Ancient Bone Proteins May Offer Insight On Megafauna Extinction

Collagen from a fossilized bone fragment can identify the animal it came from. And, some new info about our galaxy’s eventual extinction.

Speaker names marked ? are inferred from speaking time and the show’s known hosts — they are not voice-verified.

• 0:00Ira Flatow?

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• 0:16Speaker 01

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• 0:31Flora Lichtman?

  Hey, I'm Flora Lichtman, and you're listening to Science Friday.

• 0:37Flora Lichtman?

  Today in the show, wombats the size of hippos, 10-foot-tall kangaroos, and a new technique to identify mysterious biological samples.

• 0:46Speaker 03

  In museums and universities over the world, there are so many of these bags of bone scraps that no one really has looked at since, so there's still a lot of work to do.

• 1:00Flora Lichtman?

  If you think about Australia, one thing that probably comes to mind are the animals that live there, from koalas to kangaroos to a surprisingly large selection of creatures that can kill you. But once upon a time, the Australian landscape had some even weirder fauna, like a marsupial with immense claws and a small trunk, or a slow-moving kangaroo-like creature that walked on all fours, a wombat the size of a hippo. They're all extinct now, and researchers are trying to figure out why. Writing this week in the journal Frontiers in Mammal Science, researchers describe one tool they're using to hunt for clues. It's called ZooMS, and it uses samples of ancient protein,

• 1:44Flora Lichtman?

  not DNA, to identify what animal a bone came from. Joining me now to talk about it is Dr. Carly Peters. She worked on this project at the Max Planck Institute of Geoanthropology in Jena, Germany, and is now a postdoctoral researcher at the Interdisciplinary Center for Archaeology and the Evolution of Human Behavior at the University of Algarve in Faro, Portugal. Welcome to Science Friday.

• 2:06Speaker 03

  Thank you so much for having me. It's great to talk to you more about what we've been doing.

• 2:11Flora Lichtman?

  Well, you had me at giant wombats, obviously. Tell me a little bit about them.

• 2:15Speaker 03

  So basically, the animals that we studied are all extinct now. And they're all giant versions of what you could still find in Australia today. So you would have the giant wombat or a giant kangaroo. And you also have creatures that don't really have anything similar today, like the paloquestas, the creature with the giant claws that you were talking about. There's not really any closely related animal alive anymore today.

• 2:46Flora Lichtman?

  When you say giant wombat or giant kangaroo, how giant are we talking?

• 2:51Speaker 03

  We generally put the term megafauna on any animals that are larger than 45 kilograms. What we're talking about here, for example, the giant wombat, you can kind of think like hippo sized, so a lot bigger than your average wombat today.

• 3:08Flora Lichtman?

  And the kangaroo, I must know.

• 3:10Speaker 03

  I believe it's about two to three meters tall, really big. You wouldn't want to run into it.

• 3:16Flora Lichtman?

  That's like almost 10 feet tall. Yeah, you're right. I don't think I'd want to run into it. When did they live?

• 3:24Speaker 03

  So many of these animals went extinct during the late quaternary, which is the period before the one we live in now. So basically, they went extinct around 50,000 years ago. And they lived for hundreds of thousands of years before that, of obviously multiple different species of the same type of animal. But they ultimately went extinct about 50,000 years ago.

• 3:49Flora Lichtman?

  You know, I think when listeners hear giant wombat, the burning question on everybody's mind is obviously, would a giant wombat have giant cube-shaped poop?

• 4:00Speaker 03

  This is something I've wondered myself as well. And unfortunately, I don't have a good answer to that. We haven't found any of their coprolites, which are fossilized poop.

• 4:11Flora Lichtman?

  Uh, let's keep hoping.

• 4:13Speaker 03

  Yeah, it would be really cool to get the answer to it, though.

• 4:16Flora Lichtman?

  What are the other big questions about these animals?

• 4:19Speaker 03

  So there is a big debate mostly about, first of all, their exact timing that they all went extinct. But the other burning question is what actually caused their extinction? About fifty thousand years ago is also around the same time period that humans first entered Australia. So there are people who argue that human colonization of Australia caused the extinction of these animals. But there was also climate change at around the same time, so that could have also been a factor. There's people who argue that it's a little bit of both. But really, we don't know why they went extinct.

