Host: Benjamin Thompson
Welcome back to the Nature Podcast. This week, million-year-old mammoth DNA…
Host: Shamini Bundell
And how art can complement science. I’m Shamini Bundell.
Host: Benjamin Thompson
And I’m Benjamin Thompson.
[Jingle]
Interviewer: Benjamin Thompson
When it comes to piecing together evolutionary family trees, one of the best clues as to what goes where can be found in DNA. By comparing the long strings of As, Ts, Cs and Gs, researchers can peer back in time and learn how different species evolved and how populations intermingled. But sadly, DNA sequencing can only take researchers back so far. It’s a pretty fragile molecule and, if not locked away in the right sort of environment, will quickly break down. Back in 2013, a team of scientists set a new record for recovering and sequencing an ancient genome extracted from the bone of a relative of the horse and estimated to be up to 780,000 years old. That record stood for eight years. But this week, a paper in Nature suggest it’s been broken, as a team of researchers has managed to sequence the DNA from some ancient relatives of the woolly mammoth. To find out more, I called up Love Dalén from the Centre for Palaeogenetics in Stockholm, Sweden, one of the paper’s authors. I mean, we have to start really with talking about the record. I mean, you’ve sequenced the oldest DNA ever recovered thus far. How old are we talking and where did it come from?
Interviewee: Love Dalén
So, we have three specimens. They’re all from northeastern Siberia. One of them is approximately 700,000 years old, the second one is 1.1 million years old, and the third one is approximately 1.2 million years old, and we got this DNA out of mammoth teeth that were recovered from the Siberian permafrost. And so, what our late colleague Andrei Sher did when he collected these specimens back in the 1970s actually was that he was excavating the permafrost where he knew that these sections were really old, and so he found these individual teeth coming out of the permafrost.
Interviewer: Benjamin Thompson
Well, where does that sort of put things in a geologic time? What is 1.2 million years ago?
Interviewee: Love Dalén
Well, 1.2 million years ago is 1,000 times older than the Viking era, so it’s really old. It even predates the existence of modern humans and Neanderthals. We are then in the sort of early half of the period called the Pleistocene, which is the era of ice ages.
Interviewer: Benjamin Thompson
So, these teeth date back to then but they were excavated in the 1970s. Why did you decide that now was the right time to investigate them?
Interviewee: Love Dalén
Well, we’ve known, I’ve known, about these specimens since 2007, but back then the technology simply wasn’t there to even try to do this. So, there’s been this big revolution in DNA sequencing technology and that, coupled with both advances in the sort of lab methods of how to extract the DNA and in perhaps especially important advances in bioinformatics methods on how to actually authenticate and handle this DNA, it wasn’t really time to do this until in the last years.
Interviewer: Benjamin Thompson
I mean, you have these three teeth. How do you go about successfully extracting ancient DNA and getting this sequence? I mean, I imagine it must be incredibly fragile.
Interviewee: Love Dalén
Yes, it is rather fragile. What happens with DNA, even when its frozen, over time is that it breaks down into smaller and smaller and smaller pieces. So, essentially the genome of the mammoth when we recover it is broken down into anywhere between 20 and 50 million pieces, so it’s a rather big jigsaw puzzle to sort out. The most difficult problem is contamination. So, the first step is actually taking these teeth and using a dentist drill to remove the surface of the tooth because the surface is covered with contaminants. Then we drill into it, collect a little bit of powder, about 50 milligrams which is like a pinch of salt kind of in the amount that we’re taking, and we collect that and hopefully that is relatively clean from contaminants. That means that for the oldest tooth specimens we have in the study, 99% of the DNA we get is still contaminants and roughly 1% of the DNA is actually from the mammoth. So, we take this powder and we then mix it with different chemicals, and then we use various methods to clean this DNA so that eventually we have the DNA in a pure form in dissolving water, essentially.
Interviewer: Benjamin Thompson
So, you’ve got your three teeth. How do you know that they are that old? Do you know this from looking at the DNA sequence or is it where they were found that gives you these clues?
