Podcast: Genomic sequencing and the source of solar winds

Host: Benjamin Thompson

Welcome back to the Nature Podcast. This week, we’re exploring two very different issues surrounding genomic sequencing…

Host: Shamini Bundell

And learning more about NASA’s mission to the Sun. I’m Shamini Bundell.

Host: Benjamin Thompson

And I’m Benjamin Thompson.

[Jingle]

Host: Benjamin Thompson

First up this week, reporter Geoff Marsh has been investigating a project that aims to help even up global genomics.

Interviewer: Geoff Marsh

In 2003, when the results of the Human Genome Project were reported in Nature, it heralded a new era for biology and opened up the possibility of precision medicine – therapeutics that could be tailored to an individual’s needs based on their particular genetics. Since then, hundreds of thousands of genomes have been sequenced, and big data holds great promise for therapeutics, but up until now, this data has been most useful for a fraction of the world’s population. Here’s Nature’s editor in chief, Magdalena Skipper.

Interviewee: Magdalena Skipper

Traditionally, the focus was very much on individuals of European descent, and in fact, there were studies – one of them published in our pages about three years ago – which estimated that as recently as indeed three years ago, 80% of genetic studies and whole genome sequencing was still done in individuals of European descent.

Interviewer: Geoff Marsh

Considering that less than 10% of the global population is European, it’s clear that these proportions represented in our genomic libraries are out of balance, but it’s not just an issue of equality. Andrew Peterson is one of the researchers on the GenomeAsia 100K Project, which is part of an effort to redress this balance. I called him up to ask why only studying a small proportion of the human population is bad for science and medicine.

Interviewee: Andrew Peterson

There’s two very obvious areas that we miss out on by not focusing on different populations when we carry out genetics studies. So, our ability to predict for an individual their genetic risk for disease is based on a large number of studies that are done in the same population group. On the other side, all of humanity loses out when we don’t carry out genetic studies in other population groups because the biology of disease that we understand from one population can be particularly unique and illuminating but it applies to all of humanity.

Interviewer: Geoff Marsh

And that’s because while great variation exists between different groups of people – we’re all clearly very different – the underlying code of our DNA is the same. By sequencing diverse groups of people, certain associations between genes and traits may be more obvious in particular populations, but those results will apply across the board. As the name implies, GenomeAsia 100K has the lofty aim of sequencing 100,000 genomes from Asian people. This week, they’ve published their pilot study. Now, at the moment, this has included less than 2,000 people, so it hasn’t tipped the scales just yet. But those nearly 2,000 genomes represented 64 countries across Asia and they’re already reshaping our understanding of the sheer diversity present in Asia. Here’s the scientific director of the project, Stephan Schuster.

Interviewee: Stephan Schuster

The big discovery that has been made is that before the start of the project, people thought of Asia more or less as an extension of the European genetic diversity, very different from Africa, but not distinctly different from European. What we now show is that there is an unprecedented amount of diversity that is truly unexpected, and the best way to describe it is that if you think of all the Europeans and their descendants in the different parts of the world make a little less then 1 billion people, they all go back to a single ancestral lineage. If you take the same level of resolution, you would get ten or more lineages for Asia.

Interviewer: Geoff Marsh

This huge amount of variation holds great promise for our understanding of disease, and the results of this pilot study suggest that the reason for all this variation is Asia’s high number of so-called founder populations. Here’s Andrew Peterson again to explain what we mean by these founder populations.

Interviewee: Andrew Peterson

Iceland is one of the easiest to describe because Iceland was founded by a few couples and they then expanded to fill the whole island. That’s very useful because something that was a rare variant in the general population now becomes common. That’s essentially what the founder effect is. So, we know about Iceland and a company called deCODE has been very successful at studying genetic bases of disease by using that founder effect, but what we discovered was although that seems to be a somewhat unusual characteristic in European populations, there are thousands of founder populations in Asian populations.

Interviewer: Geoff Marsh

Is that just because of the sort of dotted island nature of the region?

Interviewee: Andrew Peterson

It is in Indonesia. In South Asia, there are no geographic barriers and really the barriers are cultural barriers so, in other words, strong cultural barriers to marrying outside of the groups that cultural patterns dictate that you marry in, so marrying within your own group. So, it’s very interesting in terms of how cultures and societies and how humans interact, but it’s very, very useful for understanding the biology of disease.

Interviewer: Geoff Marsh

Whilst these results sound promising for our basic science understanding of disease, I wondered whether it would be prohibitively expensive, in developing countries for example, for people to use this information for personalised medicine.