• 4:55Flora Lichtman?

  And how does your technique, Zoo MS, help with figuring that out?

• 5:00Speaker 03

  One of the major issues that we have when we try to look at why these animals went extinct is that we don't really have a lot of data for them. So for example, the Proton, which is another one of these extinct marsupials, they're best represented in the fossil record. And there's about 12, 13 well-dated fossil remains for them all over Australia. So that's not really enough data points to get to a good theory testing of why they went extinct. So now that we have the collagen peptide markers that we developed for our study, we can use them to find more of these animals in fragmented fossil remains.

• 5:44Flora Lichtman?

  So your method is a way of identifying bones, what animal they come from, and it uses collagen, not DNA. Is that right?

• 5:54Speaker 03

  Yes, that's correct.

• 5:56Flora Lichtman?

  Why not use DNA? What does collagen offer that DNA doesn't have?

• 6:00Speaker 03

  There's two main things. The first one is that proteins, and that includes collagen, but also other proteins, they tend to preserve better in the fossil record. So for example, the oldest DNA that's been recovered at the moment is from a permafrost of about a million years old, if I'm correct. But proteins can preserve for a lot longer. The oldest preserved proteins so far are up to four million year old eggshells.

• 6:27Speaker 03

  Um. They also preserve better in harsher environments. So for DNA, you often have to look at really cold regions of the world. But obviously, Australia is not very cold. So that doesn't really help you there. And the other reason is that this technique is a lot cheaper to do. So with this technique, you can analyze thousands of bones for a fraction of the cost of what you would get if you would do DNA analysis on them.

• 6:52Flora Lichtman?

  That's fascinating, because I think I would have assumed, when I think of collagen, I think of my skin, I think of it in my cartilage, like, stuff I assume breaks down actually more easily.

• 7:03Speaker 03

  Yeah.

• 7:04Flora Lichtman?

  So this is, this is surprising to me.

• 7:05Speaker 03

  Yeah, it's, you are correct. Collagen is the main protein component in skin and in cartilage, but it's also actually the main protein in your bones. It's what keeps your bones flexible. And because it's in this mineral environment of the bone, it preserves well over time.

• 7:24Flora Lichtman?

  And is one animal's collagen different from another's?

• 7:27Speaker 03

  It depends a bit on how evolutionarily distant they are. So, for example, you wouldn't be able to tell apart a wolf from a dog. They're too similar. But you can tell apart a horse and a donkey, or a sheep and goat. So it depends a bit. It's variable.

• 7:47Flora Lichtman?

  What about ancient humans? Can you tell the, the difference between a Neanderthal and a modern human using this?

• 7:53Speaker 03

  No, unfortunately, we can't. But we can identify that it's a human or closely related to a human. So then you could still send it for DNA afterwards, once you've identified it as a human. That's what people tend to do. So to then get more detailed data on it.

• 8:12Flora Lichtman?

  So is this technique that you're using, is it made possible by new technology? Or was it a new idea? Like, what advance led us to this technique?

• 8:22Speaker 03

  So the technique itself was first developed in 2009, and it was mostly brought on by developments in mass spectrometry, which allowed people to actually study in more detail the protein sequences and mass from a lot of different materials.

• 8:43Speaker 03

  And because of all of these developments, people on the brink between archaeology and chemistry, were looking into whether we could use it in archaeology as well. And that's why it was first developed mostly for European animals.

• 8:58Flora Lichtman?

  Hmm. Are there other proteins that you could use in this way to, you know, figure out what animal a remain is from?

• 9:05Speaker 03

  Yes, you can. You can use keratin, which is obviously in your hair and nails. And people use it sometimes to look at old textiles to see from which animals the textiles were made from. You could also do a similar thing with eggshell. So you have specific proteins in eggshell and then you can tell from which species a specific shell is from. So for example, if you want to look at which birds were exploited by people in the past, you could look at eggshell remains from archaeological sites in that way.

• 9:38Flora Lichtman?

  So here's the thing I don't understand. I mean, I understand you're sort of making a reference library. So you can say, okay, this bone is from this animal. And so then I can sort of like map the signature of this protein that corresponds to this animal. But what if you encounter an animal you've never seen before?