Interviewee: Love Dalén
So, there are mainly two ways we know the age of these specimens. One is that our palaeontology colleagues have been using geological methods to date these samples, so we knew beforehand approximately how old these samples were. But then when we got the genetic data, we also could use the molecular clock – the assumption that mutations happen at a relatively constant rate – to perform our molecular dating that was independent of the geological dating. And when we do that, we find that the two younger specimens, we get more or less exactly the same age, plus or minus a few hundred thousand years, but in the grand scheme of things we basically get the same age. For the oldest specimen, our DNA data actually says that it’s a bit older at 1.6 million years. And so, we don’t know why that is, but it’s still very comforting that these two different, independent methods basically give us the same result in the sense that two of these specimens are more than 1 million years old and to be honest, it’s not that important for our analysis whether the older is 1.2 or 1.6 million years old. It’s really old.
Interviewer: Benjamin Thompson
I mean, presumably you didn’t do this just to get the record, right? You actually wanted to get some data on the mammoth family tree. Now, I obviously am familiar with woolly mammoths, I guess – that’s what we learn about at school – but they’re maybe some of the more recent species of mammoth. And what you’ve done here is you’ve been able to really get a sense of how the different species that go all the way back to a million years ago fit into the tree. I mean, what’s the story here?
Interviewee: Love Dalén
So, roughly between 1 and 2 million years ago in Siberia, we have a type of mammoth that has been called the steppe mammoth, and the classic model of mammoth evolution is that these steppe mammoths were the ancestors of the woolly mammoth and the Columbian mammoth of North America. And so, what we wanted to do was to test hypotheses about the relationship between these ancestral mammoths and the woolly mammoth and the Columbian mammoth. To our great surprise, what we find is that one of these specimens, the one that is 1.2 million years old, which we now call the Krestovka mammoth, belonged to a genetic lineage that was completely unknown to us. And we look at the other really old specimen, the one that was 1.1 million years old, this one seems to be directly ancestral to the woolly mammoths. And so, we have two specimens, one is 1.2 and one is 1.1. million years old, and they belong to completely different lineages of mammoth. And then it turns out that the Columbian mammoth in North America turns out to be a hybrid between this Krestovka mammoth and the woolly mammoth, and what we can see in the genetic data is that the Columbian mammoth actually is 50% of its genome comes from Krestovka and 50% of the genome seems to come from the woolly mammoth. We think that this hybridisation happened roughly 420,000 years ago, presumably in North America.
Interviewer: Benjamin Thompson
You’ve been able to go back in time a very long way then. Obviously, that’s very, very useful. It’s given you a lot of information about the mammoth family tree, but where does it leave the field of ancient DNA? What else might we be able to learn as a result?
Interviewee: Love Dalén
This really is a time period, around 1 million years, when many mammal species and bird species evolved, so I think in a broader sense, we are kind of opening the door to a future research discipline where we can go deep into time and study macroevolutionary changes, such as speciation events, on many other species that also went through these big evolutionary changes around a million years ago.
Interviewer: Benjamin Thompson
Finally then, how far back do you think we can go? We’re at about 1.2 million years old now. Theoretically, what do you think the limit is and how close do you think we’ll get to it?
Interviewee: Love Dalén
If I remember correctly, I think theoretical models put the limit in frozen conditions at up towards, I don’t know, 3-4 million years, something like that. The problem here is of course that you need to have a sample that has been frozen more or less continuously and, beyond 2.6 million years, to my knowledge, there is no permafrost. So, I think maybe the sort of environment puts an upper limit to this, but we can definitely go more than 1.2. My guess would be that it should be possible to go beyond 2 million as well, but exactly how far back is of course impossible to say. There are so many assumptions there.
Interviewer: Benjamin Thompson
That was Love Dalén. To find out more about the million-year-old mammoth genome, look out for a link to the paper in this week’s show notes.
Host: Shamini Bundell
Coming up, we’ll be hearing why having a bit of art in your science or a bit of science in your art can be a great thing. Right now, though, it’s time for the Research Highlights with Dan Fox.
[Jingle]
Dan Fox
As the most massive planet in the Solar System, Jupiter is regularly pelted by objects. Now, a team of researchers have recorded one of these celestial impacts. Previously, astronomers needed to be content with watching these cosmic collisions from afar, but this impact was captured by NASA’s Juno spacecraft, which has been orbiting Jupiter since 2016. An ultraviolet instrument aboard Juno recorded a short flash in Jupiter’s northern hemisphere in April last year. The researchers believe it probably came from a fireball created as a space rock between one and four metres across, burned up in the Jovian atmosphere. The team estimate that there could be 24,000 of these impacts every year. If that research has made an impact, read it in full at Geophysical Research Letters.
