All Of Life Has A Common Ancestor. What Was LUCA?
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Hey, short ravers, 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, great grandparents. No, we're talking about the ancestor of all life. 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?

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. When you say last universal common ancestor, what does that mean? So imagine for a second the tree of life. All life. Yeah, so everything. Yeah. So let's start at the branches. ♪

Every living thing on Earth is represented as a tip on the branch of that tree. Right. And if you follow any two branches back in time, they converge on their most recent common ancestor. So like chimps and humans, for instance, converge on a common ancestor that lived like 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. Grandma. Wow. That's awesome.

Why do we want to know about LUCA? 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.

So today on the show, how scientists use clues from life today to uncover what our last universal common ancestor may have looked like. 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. Dun, dun, dun. You're listening to Shortwave, the science podcast from NPR. ♪

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? 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.

I thought it was the desire to belong and, you know, have friends. Not that. 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. Right. If we share genes with bacteria, we must have gotten that from a shared ancestor way back when. So it was

Look at just another term for the origin of life. 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. 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. Wow. Yeah, and understanding the nature of the end of that story can still tell researchers a lot about early evolution.

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

But that kind of inference gets a lot more complicated the further back in time you go. What do you mean?

Well, genes get up to a lot of shenanigans that can throw off that detective work. Well, what kinds of things can genes do to throw the scientist detective off their scent? 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. Oh, okay. 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. So that muddies the waters of the quest to draw a clearer picture of Luca. What else does that? 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. I know enough about science as a non-scientist to know that this essentially means the data is really cluttered. Or like scientists would say, the data is really noisy. Exactly. Lots and lots of stuff that muddies the waters. So what are researchers doing to make that picture more clear?

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.

Was she a beautiful brunette like me? No, she was not a brunette. But the researchers did suggest that Luca was like half alive and relied on hydrothermal vents for energy. We love a resilient queen. Oh, I'm not surprised she was in hydrothermal vents. How accurate do you think this picture is?

So that's debated, and some researchers think it's probably a little too simple a picture. Phil Donoghue, 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.

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. And we draw accuracy rather than precision. Hmm. Okay. So they're precisely consensing on the same thing, but that is not necessarily the right thing, making this finding not as accurate. Yeah, exactly. Exactly. All right.

All right. Well, how do we try to get a more accurate picture? 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. Okay. How does this probability strategy work? Yeah. So the team looked at nearly 10,000 different gene families from 350 bacteria species and 350 archaea species. Oh, we love archaea on this show. And from that, they did some fancy probabilistic modeling to account for horizontal gene transfer.

that gene sharing we talked about earlier. Uh-huh. And they assigned each gene a probability of having been a part of Luca's genome. Oh.

This created like a fuzzier picture, but probably a more accurate one. So what did the picture look like? LUCA was pretty complicated. They estimate this single cell, our last common ancestor, had a genome roughly the size of some modern bacteria. Whoa. It had like 2,600 proteins, so quite a bit bigger than many scientists thought. Okay. And one of the coolest things they found was that LUCA had all of these different CRISPR-Cas9 genes. Wait, isn't CRISPR like...

The human-made gene editing tool? What do you mean? 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. 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. Yeah. So Luca likely made its living without oxygen and converted carbon dioxide or hydrogen gas into energy. Wow.

Wow. Many scientists think that life might have emerged at hydrothermal vents deep in the ocean. Yes. 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. Okay. 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. Totally, totally. And another theory is that Luca might have dined on the waste of other organisms. Oh, so, whoa, so Luca may not have been alone. Like, it just wasn't all the Lucas swimming around. 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. Huh.

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. 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?

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 carbon-dated fossils. Right, the fossils whose age they know for sure. 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. Wow. That is old.

What was happening on Earth around that time? 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 one 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. Oh.

So in general, this period was once thought probably like too harsh for life to emerge. 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 and…

evolution to reach something as complicated as this Luca? I don't know. It just seems like not a lot of time, evolutionarily speaking. Yeah, it really isn't. And that makes some researchers skeptical that this dating was accurate. That this 4.2 billion years ago date is right. 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. Like what? So it could mean that those early steps of evolution might...

Wow.

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. Plus one for Team Alien. Thank you so much, Jonathan Lambert. It was a pleasure talking to you about this and about LUCA. Thank you. 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 Shortwave on whatever podcast platform you're listening to. And if you have a science question, send us an email at shortwave at npr.org.

This episode was produced by Burleigh McCoy, who we're so happy to have back from parental leave. It was edited by our showrunner, Rebecca Ramirez. Tyler Jones checked the facts. The audio engineer was Gilly Moon. Beth Donovan is our senior director, and Colin Campbell is our senior vice president of podcasting strategy. I'm Emily Kwong. And I'm Jonathan Lambert. Thank you for listening to Shortwave, a science podcast from NPR.

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