• 9:53Speaker 03

  Yes, I've had this in my research in the past. Sometimes you can kind of tell what broader taxonomic group it's in. So for example, in Australia, sometimes I've had where I can tell it's a marsupial, but I just can't really say which one, because it's not, we don't have the reference data available for it. But sometimes you really can't tell and it's just a question mark still.

• 10:17Flora Lichtman?

  Are there huge protein databases, the way that there's like DNA databases? You know, a reference library, basically?

• 10:24Speaker 03

  Yeah, there is some stuff, but it's still very much in its infancy. It also very much depends on whether a specific animal is interesting for modern clinical trials as well. So the databases are lacking a lot. And at the moment, if you want to specifically do this type of work that I do, you're best off if you want to focus on European medium sized mammals. That's the best.

• 10:51Flora Lichtman?

  They're the best represented in the library.

• 10:53Speaker 03

  Yeah, yeah, that's where it started and it's still best represented.

• 10:57Flora Lichtman?

  Okay, so how do you apply this? Is it like you go in the field and you dig stuff up and you use this method or are you going back to museum collections? Like, what's the use case?

• 11:08Speaker 03

  So for what I've done, I've mostly worked with museum collections. So basically, an archaeologist or a paleontological team will work at a site, they dig up everything they find, their remains, and then first a paleontologist or a zoo archaeologist, which is someone who looks at the animal remains at archaeological sites. They would look at the material and based on specific elements or features of a bone, they would be able to tell which bone it is and from which animal. But then there are a lot of remaining fragments that are too tiny to say what they are from. So they normally they get bagged up and they get put in either museum storage or university storage. They'll be saved, but they'll never really be looked at again.

• 11:54Flora Lichtman?

  They're like the scraps, the bone scraps.

• 11:56Speaker 03

  Yeah, that's that's normally what I call it too, the bone scraps. And then what I've done is I've gone through these museum collections to select from these bone scraps material to sample and to then identify later on.

• 12:10Flora Lichtman?

  That's so cool. So you're using all of these parts of the collection that would have just maybe, you know, collected dust and not told us anything.

• 12:18Speaker 03

  Exactly. That's also what I find very fascinating about it. And of course, in museums and universities over the world, there are so many of these bags of bone scraps that no one really has looked at since. So there's still a lot of work to do.

• 12:33Flora Lichtman?

  Is there a bag of bone scraps you're dying to test?

• 12:36Speaker 03

  I know, it's difficult to tell because you don't know what you'll find, right? At the moment, I'm working at a new institute, working on new projects, and it's really cool to see, hopefully, some ancient human remains or from these extinct animals where we don't really get much data from them. I don't know, there are so many interesting things that you could in theory find. I don't know, there's so many cool sites. I'm an archaeologist, I love all the sites.

• 13:03Flora Lichtman?

  Thanks so much for joining us today.

• 13:05Speaker 03

  Yeah, thank you so much for having me.

• 13:06Flora Lichtman?

  And good luck. Good luck with the scraps.

• 13:09Speaker 03

  I will. There's so many waiting for me.

• 13:12Flora Lichtman?

  Dr. Carley Peters, postdoctoral researcher at the Interdisciplinary Center for Archaeology and the Evolution of Human Behavior at the University of Algarve in Faro, Portugal. After the break, some maybe good news. The Milky Way might be safe from a cosmic collision. Although, key word, "might."

• 13:34Speaker 04

  The old calculations were not wrong. We just explore a bigger space of possibilities. And what was predicted in the past is definitely one of the possible outcomes. It's just not the only possible outcome.

• 13:48Ira Flatow?

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• 14:29Speaker 01

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• 16:11Flora Lichtman?

  Before we go, some good news, or news that sounds good, anyway. Our galaxy may not be heading for a smash-up with neighboring galaxy Andromeda after all. Andromeda is hurtling at us at over 100 kilometers per second, and it was long thought that we were in for a collision, but new calculations suggest that's not a sure thing. Joining me now to talk about it is Dr. Til Sivala, astrophysicist at the University of Helsinki. He recently wrote about this in the journal Nature Astronomy. Welcome to the show.

• 16:42Speaker 04

  Thank you very much for having me.

• 16:44Flora Lichtman?