Interviewee: Stephan Schuster

I would say no, and see, this is the other thing that I am feeling very, very positive about because in the developed world, it is always about the patient or the wealth of the healthcare system that the person is associated with, but if we, for example, can make this distinction, that this ethnic group has this high allele frequency for certain variants, you can give recommendations back to all the doctors who are practicing in that area and say, you need to be aware of this adverse effect and also watch out for other things. So, in the end, you don’t need to have every single person sequenced.

Interviewer: Geoff Marsh

Understanding the unique variation within a particular group of people has clear benefits for the members of that population. This pilot study represents a positive step towards expanding our genomic data beyond the borders of Europe, but the effort is far from finished. Here’s Nature’s editor in chief, Magdalena Skipper.

Interviewee: Magdalena Skipper

As wonderful as it is to see this study, and it’s really important and the whole project, I would love to see greater attention paid to similar studies focused on populations in Africa and on individuals of African descent who live elsewhere. These populations are some of the most genetically understudied populations. Those individuals deserve to have those genetic associations surfaced and studied, and also, of course, because we all came from Africa, there is the greatest genetic diversity and amount of genetic variation present in Africa, and we still have not tapped into that.

Interviewer: Geoff Marsh

Do you think these kinds of projects are going to start happening now?

Interviewee: Magdalena Skipper

Oh, definitely, and a number of projects focusing on Africa are taking place already. One that comes to mind immediately is H3 Africa, which is largely funded by the NIH and the Wellcome, but of course there are many others.

Host: Benjamin Thompson

That was Nature’s editor in chief Magdalena Skipper. You also heard from Andrew Peterson and Stephan Schuster, who are both members of the GenomeAsia 100K consortium. You can read their paper over at nature.com.

Host: Shamini Bundell

If you missed last week’s show, we announced our 2019 listener survey. Thanks so much to all of you who have filled it in so far. We’ve had some fascinating feedback but we want even more. To fill it out, just head over to go.nature.com/podsurvey19, and you can also watch our special behind-the-scenes video showing us all in action. Now though, it’s time for the Research Highlights, brought to you by Anna Nagle.

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Anna Nagle

Rivers sculpt the landscape they cut through, but rivers in barren landscapes are more restless than those surrounded by vegetation, altering their course more often. To get an idea how the bends in rivers – known as meanders – alter over time, a team of researchers studied images of rivers flowing through environments ranging from the Arctic to the Amazon. The team showed that meanders in waterways devoid of vegetation shift ten times more quickly than rivers that have plants stabilising their banks. As little is known about the way that rivers behaved before plants arose on land, the team behind this work hope that their findings will provide more information about the evolution of arid terrain, such as that of the early Earth or even Mars. Meander over to Nature Geoscience to find more.

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Anna Nagle

The diet of picky penguins in Antarctica may be the cause of their plummeting population, according to new research. Gentoo penguins and chinstrap penguins both live in Antarctica and both share a taste for krill. However, human activity in the region has led to krill levels fluctuating over the past century, causing a dietary quandary for the creatures. By analysing nitrogen isotopes in penguin feathers from museum specimens of different periods, researchers were able to show that both penguin species feasted on krill when it was plentiful. However, as krill levels declined over the past 40 years, gentoo penguins shifted to a more diverse diet, but the chinstraps didn’t. Over the same period, populations of gentoos flourished, while chinstrap populations are estimated to have decreased by at least 30%. The researchers behind this work suggest that species with more varied diets are less vulnerable to the impacts of human activity such as climate change. Check out that research over at the Proceedings of the National Academy of Sciences.

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Host: Shamini Bundell

Next up on the show, while genomic datasets like the one we heard about earlier can be really useful for geneticists and for doctors, the technology used to profile DNA can have a darker side. Reporter Nick Howe has the story.

Interviewer: Nick Howe

I’m going to start this next bit with a bit of an anecdote. My wife is Serbian and so to stay with me in the UK, she needed a visa. To get it, in amongst all the vast number of things we had to send to the government, she also had to submit her fingerprints. I’m going to be honest – I was a bit uncomfortable about that. I mean being born here, I’d never had to anything like that, so why did she? She thought I was being naïve. These biometric checks are fairly routine in a lot of places. But it seems to me that everyday there’s a new story about how more and more of our privacy is being eroded, with social media data being sold off, huge data leaks, and the emergence of facial recognition technology. I’m starting to become aware that I need to be careful about what kind of personal data I give away and what it could be used for. Does it matter if the government has my fingerprints? Should I let Facebook use an algorithm to automatically detect my face in uploaded images? Should I give away details of my personal life on a podcast? This week, I’ve got a new worry to add to that list, something I hadn’t considered could even be the subject of surveillance, and that’s the vast set of information that is contained in every one of our cells – our DNA.