[Jingle]
Dan Fox
The long-snouted, shark-like predators called sawfish have vanished from nearly 60% of their historical habitat and are nearing extinction, according to new research. Sawfish are rays known for their chainsaw-like noses and their large size. Some species routinely reach 5 metres in length. They live near seashores and in mangrove forests, habitats that are rapidly disappearing. To study what this means for the five species in the family, scientists reviewed sawfish research conducted between 2014 and 2019 in 64 countries. From this, they estimated the distribution of these fishes. They found that fishing and habitat loss have driven sawfish to extinction in 55 of the 90 countries whose waters they once occupied. Saving the sawfish, the researchers say, will require countries to protect the creatures’ offshore habitats and to ban fishers from keeping sawfish that are caught in their nets. Read that research in full at Science Advances.
[Jingle]
Host: Shamini Bundell
Art and science. To some, these are polar opposites, as different as chalk and cheese. But to others, these two disciplines are a perfect pair which complement and benefit one another. The relationship between art and science has been perennially discussed and today, it’s caught the attention of Nature’s very own Nick Petrić Howe, who’s been talking to an artist and a scientist reaching across the divide.
Interviewee: Abrian Curington
Hello, this is Abrian.
Interviewer: Nick Petrić Howe
This is Abrian Curington. She is an illustrator from Washington State in the US who writes fantasy graphic novels, has a penchant for cartography, and loves the oceans and the stars.
Interviewee: Muzz Haniffa
Hello.
Interviewer: Nick Petrić Howe
And this is Muzz Haniffa. She is a researcher of dermatology and immunology at Newcastle University in the UK who investigates the function of immune cells in the skin. Despite being separated by a metaphorical and literal ocean, these two women have an interest in the intersection between art and science. Abrian is an artist but also a self-described nerd who has always had in interest in science.
Interviewee: Abrian Curington
Growing up, I seemed to split my time between reading and making up stories and studying cool rocks that I picked up on my walks.
Interviewer: Nick Petrić Howe
And Muzz is a scientist who has an artistic side.
Interviewee: Muzz Haniffa
I have always been interested in the interface between art and science.
Interviewer: Nick Petrić Howe
So, when opportunities arose for this scientist and this artist to combine these so-called disparate disciplines, they jumped at the chance. For Muzz, this occurred when she attended a welcome conference that brought together artists and scientists.
Interviewee: Muzz Haniffa
And I just happened to sit at lunch next to a professor of modern and American literature, Linda Anderson, and I started talking to her, and the rest really was history.
Interviewer: Nick Petrić Howe
That history she’s referring to was a collaboration between Muzz and many artists to try and find new ways to communicate her research to people, to expand beyond the typical writing of papers for your peers that is so central to science. This effort culminated in an event called Inside Skin, where artists transformed Muzz’s work on the gene expression of immune cells in the skin into interactive exhibits.
Interviewee: Muzz Haniffa
We had a booth which had like sound and LED visual display, and the light display and the sound was essentially a transformation of the gene expression data, so the intensity of the genes that were expressed were transformed into this. And the idea of going into a booth and putting headphones on so that you can hear the cells and see the visual display of the cells in a way that was almost engulfing you was very much about the immune cell called macrophage and dendritic cells, and their job is to engulf substances around them, and so this was a way of you kind of being engulfed, to hear them and see them. Another one which was one which is a bit more sensory, so you can touch these circuit boards which would then send electric circuits across other panels, and that meant that, depending on the pressure, how much you touch, where you touch, it would send different patterns, and this was to depict how cells communicated with one another.
Interviewer: Nick Petrić Howe
The response from the public was overwhelmingly positive, and it showed Muzz the ability of art to communicate science. For artist Abrian, science has always played a role in her artwork. She includes science in her illustrations, even in places where you might not think it would fit.