  This is a thing that I didn't have on my worry list, and now I feel like I just get to write it down and cross it off.

• 16:50Speaker 04

  I guess it's possible to answer this question in several ways. So the merger, even if it happens as was previously predicted, would still take about four and a half billion years. So I don't think that's something any of us have to worry about. But we do find indeed that even this merger in the far future is not certain. We find, in fact, only about a 50% chance that there's any merger in the next 10 billion years. And for merger in less than 5 billion years, we now see only about a 2% chance.

• 17:19Flora Lichtman?

  Was this a surprise?

• 17:21Speaker 04

  The short answer is yes. I was initially interested in a completely different question related to the future evolution of the Milky Way and Andromeda. I wanted to understand how the cosmic environment might influence this. But as a starting point, I thought I would revisit this prediction. I had expected that we'd basically be able to confirm this prediction. But we found that in fact, when we included all the observational uncertainties and also when we considered a more complete system, including the effect of the Milky Way's most massive satellite galaxy, yeah, we only found a 50/50 chance, and that was a big surprise.

• 17:55Flora Lichtman?

  So it sounds like the old calculations weren't wrong. You just have now more data to work with.

• 18:00Speaker 04

  Yeah, exactly. In the past, people have considered the effect of the next most massive galaxy in the local group, the Triangulum galaxy or M33. But we find that actually we need to go one step further and also include the effect of the Large Magellanic Cloud, which is a dwarf galaxy, a satellite galaxy of the Milky Way. It's important to stress that the old calculations were not wrong. We just explore a bigger space of possibilities. And what was predicted in the past is definitely one of the possible outcomes. It's just not the only possible outcome.

• 18:30Flora Lichtman?

  Well, what are we missing out on if we don't collide with Andromeda?

• 18:34Speaker 04

  What would happen precisely depends a lot on when that merger will happen, what the energy of the orbit will be at that time, what the relative inclination of the two galaxies will be at that time. So how precisely the merger will play out, I would say it's too early to say that. We currently have two large disk galaxies in the Milky Way and Andromeda. And the most likely outcome of such a merger is that they would essentially be destroyed and constitute a new elliptical galaxy that would form after some time. For a brief period, there would be an intense period of star formation, a so-called star burst. But that would produce a lot of young stars, which would result in intense radiation. The two

• 19:16Speaker 04

  supermassive black holes in the center would also find each other and merge. That would create even more radiation, which would eventually shut off star formation. So the the long-term result of that merger would be basically that the two Large disk galaxies that currently constitute the local group, including our own galaxy, the Milky Way and Andromeda, they would cease to exist and in its place after some billions of years would be an elliptical galaxy that would not have much new star formation and would basically slowly, slowly fade. So that would be the long term future. And yeah, it's important to say that's still very much one possible scenario.

• 19:53Flora Lichtman?

  You know, this is a thing that may or may not happen in the next 10 billion years. Why do you care about this?

• 20:01Speaker 04

  I think it's a really good question. So, I mean, on one level, we know for certain that the sun will explode in about eight billion years. Even before that, it will make Earth uninhabitable. The calculations are on about maybe one billion years. So, so this is all beyond human lifetimes. I think it's just something that I'm curious about because it affects my own galaxy, even though I might not be around when that merger will happen. I think it's just part of human curiosity that we like to know. And what actually fascinates me is, yeah, the question of why we are interested and why we might even prefer one outcome over another. Um, at least personally, I can say I prefer the Milky Way to, to continue,

• 20:44Speaker 04

  uh, to live, even if there's no impact on, on my life or, or human lifetimes, I think. And, but why that is, I think is more a question for, for maybe psychologists compared to astrophysicists.

• 20:55Flora Lichtman?

  Thank you so much, Til.

• 20:57Speaker 04

  Okay.

• 20:58Flora Lichtman?

  Dr. Til Savala, astrophysicist at the University of Helsinki.

• 21:05Flora Lichtman?

  Thanks for listening. If you like the show, rate and review us wherever you listen, or just go straight to guerrilla marketing. Take a friend's phone and subscribe them to this podcast. Please help us get the word out about Science Friday. Today's episode was produced by Charles Burquist. I'm Flora Lichtman. Thanks for listening.