Genomics unwraps mystery of the Tarim mummies

Host: Nick Petrić Howe

Welcome back to the Nature Podcast. This week, genomics reveal the origin of some mysterious mummies.

Host: Shamini Bundell

How to keep up your digital hygiene.

Host: Nick Petrić Howe

And what to expect at the UN’s latest climate conference. I’m Nick Petrić Howe.

Host: Shamini Bundell

And I’m Shamini Bundell.

[Jingle]

Interviewer: Nick Petrić Howe

The year is 1934, and explorers are crossing the inhospitable Taklamakan Desert in Central Asia. In a region known as the Tarim Basin, they come across an unusual sight. What appear to be great oars pierce the sky and amidst them lie boats, or so it appears. They weren't just boats. They were coffins.

Interviewee: Paula Dupuy

So, we have these naturally mummified individuals that are exquisitely preserved, and in having this amazing preservation we get this window into this period in the past, the Bronze Age, so around 4,000 years ago.

Interviewer: Nick Petrić Howe

This is Paula Dupuy, an archaeologist of Inner Asian prehistory. The individuals found are known as the Tarim Basin mummies. For 66 years they remained forgotten but in the early 2000s, archaeologists rediscovered and re-examined the site, revealing many other unusual aspects of the mummies.

Interviewee: Paula Dupuy

So, generally, the mummies are described as having Western physical appearance, so they were quite tall, fair-skinned, fair-haired, long noses, so all these things we associate with western Eurasia and not Asiatic populations. And so, from early on, the question was where did they come from?

Interviewer: Nick Petrić Howe

Seemingly European people mummified in a desert, right in the heart of Asia. The Tarim Basin mummies have puzzled archaeologists for decades. Although they appeared to have a so-called Western appearance, their diet had traces of both East and West.

Interviewee: Paula Dupuy

And this is one of the really unique aspects of this region, is that they’re growing crops that originate both in southwest Asia as well as in central China, so you get this kind of crossover of eastern and western domesticates.

Interviewer: Nick Petrić Howe

Most hypotheses about the Tarim mummies’ origin centre around migration from somewhere to the North or West. Particular attention has been paid to a people known as the Afanasievo from the Eurasian steppe – modern day southern Siberia. This has been particularly compelling as, like the Tarim Basin mummies, they kept goats, sheep and cattle, and they shared the so-called Western physical appearance. Also, evidence has been found in the Tarim Basin, albeit much later than the mummies were around, of the Tocharian language – a now extinct tongue that is thought to be closely related to European languages – possibly spread by the Afanasievo. Now, scientists are turning to biology for answers. After all, where there is migration of people, there are genes.

Interviewee: Choongwon Jeong

If this migration from a certain proposed source really contributed to Tarim mummies’ gene pool, then we should be able to find it.

Interviewer: Nick Petrić Howe

This is Choongwon Jeong, an evolutionary geneticist who has been delving into the genomes of the Tarim mummies. Now, previous genetic studies have relied on mitochondrial and Y chromosome DNA and indeed have found genes associated with both East and West. But Choongwon says these studies lack the resolution that can be offered by genomic DNA. By comparison, Choongwon’s study sequenced genomic DNA from 13 Tarim Basin mummies. He compared these with DNA from a different set of mummies that were slightly older and from further north. Choongwon’s analysis suggested that the older, more northerly mummies’ genomes supported the theory of Afanasievo migration.

Interviewee: Choongwon Jeong

And it’s pretty clear that they have a large fraction of their genome descended from an Afanasievo gene pool.

Interviewer: Nick Petrić Howe

But for the Tarim mummies…

Interviewee: Choongwon Jeong

I was really surprised.

Interviewer: Nick Petrić Howe

The Tarim mummies, well, they were quite unique.

Interviewee: Choongwon Jeong

Basically, they have zero contribution from the Afanasievo herders.

Interviewer: Nick Petrić Howe

Choongwon found no evidence of Afanasievo genes in the Tarim Basin mummies, but that isn’t all. His data didn’t support any of the leading hypotheses for the origin of the Tarim Basin mummies. Instead, they appear to be a remnant of a group of ancient North Eurasians, a thought-to-be nomadic population that was once widespread across northern Europe and Asia. This group’s genetic legacy has been found throughout Europe and even the Americas. They are also suggested to be the first people to develop blond hair, which fits in with the appearance of the Tarim Basin mummies. But the lack of Afanasievo genes suggests that the Tarim mummies remained genetically isolated from their neighbours. And yet, there’s lots of archaeological evidence to suggest that they were culturally very similar to Afanasievo and other peoples around them.