Interviewee: Abrian Curington
I’ve spent an inordinate amount of time on a scene where my main character was trying to calculate the physics of a minotaur smashing into a wall. I actually contacted a mathematician like, ‘How are we going to work this out?’ So, I have this whole thing about calculating fantasy physics just for fun because I just think its delightful.
Interviewer: Nick Petrić Howe
So, when Abrian discovered a possibility to join a scientific expedition aboard a research vessel, she figured it was a great way to expand her artwork whilst also exploring her passions of the oceans and the stars.
Interviewee: Abrian Curington
I actually got put on, somehow, the most perfect expedition. It was seeking space rocks, and we worked with a NASA team to search for meteorites on the seafloor. It was a perfect blend of sea and space, and I was just delighted to work with them and learn about all of their research.
Interviewer: Nick Petrić Howe
For Abrian, the expedition mostly involved asking interesting questions and observing the researchers, and to cap off the experience she illustrated the voyage.
Interviewee: Abrian Curington
I painted a scene of the remote operated vehicle SuBastian underwater, scooping up sediment. They’re essentially using a sieve to scoop up sediment and shake it around and look for meteorites. Then I showed the research vessel, Falkor, above the ocean, and all around that I have a border that showcases little moments, little sea creatures that were found, the maps that were used, a scene of the Moon over the midnight sky, which was amazing because it was just pitch black darkness but you had this shining Moon and the white waves, just a falling meteorite, just little snippets of the adventure. And so, all parts of the team were able to say, ‘I remember that,’ and, ‘I remember that.’ So, I printed a bunch of them and gave them to the crew and science team as a thank you.
Interviewer: Nick Petrić Howe
This, and other experiences with scientists, have helped Abrian become more comfortable showcasing science in her artwork.
Interviewee: Abrian Curington
At the moment, I’m looking into writing a story that involves different dimensions, and so I can write that, but I always like to research about whatever I’m studying. So, I’ll research different dimensions, and usually, I’ll find information that makes whatever I’m making up even more interesting because real life is infinitely more fascinating, typically, than anything that we can come up with. So, I’ve definitely taken more interest in the world around me even more so that I have before, and in having to talk to people about visual storytelling and visual communication in non-fiction settings, I’ve actually had to up my game on visual storytelling. You can kind of cheat around a little bit, but if you’re having to explain it to somebody else, you have to bone up some more on what you already know. So, I’ve definitely grown as an artist and as a visual storyteller, and I’ve gotten to do things that I never thought I would do, speak at conferences, go out at more expeditions, so just great all around.
Interviewer: Nick Petrić Howe
For scientist Muzz, by working with artists to showcase her work to the public, she has changed the way she things about her science and how to identify what’s important.
Interviewee: Muzz Haniffa
Yeah, I mean, the way that it has shaped my research since is to kind of think of the concepts that you have. I mean, it sort of a) directed me to kind of what people kind of think is important, b) research areas that are important because although these are kind of like art exhibits, there are biological messages and also kind of the focus on people who have skin disorders, so homing in on to kind of what is actually important for the public and patients in general. Also, thinking about the reason why we do research and how I can communicate the research ideas and findings in a more meaningful way, that has been shaped by those interactions.
Interviewer: Nick Petrić Howe
For both Muzz and Abrian, the experience of intertwining their fields has been extremely positive, and they both feel that they have grown as a result. Maybe your research could benefit from art too. If you’re intrigued, Muzz has this advice.
Interviewee: Muzz Haniffa
Go for it. Don’t feel that you can’t do this because I never thought I could go on this journey and find myself enjoying it and thinking that it’s such a fantastic experience. There are lots and lots of individuals and organisations that are going to be able to help you, and it’s such a fantastically enriching experience and it will change how you approach science and how you approach public engagement in the future.
Host: Shamini Bundell
That was Muzz Haniffa from Newcastle University. You also heard from Abrian Curington who’s based in Washington State. If you’re interested in reading more about artists and scientists coming together, then make sure you check out the show notes where there’ll be a link to Nature careers article with many more examples. Also, we’ll include some links to a few resources for any of you who might be interesting in doing something similar.
Host: Benjamin Thompson
Finally on the show, it’s time for the weekly Briefing chat, where we discuss a couple of articles that have been highlighted in the Nature Briefing. Shamini, what have you been reading this week?
