All Of Life Has A Common Ancestor. What Was LUCA?

Imagine the tree of life. The tip of every branch represents one species, and if you follow any two branches back through time, you'll hit an intersection. If you keep going back in time, you'll eventually find the common ancestor for all of life. That ancestor is called LUCA, the last universal common ancestor, and there is no fossil record to tell us what it looked like. Luckily, we have Jonathan Lambert. He's a science correspondent for NPR and today he's talking all things LUCA: What we think this single-celled organism may have looked like, when it lived and why a recent study suggests it could be older and more complex than scientists thought. Have other questions about ancient biology? Email us at [email protected] mailto:[email protected] — we'd love to hear from you! Listen to every episode of Short Wave sponsor-free and support our work at NPR by signing up for Short Wave+ at plus.npr.org/shortwave http://plus.npr.org/shortwave. In a previous version of this episode, we said that the research team used carbon-dated fossils to calibrate a molecular clock aimed at estimating the age of LUCA. In fact, the researchers used radio isotopic-dated fossils for that purpose. 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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• 0:00Emily Kwong?

  This message comes from NPR sponsor Viore with the Halo Essential Wide-Like Pant. Receive 20% off your first purchase at viore.com/NPR on any US orders over $75 and free returns. Exclusions apply. Visit the website for full terms and conditions. You're listening to Short Wave from NPR. Hey, Shortwavers. Emily Kwong here with a story about your ancestors, but not your grandparents and not your great-grandparents, nor your great-great-great-great-great-grandparents.

• 0:33Speaker 01

  No, we're talking about the ancestor of all life.

• 0:36Emily Kwong?

  All life. And you're just the right person to talk about this with us, Jonathan Lambert, because before your current stint on the NPR Science Desk, you wrote about this ancestor for Quantum Magazine. Is this where all living things descended from?

• 0:51Speaker 01

  Yes. So they call it LUCA, which stands for the Last Universal Common Ancestor, which is no longer alive, but it would have existed billions of years ago as some kind of single-celled organism.

• 1:03Emily Kwong?

  When you say "last universal common ancestor," what does that mean?

• 1:07Speaker 01

  So imagine for a second the tree of life.

• 1:09Emily Kwong?

  All life.

• 1:10Speaker 01

  Yeah, so everything. So let's start at the branches. Every living thing on Earth is represented as a tip on the branch of that tree.

• 1:18Emily Kwong?

  Right.

• 1:19Speaker 01

  And if you follow any two branches back in time, they converge on their most recent common ancestor. So chimps and humans, for instance, converge on a common ancestor that lived less than 10 million years ago. If you keep tracing any path of ancestry back far enough, whether you start with gorillas, or sharks, or ginkgo trees, or those neat bacteria that live in the bowels of the Earth, you'll eventually reach the same single point. That's LUCA. That's the ancestor of every living thing and every dead thing that we know about.

• 1:52Emily Kwong?

  Wow, that's awesome. Why do we want to know about Luca?

• 1:57Speaker 01

  Scientists want to understand what it was like because it gets at this really fundamental question of where we, as in all life on Earth, came from. And here's a new development. A team of scientists took the biggest swing yet at trying to paint a picture of Luca through some pretty tricky detective work.

• 2:14Emily Kwong?

  So today on the show, how scientists use clues from life today to uncover what our last universal common ancestor may have looked like.

• 2:23Speaker 01

  How it could be a bit older and more complicated than we thought, and if true, could hint that we're not the only life in the universe.

• 2:30Emily Kwong?

  Dun, dun, dun. You're listening to Short Wave, the science podcast from NPR.

• 2:42Speaker 02

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• 3:54Emily Kwong?

  All right, let's back up a second, John. How do we even know that Luca, who I fully believe in, but still, how do we know that Luca existed?

• 4:02Speaker 01

  Evidence that it existed is hidden in every living thing. So we all share some basic fundamental machinery of life, things like a genetic code or using amino acids to build proteins.

• 4:14Emily Kwong?

  I thought it was the desire to belong and, you know, have friends. Not that.

• 4:20Speaker 01

  Yeah, yeah, not that. And given what we know about how evolution works, that genes get passed down from generation to generation, it follows that something like Luca must have existed.

• 4:32Emily Kwong?

  Right, if we share genes with bacteria, we must have gotten that from a shared ancestor way back when. So is Luca just another term for the origin of life?

• 4:41Speaker 01

  No, it's not the origin of life. It's not even the first cell or the first microbe or the first of anything, really. But it is the furthest back that we can push towards the origin of life by looking at what's alive today. Greg Fournier, a biologist at MIT, put it well.

• 4:59Speaker 06

  In a way, you can think of it as almost the end of the story of the origin of life as we know it. Because all of the things that are in common across all of life that exists today would also have been already present by Luca.

• 5:14Emily Kwong?

  Wow.

• 5:15Speaker 01

  Yeah, and understanding the nature of the end of that story can still tell researchers a lot about early evolution.

• 5:22Emily Kwong?