Interviewee: Choongwon Jeong

In contrast to this clear genetic separation, we see the very strong cultural connection with other groups. So, basically, they were not like isolated, isolated. They knew what was happening in the nearby regions, and then they actually imported and got all these animals and plants and knew how to grow and cultivate these animals and plants.

Interviewer: Nick Petrić Howe

Cultural mixing does not, it seems, always lead to, well, mixing of genes.

Interviewee: Paula Dupuy

I think that we need to not assume that when you get a new cultural practice or a new tradition, that it means that people moved and brought their ideas with them and then local people adopted them. Now, we have to think about how this may have happened, so potentially down the line exchange, so from one hand to another, or non-regular interactions where you get people coming together for certain events, so ritual moments of the year where people gather, congregate, share ideas and then go their own separate ways.

Interviewer: Nick Petrić Howe

This is not unprecedented. In a previous study in Mongolia, Choongwon found people adopted cultural practices from elsewhere with little movement of genes. For these unusual people who buried their dead in boats in the middle of desert – the Tarim Basin mummies –there are still many mysteries to unpick.

Interviewee: Paula Dupuy

One of the big questions is what’s happening before 2100 BC. You have this third millennium. The third millennium has a big question mark on it. What was there before the Tarim Basin mummies are living there? Is there a hunger-gatherer population that we haven’t picked up. Is there other populations just outside the basin from the early third millennium that can help us make this connection as to how this culture emerges? What are its cultural origins? And so, it’s really finding those earlier sites that are going to be really crucial going forward.

Interviewer: Nick Petrić Howe

That was Paula Dupuy from Nazarbayev University in Kazakhstan. You also heard from Choongwon Jeong from Seoul National University in South Korea. To find out more about the genetics of the Tarim Basin mummies, check out the paper, along with a News and Views article written by Paula, in the show notes.

Host: Shamini Bundell

Coming up, we’ll be hearing about some unscrupulous publication practices and how you can you help protect yourself. Right now, though, it’s the Research Highlights with Dan Fox.

[Jingle]

Dan Fox

As a material, wood has a lot of things going for it, but it isn’t very easy to shape. Now, a team of researchers have found a way to make wood mouldable. The researchers first removed more than half of wood’s stiff and water-repelling components, leaving behind the softer cellulose. Then they allowed the wood to dry, causing the hollow cellulose fibres to collapse. When this dried wood was dipped in water, the cellulose-rich regions quickly rehydrated, allowing the wood to be moulded or folded into various shapes that then set when the wood dried again. A 3D wooden lattice produced with this process, when sandwiched between two sheets of aluminium, was strong enough to support a car. The authors hope that their process could help wood, a renewable resource, to compete for roles conventionally filled by plastics and metals. Branch out and read that research in Science.

[Jingle]

Dan Fox

Sixty-six million years ago, a devastating mass extinction wiped out roughly 75% of all Earth’s species, including the dinosaurs. But snakes survived and thrived, after developing a taste for a bountiful array of creatures. To find out more about the reptiles’ dietary shifts, researchers compiled data from dissections of museum specimens’ gut contents and field observations of 882 modern snake species. The authors merged those data with information about the evolutionary history of snakes. Their results suggest that the most recent common ancestor of living snakes dined exclusively on insects and other invertebrates. But shortly after the mass extinction, snakes developed the striking variety of dietary preferences that they have today. Devour that research at PLoS Biology.

[Jingle]

Host: Shamini Bundell

Guillaume Cabanac is a computer scientist from the University of Toulouse in France and this week in Nature he’s written a World View, looking at a very particular unscrupulous academic practice – attaching a researcher’s name to something without them knowing. This practice can have serious career and reputational repercussions, especially in a world where predatory journals and things like fake conferences and editorial boards exist. But Guillaume is fighting back, and is calling on researchers to do what he calls a ‘digital hygiene’ check every month to protect themselves from practices like this. Benjamin Thompson gave him a call to find out more, and started by asking him why someone might get unknowingly added as an author.