Host: Shamini Bundell
So, I have found some really fascinating research this week. It’s a really fun and sort of quite creative paper in Science, and it’s all about how do we figure out what our ancient relatives’ brains look like, so Neanderthals, say. Ben, if you wanted to figure out what a Neanderthal’s brain looked like, how would you go about that?
Host: Benjamin Thompson
I mean, it’s a tricky one, right? We talked about ancient DNA earlier in the show, so maybe you could go back into that and have a look and try and piece something together? I don’t know, really.
Host: Shamini Bundell
Yeah, so DNA is kind of really limited because all you’re looking at is sort of genes and sequences. How do you know what that actually appears as in an actual brain? It’s really hard to hypothesise about what that might be. So, some researchers have sort of tried quite an ingenious way to get around that by growing brain organoids with a Neanderthal gene in.
Host: Benjamin Thompson
Right, I mean we covered brain organoids, these mini-brains, on the pod a few months back. They’re fascinating things. So, now we’ve got a mini-brain with a little bit of a Neanderthal flavour as well.
Host: Shamini Bundell
Yeah, and what they’re sort of trying to do is see if there are any obvious changes with one Neanderthal gene involved compared to the sort of human brain organoids. So, these are tiny, like half-centimetre clusters of stem cells that have been sort of induced to crate brain-like tissue. It’s not a full-grown brain or anything. But they’ve grown up one set of organoids with the Neanderthal version of this gene called NOVA1, and one set with the human version of this gene.
Host: Benjamin Thompson
Right, I mean, compare and contrast then. What has this one difference made between the two?
Host: Shamini Bundell
It’s quite surprisingly a really obvious visual difference. So, there are actually photos in this article and you can see that the shape of these tiny little clusters of cells is completely different. So, the organoids with the Neanderthal version of NOVA1 are basically like really bumpy looking compared to the sort of smooth, round human ones. They are potentially a little bit smaller and they might even more mature more quickly.
Host: Benjamin Thompson
But obviously, this is only one gene that’s changed, and these aren’t sort of fully-fledged brains. These are, as you say, very small organoids, mini-brains, in a petri dish. What else can be learnt from this other than they look a bit different?
Host: Shamini Bundell
Yeah, so, on the one hand, it is only one gene. The researchers have sort of picked a gene that they think is very significant in the differences between Neanderthals and humans. So, the Neanderthal version of this gene is common to Neanderthals and Denisovans, whereas humans have a lot of Neanderthal genes in us, but every single human has the modern human version of this gene. So, it seems like it’s significant that our NOVA1 is this way. It seems really important in our evolution. But then again, it’s only one gene that you’re changing, whereas in our DNA, a whole load of genes have changed, so we don’t know whether changing that one gene in otherwise modern human cells has a sort of cascade effect on loads of different genes that wouldn’t be the case in a Neanderthal. Plus, of course, as you say, it’s not a brain, it’s an organoid.
Host: Benjamin Thompson
Well, yeah, of course, Shamini, brains, as we know, are fantastically complicated things. Is the plan now to maybe put in different genes, more genes, to work out maybe a bit more about Neanderthal brains?
Host: Shamini Bundell
Yeah, and to some extent the idea isn’t just to figure out what a Neanderthal brain is like but to figure out how our brains evolved, and this technique, done on sort of different genes, maybe different species, sort of combined together could give us a lot more insight into things like that. And so, what research have you got for us today?
Host: Benjamin Thompson
Well, Shamini, as you know, I love a stone circle or really anything stone circle adjacent to be honest with you. I’ve been to ones on the Hebridean islands off the coast of Scotland, I’ve been to a stone circle in the Lake District. Sea Henge off the coast of near where I used to live is fascinating to me as well.
Host: Shamini Bundell
I didn’t know this about you. This is a well-kept secret. I’m not even sure I’ve even heard of all of the different henges that exist.
Host: Benjamin Thompson
There is, though, the one right at the top – Stone Henge. You’ve heard of that one of course.
Host: Shamini Bundell
The one, yes, I know that one, the big one.
Host: Benjamin Thompson
Yeah, well, some new research has come out published this week in Antiquity and written about in Science, suggesting that Stone Henge, in some cases, is kind of second-hand.