Interviewee: Yves Moreau

My name is Yves Moreau and I’ve been working for about fifteen years on genome analysis related to rare human diseases and in that framework, I started working on genetic privacy solutions.

Interviewer: Nick Howe

Yves has written a Comment article in this week’s Nature arguing that growing DNA databases are aiding human rights abuses.

Interviewee: Yves Moreau

The biggest example is in Xinjiang in western China, where DNA databases and DNA profiling – the kind of profiling that you use for law enforcement – is being rolled out on a massive scale and Human Rights Watch and others have established that blood samples from the whole population aged 12-65 had been collected in 2016-2017, making it possible to create this massive DNA database of the entire population.

Interviewer: Nick Howe

Human Rights Watch have raised specific concerns about the minority Muslim Uyghur population, as they report that it’s not clear that people are truly consenting to having their DNA catalogued. Also, it has been widely reported that these people are closely monitored by the Chinese government and many have been detained in what the authorities call ‘vocational education and training centres’. The concern is that the inclusion of DNA profiling to existing monitoring may further invade upon the privacy of Uyghur people, but potential abuses aren’t limited to China.

Interviewee: Yves Moreau

I would say that the second biggest concern I have today is on the US-Mexico border. Even people who apply for refugee status at the legal port of entry, all these people will be put in a database next to criminals, as if these people were criminals or at least potential criminals.

Interviewer: Nick Howe

This plan by the US government hasn’t yet been rolled out. But once in place, DNA from immigrants would be put in an FBI database. The Department of Homeland Security claims that this move would help solve crimes, but human rights activists and lawyers have raised concerns about the privacy of immigrants. There are moves to build or create large DNA databases across the world too. Perhaps more so than any other surveillance technology, DNA gives insights into all sorts of aspects of a person – your susceptibility to disease, your ethnicity, your family relationships. In fact, you don’t even have to have your own DNA on file to be identifiable – your family’s data can be used to track you down.

Interviewee: Yves Moreau

This surveillance affects something extremely important, and this is our personal autonomy or ability to behave as we choose. That ability is deeply perturbed when you’re being under constant surveillance, and obviously, this can have benefits, like the ability to commit illicit actions will be limited through surveillance, but also the ability to carry out legitimate actions like political dissent will be very quickly extremely limited through constant surveillance.

Interviewer: Nick Howe

And the danger here isn’t just government officials coming along and demanding cheek swabs. Increasingly, we’re also giving our DNA away. There are now dozens of companies offering you insights via your genetic code. Most have very strict privacy policies, but these can be overridden by the courts for use in criminal investigations. Yves worries this might be the thin end of the wedge. Birgit Schippers is a political scientist who works on human rights implications of surveillance technologies and biometric information. She, like Yves, thinks that we should be concerned.

Interviewee: Birgit Schippers

Surveillance technology can assist human rights abuses. I also share some of the key concerns that have been outlined over the creation of national databases, so this is the kind of databases, whether they’re of DNA or other biometric data, contribute to the creep of surveillance technology.

Interviewer: Nick Howe

Birgit also worries that DNA profiling could be combined with other types of surveillance technology using artificial intelligence.

Interviewee: Birgit Schippers

We can, for example, combine biometrics collected through facial recognition technology with data collected via voice recognition technology and that is actually enabling us to provide a much more effective, efficient, and also accurate tracking of individuals and even whole communities, so that’s why this issue is so particularly worrying.

Interviewer: Nick Howe

With increasing surveillance, are ‘Big Brother’ states inevitable? Well Yves and Birgit hope not. They think that the technology involved in DNA profiling, and other surveillance, should meet ethical and independently verifiable guidelines. If something can lead to human rights abuses then we should think more carefully about how it’s employed at every stage. Yves and Birgit believe that the scientists who work on these technologies should consider how their research could be abused.

Interviewee: Yves Moreau

A lot of questionable research is being published on surveillance technology, on DNA profiling and we as academics, we have to take our responsibilities. What I’ve seen is that while the biomedical community has realised that they hold serious responsibility, in engineering and computer science, we have grown with the idea that what we were doing was benign and that there was nothing to worry about.

Interviewer: Nick Howe

For Yves, if there’s a foreseeable abuse of a technology, then we should act to limit it.