Interviewee: Guillaume Cabanac

There are some cases where authors put other people in the by-line for increasing the perceived prestige of the submission. In some cases, we can find the names of researchers being acknowledged in the acknowledgement sections of the papers, and when you go and ask the people what did they contribute, sometimes they say, ‘I don’t really know. I don’t even know the researchers who acknowledged me.’

Interviewer: Benjamin Thompson

Why is this a problem then if your name is attached to a paper like this?

Interviewee: Guillaume Cabanac

Imagine you have a paper that is used for public health policy, for instance, and your name is attached to it, and the paper is really buggy, for instance. Imagine what will be the reaction of your institution. In some countries, you could get fired for publishing a paper that is wrong, that will be retracted, or the other colleagues of yours who don’t know that you didn’t contribute at all might change their point of view about your work.

Interviewer: Benjamin Thompson

And so, this is clearly a practice that is going on and, in your World View, you argue that funders and institutes have a role in rooting this out, in protecting their researchers. But you also say that there is a role to play for individuals as well, and you talk about something that you do yourself every month, and it’s described as a digital hygiene check, and this kind of involves Googling your own name which, in your case, very much isn’t a vanity exercise. What are you doing it for?

Interviewee: Guillaume Cabanac

I realised that these cases involving the deception of scientists could be counteracted fairly simply. As a researcher, you need to take care of your digital presence they call it in the business industry. So, you appear on webpages. Maybe without knowing, your name might appear in the webpage of a fake conference to give the impression that they are supported by scholars around the world, and you need to know about that because that might harm your reputation. And how to see a paper popping up, simply you go and Google your name or you go to Google Scholar or Dimensions, the academic search engine, and the idea is to turn on the notifications so that any time these software index papers bearing your name, you will be notified. And if it captured a non-paper of yours, something that you are not aware of, you have to react. You shouldn’t wait until dozens of papers bearing your name are published to realise that something is happening.

Interviewer: Benjamin Thompson

Has anything ever come up with your name on it that you weren’t aware of?

Interviewee: Guillaume Cabanac

With my name on it, nothing really serious. But there is a positive outcome of doing it. When you turn on the notifications, you can see the researchers who will cite you formally, but you can also look at the metrics to know that your paper was mentioned in a blog, on Wikipedia or in other places on the internet.

Interviewer: Benjamin Thompson

And so, you give an example of this positive aspect then on another sphere of your work because you’re also getting quite a name for yourself as a bit of a sleuth, looking for papers that have been maybe falsified but in a very particular way – by rewording an existing paper and submitting it as a new piece of work. And the giveaways are things that you’ve been calling ‘tortured phrases’. Tell us a bit about that.

Interviewee: Guillaume Cabanac

Yeah, we noticed in the published literature in the elite publishers that some papers would contain nonsense. So, sometimes it’s the entire paper that is nonsensical. Sometimes it’s only a paragraph with an equation that has no meaning at all. And when we looked at the nonsensical text, we could find tortured phrases in the text. What does it mean? It means that, for instance, instead of using ‘artificial intelligence’, you read ‘counterfeit consciousness’. That’s crazy. And then you go to the statistics and you see ‘p-esteem’ instead of ‘p-value’. So, you understand because of the context but you really wonder why did the authors change? So, we found these tortured phrases in many publications by top publishers, and we discovered that they result from the tentative to deceive plagiarism detection software by using paraphrasing software that change the words into synonyms, and that’s how you have ‘enormous data’ instead of ‘big data’ or ‘enormous information’ instead of ‘big data’.

Interviewer: Benjamin Thompson

And you’ve been searching for these for quite a long time now and suggested maybe hundreds of papers that need to be taken a second look at. But how has the digital hygiene work and this work come together?

Interviewee: Guillaume Cabanac

We published a preprint on arXiv in July, and we weren’t very sure that it would attract some viewers but, by doing the digital hygiene, I became aware of citations and mentions outside of the academic sphere, and it gained attention, and this had led me to re-prioritise my work.

Interviewer: Benjamin Thompson

Now, there are options for researchers if they find themselves misattributed, either accidentally because of having the same name as someone else or more maliciously as you’ve described, and they should speak to their institutions to find out about them. But of course, academics are very, very busy people, and there will be folk listening to this now who will be thinking, ‘Well, I haven’t really got time to go ahead and do this every month,’ to look until page six of Google to look where their name might be appearing. What would you say to them? Why is doing this important?