  Let's pick up that story, then. How are researchers trying to tell it and figure out what Luca may have looked like?

• 5:28Speaker 01

  So in general, all these efforts try to guess the genes and proteins that Luca had by looking for what's shared across different organisms. Like, for example, if you compare a gene that's basically the same in us and chimps, it's pretty safe to say that we inherited it from our common ancestor. That's the simplest explanation. But that kind of inference gets a lot more complicated the further back in time you go.

• 5:51Emily Kwong?

  What do you mean?

• 5:52Speaker 01

  Well, genes get up to a lot of shenanigans that can throw off that detective work.

• 5:58Emily Kwong?

  Well, what kinds of things can genes do to throw the scientist detective off their scent?

• 6:02Speaker 01

  Yeah, so there's horizontal gene transfer, which is this thing where instead of passing genes vertically from one generation to the next, some microbes can pass them horizontally to their neighbors. Like, a bacterium can give its other bacteria friends antibiotic resistance, for example, when it butts up against them and shares that little bit of DNA.

• 6:23Emily Kwong?

  Oh, OK.

• 6:24Speaker 01

  And so that can make it seem like a bunch of species all inherited this gene from a common ancestor, when, in reality, it just got shared a bunch.

• 6:31Emily Kwong?

  So that muddies the waters of the quest to draw a clearer picture of Luca. What else does that?

• 6:35Speaker 01

  Yeah, and then there's the issue of genes getting lost, but only for some species. Like, if genes that were in Luca get lost down the line in certain species, it could lead researchers to falsely conclude that the genes evolved after Luca, since it's not shared by all its descendants.

• 6:53Emily Kwong?

  I know enough about science as a non-scientist to know that this essentially means that the data's really cluttered. Or like, scientists would say, the data's really noisy.

• 7:02Speaker 01

  Exactly. Lots and lots of stuff that muddies the waters.

• 7:05Emily Kwong?

  So what are researchers doing to make that picture more clear?

• 7:08Speaker 01

  So one way to tune out all that noise is to be really stringent and focus only on genes that show little evidence of horizontal gene transfer. And a really prominent analysis of this sort back in 2016 painted a pretty simple picture of Luca.

• 7:23Emily Kwong?

  Was she a beautiful brunette, like me?

• 7:26Speaker 01

  No, she was not a brunette. But the researchers did suggest that Luca was like, half-alive and relied on hydrothermal vents for energy.

• 7:36Emily Kwong?

  We love a resilient queen. Oh, I'm not surprised she was in hydrothermal vents. How accurate do you think this picture is?

• 7:43Speaker 01

  So that's debated, and some researchers think it's probably a little too simple a picture. Phil Donaghy, a paleontologist at the University of Bristol, told me that he thinks that being too picky could lead researchers to dismiss lots of proteins that Luca actually had, which would lead to kind of like an artificially simple picture of Luca.

• 8:04Speaker 07

  And so what I'd argue is that people have come up with a very high-definition, high-resolution picture in the past, which is much more precise, but... Arguably far less accurate. We draw accuracy rather than precision.

• 8:18Emily Kwong?

  Hmm, OK. So they're precisely consensing on the same thing, but that is not necessarily the right thing, making this finding not as accurate.

• 8:28Speaker 01

  Yeah, exactly, exactly.

• 8:29Emily Kwong?

  All right. Well, how do we try to get a more accurate picture?

• 8:32Speaker 01

  So basically, by being less picky. So instead of trying to definitively predict whether Luca did or didn't have a given gene, they assigned a probability.

• 8:41Emily Kwong?

  OK, how does this probability strategy work?

• 8:44Speaker 01

  Yeah, so the team looked at nearly 10,000 different gene families from 350 bacteria species and 350 archaea species.

• 8:51Emily Kwong?

  Oh, we love archaea on this show.

• 8:52Speaker 01

  And from that, they did some fancy probabilistic modeling to account for horizontal gene transfer, that gene sharing we talked about earlier.

• 9:00Emily Kwong?

  Uh huh.

• 9:01Speaker 01

  And they assigned each gene a probability of having been a part of Luca's genome. This created like a fuzzier picture, but probably a more accurate one.

• 9:10Emily Kwong?

  So what'd the picture look like?

• 9:11Speaker 01

  Luca was pretty complicated. They estimate this single cell, our last common ancestor, had a genome roughly the size of some modern bacteria.

• 9:20Emily Kwong?

  Whoa.

• 9:20Speaker 01

  It had like 2,600 proteins, so quite a bit bigger than many scientists thought.

• 9:25Emily Kwong?

  OK.

• 9:26Speaker 01

  And one of the coolest things they found was that Luca had all of these different CRISPR-Cas9 genes.

• 9:31Emily Kwong?

  Wait, isn't CRISPR like the human-made gene editing tool? What do you mean?

• 9:36Speaker 01

  Yeah, yeah. So we humans hijacked it to bioengineer, but in nature, bacteria use these CRISPR genes to slice and dice viruses. And so the fact that Luca had these genes suggests that it might have had some kind of ancient immune system.