Host: Shamini Bundell
So, the sort of most iconic monument in England is actually just nabbed from somewhere else?
Host: Benjamin Thompson
Yeah, I mean, I don’t think necessarily it’s been nabbed, but it has come quite a long way. Now, let’s have a bit of a chat about Stone Henge here. Of course, when you think about it, you think of those kind of vertical stones with kind of a crossbar stone across the top, right, and in this case, we’re not actually talking about those ones. Stone Henge was kind of built in stages, and one of the early stages, about 3,000 years ago, I think, was this kind of ring of stones, this sort of thing called a blue stone. And it’s been a bit of a mystery as to exactly the voyage that they took from where they were quarried to Salisbury Plain where they are now.
Host: Shamini Bundell
So, yeah, I think I’ve heard something about this that one of the sort of amazing things is the fact that they were quarried so far away. The stone that they’re made of clearly came from miles away.
Host: Benjamin Thompson
Yeah, absolutely right. So, it’s known that these stones were quarried in Wales, several hundred kilometres away, but what’s been a bit of confusion is there’s kind of a gap of a few hundred years between when it was sort of estimated these stones were quarried and when they appeared at Stone Henge. And so, researchers have been trying to find out what happened in between.
Host: Shamini Bundell
And how do you go about tracing the life history of a piece of rock?
Host: Benjamin Thompson
Well, you do a lot of searching, Shamini. In this case, it took over a decade. And so, there had been some theories that there had been a sort of intermediary stone circle somewhere in Wales, and researchers have been searching for it, and it looks like they’ve found it, which is kind of amazing. In particular, they looked at one sort of area only a few kilometres from where the stones were quarried, and there was kind of four stones there that looked a little bit like kind of the Stone Henge stone circle, right, and they excavated it and excavated it, and it turns out that these four stones were part of a massive circle with a lot of holes that would have contained other stones.
Host: Shamini Bundell
Oh my gosh. This is suspicious. Were they sort of holes the same size as the Stone Henge stones by any chance?
Host: Benjamin Thompson
I mean, absolutely right, they were. In one case, there’s this one particular sort of stone from Stone Henge, they kind of scanned that and scanned the hole, and literally is like a lock and key situation. They go together. And there’s other things giving evidence that one became the other. So, both of these sort of circles, the entrance to them was oriented to sunrise on the summer solstice, and they did some kind of chemical analysis of the holes and it suggested that the stones were put there and then maybe 300 or 400 years later they were taken away and moved somewhere else, adding yet more evidence that this sort of intermediary stop was a stepping stone, if you will, to Stone Henge.
Host: Shamini Bundell
It’s strange enough to think that whoever built Stone Henge bothered to transport the materials so far, but then to build a stone circle and then take it down and then go miles away and build another one. I mean, do we have any idea what were these people doing? What was going on back then?
Host: Benjamin Thompson
Yeah, lots of questions and very few answers, I’m afraid to say. But it maybe is part of a larger migration. So, some kind of bones of animals and humans found, I think, around the Stone Henge area, analysis of those suggested that they spent at least part of their existence near the coast of Wales. And other evidence suggested that human activity dropped in this area of Wales when the Welsh circle was demolished, but the researches don’t know why that is just yet. So, I mean, potentially, it could just be it was a link to the past and they wanted to take their culture with them when they migrated from one place to another.
Host: Shamini Bundell
So, this is another one of the stories – we’ve had lots of them on the podcast today – where the easiest thing to do would just be to get a time machine and go back in time and find out what was actually going on, but it’s fascinating to see all the different methods that researchers are using to piece together the past, so thank you very much, Ben. And listeners, if you want to know about all the stories we’ve discussed, you can find links to those in the show notes. And if you’re interested in more stories like this but instead as an email, then make sure you check out the Nature Briefing. Again, we’ll put a link in the show notes to where you can sign up.
Host: Benjamin Thompson
And that’s all we’ve got time for this week. Don’t forget to keep an eye out on your podcast feed for the next edition of Coronapod, which will be coming out in a couple of days. I’m Benjamin Thompson.
Host: Shamini Bundell
And I’m Shamini Bundell. Thanks for listening.