Interviewee: Guillaume Cabanac

What did happen in an institution I know in France is that researchers had been deceived because their names appeared in dozens of papers before their institution realised that it was happening, and it’s really a bad situation. So, they didn’t spend the time to search online each and every month for a couple of minutes and now they have to deal with administrative burden. They have to deal with research integrity issues because of this bad story that is happening to them. It’s a really difficult situation.

Host: Shamini Bundell

That was Guillaume Cabanac from the University of Toulouse in France. Look out for a link to his World View in the show notes.

Host: Nick Petrić Howe

Finally on the show, we’re talking about COP26. This Sunday, the 26th UN Climate Change Conference begins in Glasgow, here in the UK. An estimated 20,000 people from 196 countries — including world leaders, scientists and activists — are expected to be in attendance. To find out what’s on the agenda, Benjamin caught up with Nature’s Jeff Tollefson, who explained the main goal of the conference.

Interviewee: Jeff Tollefson

The short answer is that this conference was designed as kind of a catchup. It’s five years after the Paris agreement was signed and of course that committed the world to trying to halt global warming to 1.5-2 °C. But everybody recognised at the time that all of the pledges and commitments fell well short of that goal, based on scientific modelling. So, the world leaders, when they signed that treaty, they also included a provision that said every five years you have to come back and you have to re-evaluate progress, you have to re-evaluate pledges and in theory you have to increase your ambition and commit to do more until the world basically reaches this goal. So, the pledges that are going to be made in Glasgow from various governments are supposed to bring the world in line with the Paris agreement.

Interviewer: Benjamin Thompson

Well, if this is the time to re-evaluate Paris agreement progress, another thing being discussed at the conference was put in motion even longer ago, and that’s the financing of climate initiatives, particularly from rich countries to those less well off.

Interviewee: Jeff Tollefson

Yeah, so this kind of dynamic between rich countries and poor countries, developed countries and developing countries, is the way you formally think about it within the UN climate convention. This dates all the way back to 1992 at the Earth Summit in Rio when I think 154 governments came together. They signed an agreement that said we’re going to try and stop global warming, and in that agreement you had a phrase that was kind of coined: ‘common but differentiated responsibilities’. And basically, the idea is that developed countries have a responsibility to kind of lead and do more and to help developing countries. It was never kind of exactly clear what that meant. In 2009, as part of kind of an agreement to get everybody to take action, developed countries said, ‘We’ll give you US$100 billion a year in climate finance.’ That was supposed to arrive by 2020. What that means is of course unclear. Everybody has got their own definitions. A lot of this money is actually coming in the form of loans when developing countries want it in the form of grants. And of course, even by their own accounting standards, the developed countries are not meeting that goal. So, this has always been a tricky negotiating point and we’re going to see it come up again in Glasgow.

Interviewer: Benjamin Thompson

And what can people expect from COP26 then? If we think back to Paris then, there was this celebratory mood that an agreement was made. If it’s very much the devil is in the details, are we looking to see something similar at the end, an eleventh hour deal, or really is there going to be a lot more smaller things that are announced as the conference goes on, do you think?

Interviewee: Jeff Tollefson

I think the honeymoon period has definitely worn off for the Paris agreement, and now everybody is kind of taking a hard look at the number and realising that we’re still not there. So, depending on whose analysis that you look at, you add up all the pledges, even the new ones that have been made before Glasgow, we’re still not at 2 °C or 1.5. So, what can we expect there? It’s a bit unclear. In some senses, a lot of the news has already happened. A lot of major emitting countries have already made their own commitments. So, in theory, if everybody holds to what they’ve already committed to then there aren’t going to be any surprises. But I think the hope is you’ll get the leaders in the room and they will all kind of do a kumbaya and everybody will agree to do a little bit more. So, that would be the surprise welcome outcome – something more than we’ve already been told.

Interviewer: Benjamin Thompson

Do you think that’s likely, Jeff? I mean, there’s a lot of talk in the newspapers about how leaders from different countries aren’t going to be in attendance and, just today, the UK prime minister Boris Johnson was maybe less than effusive about his hopes for how well the conference was going to go.