• 9:51Emily Kwong?

  So maybe Luca's not simple at all. She's complex, she's robust, and was perhaps grappling with viruses just like us. What do they have to say about how Luca fed and kept herself alive?

• 10:04Speaker 01

  Yeah, so Luca likely made its living without oxygen and converted carbon dioxide or hydrogen gas into energy.

• 10:12Emily Kwong?

  Wow.

• 10:12Speaker 01

  Many scientists think that life might have emerged at hydrothermal vents deep in the ocean.

• 10:16Emily Kwong?

  Yes.

• 10:17Speaker 01

  And this probabilistic Luca could have lived there, eating up the gas that spews from these vents. But those Gases could have also come from the atmosphere, too. So this LUCA might have lived closer to the ocean's surface, too.

• 10:29Emily Kwong?

  OK, I find this speculation deeply enjoyable. You know, Gina introduced me to this idea that hydrothermal vents may have been the cradle for the origin of life. Or, as you put it in your article, "the chemical alchemy that snapped molecules into a form that allowed evolution," loosely paraphrasing your piece. The ocean, it just seems like the cradle for all of that.

• 10:51Speaker 01

  Totally, totally. And another theory is that LUCA might have dined on the waste of other organisms.

• 10:58Emily Kwong?

  Oh, so, whoa, so LUCA may not have been alone. Like, it just wasn't all the LUCA swimming around.

• 11:03Speaker 01

  Phil and his colleagues argue no. Those researchers think that LUCA was actually part of a complex ecosystem of microbes that have since gone extinct. They don't have evidence for this, since any traces of those lineages are long gone. But essentially, they argue that something as complicated as their version of LUCA couldn't have evolved in isolation.

• 11:24Emily Kwong?

  This is an interesting picture they're painting. But what did this paper say about when LUCA may have lived? And how do they even go about figuring that out if it was billions of years ago?

• 11:33Speaker 01

  Yeah, it's really hard. And so they turned to genes. So all genes mutate over time. And the tick, tick, tick of those mutations can serve kind of like a molecular clock. And the researchers calibrated their clock with fossils.

• 11:48Emily Kwong?

  Right, the fossils whose age they know for sure.

• 11:50Speaker 01

  Right, right. And so then they estimated when LUCA lived by looking at all the genetic differences that its descendants racked up. And their clock put LUCA living about 4.2 billion years ago.

• 12:02Emily Kwong?

  Wow, that is old. What was happening on Earth around that time?

• 12:08Speaker 01

  It was really rough. So about four and a half billion years ago, a Mars-sized planet collided with Earth to form the moon. And scientists think it likely would have taken like 1 or 200 million years after that for the planet to settle down enough to support life. And in the years following, scientists think the Earth was getting continually bombarded with asteroids. So in general, this period was once thought probably like too harsh for life to emerge.

• 12:36Emily Kwong?

  But this new LUCA theory kind of complicates that. I mean, that leaves, what, like a couple hundred million years for the origin of life to happen? Evolution to reach something as complicated as this LUCA, I don't know. It just, it just seems like not a lot of time, evolutionarily speaking.

• 12:53Speaker 01

  Yeah, it really isn't. And that makes some researchers skeptical that this dating was accurate.

• 12:58Emily Kwong?

  That this 4.2 billion years ago date is right.

• 13:00Speaker 01

  Right, right, right. But other researchers think that it makes a lot of sense. And if it's true, it has some pretty profound implications.

• 13:08Emily Kwong?

  Like what?

• 13:10Speaker 01

  So it could mean that those early steps of evolution might be kind of easy. And that, yeah, and that on Earth, it didn't take all that long to go from some self-replicating thing snapping into being to a LUCA like the one painted here.

• 13:25Emily Kwong?

  Wow.

• 13:27Speaker 01

  And if it wasn't so hard for complex life to evolve here on Earth, that might mean that it's not so hard on other planets either.

• 13:37Emily Kwong?

  Plus one for Team Alien. Thank you so much, Jonathan Lambert. It was a pleasure talking to you about this and about LUCA.

• 13:45Speaker 01

  Thank you.

• 13:46Emily Kwong?

  To learn more about the origins of life, check out our episodes on hydrothermal vents and another episode on archaea. And make sure you never miss a new episode by following Short Wave on whatever podcast platform you're listening to. And if you have a science question, send us an email at [email protected].

• 14:03Speaker 01

  This episode was produced by Burley McCoy, who we're so happy to have back from parental leave.

• 14:08Emily Kwong?

  Hooray.

• 14:09Speaker 01

  It was edited by our showrunner, Rebecca Ramirez. Tyler Jones checked the facts. The audio engineer was Gilli Moon.

• 14:16Emily Kwong?

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

• 14:22Speaker 01

  And I'm Jonathan Lambert.

• 14:23Emily Kwong?

  Thank you for listening to Short Wave, a science podcast from NPR.

• 14:36Speaker 05

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