kwong?

  Which suggested something that went beyond Woz's work. It suggested that eukaryotes, like trees, mushrooms, birds, us.

• 10:26Speaker 02

  All the cool kids.

• 10:27Emily Kwong?

  May have, in fact, come from archaea, that the eukaryotic branch, in fact, sprouted from some ancient Asgardian ancestor.

• 10:37Speaker 05

  I literally went running into my grad student's office and I said, oh, my God. We have something very big.

• 10:45Emily Kwong?

  And at the time, this was very controversial. But Brett and other researchers kept doing the work and standing up to the naysayers, saying, no, this is right.

• 10:56Speaker 05

  Eukaryotes actually fall within the Archaea. We are literally Asgardians. Obviously, it's 2 billion years of evolution since we evolved from them, but they are our ancestors.

• 11:11Emily Kwong?

  And new research is continuing to bear this out when it comes to the story of how our immune system evolved.

• 11:18Speaker 02

  So bring us up to date. Give me some specifics here.

• 11:20Emily Kwong?

  So a few years ago, another microbiologist, Pedro Liao, who's from Brazil, came to work in Brett's lab at UT Austin as a postdoc. And Pedro was reading about how certain proteins that helped our ancient immune system do its job may have come from bacteria.

• 11:35Speaker 06

  And me, as someone working in the Archaea side of the origin of eukaryotes, I was like, why someone is focusing one in one player that formed the eukaryote and not a second one? I know Archaea play a role in this.

• 11:48Emily Kwong?

  He was like, why are they not looking at Archaea? Why are people always forgetting about Archaea? And he wanted to look for evidence that Archaea may bear clues for how our immune system evolved.

• 11:58Speaker 02

  I'm getting the theme with these Archaea investigators. So this guy's on a quest now, right?

• 12:04Emily Kwong?

  Yeah, they're a tenacious bunch. That's true. Pedro started looking at two classes of proteins found in our ancient immune system. And these proteins basically mess with viral DNA.

• 12:15Speaker 02

  Mess with it like they stop viruses from spreading?

• 12:18Emily Kwong?

  Yeah, they're really important. And Pedro started looking for similar amino acid sequences in these Asgard's. Using an AI tool called CollabFold, he predicted what those proteins would look like, took that work to Brett, and he found those exact protein structures in nature, in those Asgard's from the deep sea.

• 12:37Speaker 06

  Some researchers in my field wait their whole life for someone to prove their predictions were right. I had to wait less than, I don't know, a couple of weeks.

• 12:45Emily Kwong?

  The research he and Brad and a whole team at UT Austin did was published in the journal Nature Communications this summer. I'm going to show you one of the illustrations in the paper. Super exciting. This compares where the sequences for defense proteins show up.

• 13:02Speaker 06

  They are way bigger in Asgard and eukaryotes than they are in bacteria. So what that means is that they are more prevalent in Asgard and eukaryotes than they are in bacteria. So I was like, okay, if this is coming from a prokaryote, a bacteria or an archaea, it is most likely that they are coming from archaea because it is way more prevalent there.

• 13:22Emily Kwong?

  Meaning there was a symbiotic relationship between bacteria, which had these original immune systems, and Asgard's. And Pedro just did like the ancestry.com research to prove it.

• 13:32Speaker 02

  So he's pretty confident.

• 13:34Emily Kwong?

  Yeah, he's very confident.

• 13:35Speaker 06

  I, I, I fully believe this is how it happened, but how many times it happened, it did not work. This is, this is something that is a main question in biology still. And we don't know. So that's, that's the thing that keeps me up at night. I love it.

• 13:49Emily Kwong?

  These archaea scientists are tenacious, so I fully believe they'll get there. And this work could be beneficial to us someday, too. I mean, we are surrounded by viruses with the potential to infect us.

• 14:00Speaker 02

  Yeah, always have been and always will be.

• 14:02Emily Kwong?

  Yeah. And if our immunity is thanks in part to archaea, we should be looking to them for clues about how to keep us safe and healthy in the future.

• 14:11Speaker 05

  Perhaps we could use these defense systems in some therapeutic way to, you know, fight off viruses. And they've been looking in bacteria, which are very different than us. Maybe we should be looking at Asgard's for some sort of useful things to come from it.

• 14:27Speaker 02

  Well, Emily, I look forward to an Asgardian antiviral any day now.

• 14:32Emily Kwong?

  Where there's archaea, there's a way, John.

• 14:34Speaker 02

  For sure.

• 14:35Emily Kwong?

  Follow our show on Apple and Spotify. It makes a huge difference. Also, if the AI protein folding sounded cool to you, too, check out our episode on AlphaFold. We'll link to it in our episode notes.

• 14:49Speaker 02

  This episode was produced by Hannah Chin. It was edited by our showrunner, Rebecca Ramirez. Tyler Jones checked the facts. Jimmy Keely was the audio engineer.

• 14:57Emily Kwong?

  Beth Donovan is our senior director and Colin Campbell is our senior vice president of podcasting strategy. I'm Emily Kwong.

• 15:04Speaker 02

  And I'm John Hamilton.

• 15:05Emily Kwong?

  And thank you for listening to Short Wave, the science podcast from NPR.

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