Interviewee: Jeff Tollefson

I think conventional wisdom would suggest that COP26 has already generated what it’s going to generate, for the most part. That said, when you get people together and you shine a spotlight on them, and there will be a lot of pressure coming from the media, coming from NGOs, coming from scientists, it’s possible that people still have some cards in their back pockets that they’re going to negotiate with, and if they can talk other people into doing certain things then maybe they’ll come forward with additional commitments. But I wouldn’t say that that’s a likely outcome. I don’t think anybody really knows.

Interviewer: Benjamin Thompson

I mean, Jeff, obviously you’ve been covering all things climate for a very, very long time now, and been to many COPs. What’s the sense that you’re getting from the researchers that you’ve spoken to ahead of time about how they’re feeling about how things are going to go?

Interviewee: Jeff Tollefson

There are kind of two camps. You have to remember the scientists have been watching this for 30 years as well, and there’s been very little progress over that time. So, there is some scepticism and even cynicism, I think, within the scientific community about the ability of this process to really kind of push governments to do what needs to be done, and you have to remember that COP26 is just a meeting. All of these pledges and commitments, governments have to come home, political leaders have to come home, and sell them to their population. So, the United States has made an ambitious pledge to cut its emissions by 50% by 2030, but if you look at the political situation here, President Joe Biden is having a very hard time getting his climate agenda through the Congress. So, these are the types of questions that I think allow for a certain sense of scepticism. There is one other camp, and those are the folks who look at the technology and say renewable energy has been skyrocketing in recent years, prices are coming down, and in time those technologies are going to win. And I think most people would perhaps believe that clean energy will kind of come out on top in the end. But again, it’s always a question of time. The problem here is scale and time. We don’t have time to mess around, and there’s not a lot of evidence that a lot of governments are taking this as seriously as they need to be if you want to solve this problem in the next 20 years.

Interviewer: Benjamin Thompson

It almost seems a cliché to say, Jeff, but it seems like the hard yards are going to start the day after COP26 then maybe?

Interviewee: Jeff Tollefson

Exactly.

Interviewer: Benjamin Thompson

One other thing, Jeff, that I think it would be remiss not to mention of course is that we are still very much in the middle of a global pandemic. What sort of impact are we expecting the pandemic to have?

Interviewee: Jeff Tollefson

Obviously, COP26 was delayed by one year, so that’s the first impact, and some people say that was maybe not necessarily a bad thing. If the world isn’t ready for COP26 this year, it certainly wasn’t ready last year. So, governments have had more time to think, more time to plan, and that also allowed time for the Intergovernmental Panel on Climate Change to put out its science report in August. At COP26, low-income countries and particularly and especially small island states, those countries that are really pushing for aggressive action because their livelihoods are in direct threat due to rising seas and storms and things like this, they will be using that report as a hammer to try and force more aggressive action. So, all of that might be a good thing. The potential downside is we’ve heard a lot of reports that low-income countries are having a hard time getting their delegations there due to travel restrictions. So, I think, for the most part, probably the negotiating teams for most of these governments are going to be there, but oftentimes small countries rely on NGOs, on civil society organisations, on scientists, to help them negotiate this process, and a lot of those people might have a hard time coming. So, there are some expectations that, broadly speaking, poor countries are going to be less well represented at the COP than they would be in most years. Whether that turns into a political issue is unclear. We’ll have to see how it plays out. The danger would be that if it does become an issue then you kind of lose credibility for the diplomatic process at this COP, which would be a bad thing.

Host: Nick Petrić Howe

Nature’s Jeff Tollefson there, talking with Benjamin Thompson. For more on what to expect from COP26, check out a news story that Jeff has written. We’ll put a link to it in the show notes.

Host: Shamini Bundell

And look out for more COP26 coverage on the podcast in the next few weeks. We’ll be on location, speaking to scientists and letting you in on what’s happening at the conference. Not only that, next week the Nature Podcast is going mobile and for the first time ever will be coming to you from a train. Benjamin will be onboard traveling from Amsterdam to Glasgow and chatting science with some of the people heading to COP26.

Host: Nick Petrić Howe

That’s all for this week. As always, you can keep in touch with us via Twitter – we’re @NaturePodcast. Or send us an email – we’re podcast@nature.com. I’m Nick Petrić Howe.

Host: Shamini Bundell

And I’m Shamini Bundell. See you next time.