Interviewee: Yves Moreau

We’re not going to stop selling kitchen knives because people could murder someone when they come and buy a kitchen knife, but if somebody was to barge into your store and say that their wife is cheating on them and that they want to buy a knife to kill her, then if you were to sell this person a knife, you would be in trouble and you should be, and so I think that the same thing here is how foreseeable are the abuses and once they are clearly foreseeable, then you actually get some form of responsibility. That applies to businesses and that applies to academics as well. So, you cannot say, ‘I didn’t know.’

Interviewer: Nick Howe

It comes down to whether you consider technology ethically neutral. Do guns kill people or do people kill people? Yves believes that the companies selling DNA profiling technology should be held accountable for what is done with it. Otherwise we risk a slippery slope, and my wife and I could be giving up more than our fingerprints.

Host: Shamini Bundell

That was reporter Nick Howe. He spoke to Yves Moreau from KU Leuven in Belgium, and Birgit Schippers from St Mary's University College, Belfast in the UK. You can read Yves’ Comment article over at nature.com/opinion.

Interviewer: Benjamin Thompson

Finally on the show, it’s time for the News Chat and I’m joined on the line from Colorado by Alex Witze and she covers all things space for us here at Nature. Alex, thank you so much for joining me.

Interviewee: Alex Witze

Thank you for having me.

Interviewer: Benjamin Thompson

Today on the News Chat we’ve got a bit of a special about the Sun – of course, the star at the very centre of our Solar System – and a bunch of new research has come out about that. Alex, what’s the headline here?

Interviewee: Alex Witze

The headline is we’re getting our first look at the very heart of the Sun, the sort of energy, the magnetism, the particles that are roiling it and making it the thing that it is. We’re getting our first close-up look at something called a solar wind. It’s a big stream of particles, just a wind of energetic particles that washes through the whole Solar System, and here on Earth, we experience it all the time. The solar wind is what causes, for instance, the northern and southern lights if you’re up at the poles. It can cause space weather, when we have sort of radio blackouts or other sort of geomagnetic storms, as they call them, and the bottom line of what we’re learning this week is we’ve gone to the Sun and looked at it.

Interviewer: Benjamin Thompson

Well, we’ve known about solar wind and solar flares for a long time – why haven’t we been able to find this out before now?

Interviewee: Alex Witze

One of the really hard things about the Sun is, not surprisingly, it’s really hot, and its radiating all this stuff, so if you want to go there, you have to build a really, really tough spacecraft, and so that’s what NASA and a Maryland laboratory did. It took them many decades to figure out how to design a spacecraft that could withstand the heat. They’re going to go so close that it’s going to get to like 1,400 degrees Celsius, so you can’t just put your usual spacecraft instruments that are used to being in deep space and put them in an oven like that. So, NASA worked really hard to put together this mission. They’ve got this amazing heat shield that sort of shelters all the instruments as they go whizzing by the Sun, and this spacecraft, which is called Parker Solar Probe, loops by the Sun again and again, and every time it gets a little bit closer. It’s gone by three times so far and in the next couple of years it’s going to get even closer. It’s going to be flying straight through the atmosphere of the Sun, so just imagine how hot that must be.

Interviewer: Benjamin Thompson

And this intrepid probe launched in 2018. We know it’s destination, but it takes a rather roundabout way to get to the Sun for each pass.

Interviewee: Alex Witze

Yeah, it goes by Venus and then it goes by the Sun and it is sort of making these loops that go out to Venus and then inside the orbit of Mercury and closer and closer to the Sun. So, it’s kind of like a spiralling in kind of orbit. It’s kind of a mission of delayed gratification. It’s going to take many years before they can get to the closest approach, but this spacecraft has sort of done its first tastes of the Sun. It’s gotten closer than any other spacecraft has ever gotten to the Sun so far, and that’s what’s being reported this week in these new Nature papers.

Interviewer: Benjamin Thompson

Yeah, so you’re right. Four papers then and what specifically have they found?

Interviewee: Alex Witze

They basically found that the energy radiating from the Sun, this solar wind, it’s a lot more complicated than anyone had thought. So, we’re kind of downstream from the solar wind and one of the scientists I talked to described it as kind of being near the bottom of a waterfall. The water is coming down at you, you can see there’s a big sheet of water, but you don’t know where it’s coming from and you don’t know what it was like up at the top of the waterfall. With the spacecraft, by flying to the Sun and looking at where the solar wind is being born, it’s like almost kayaking up the waterfall, if you could do that. But you’re getting closer and closer to the source of this powerful energetic stuff that’s constantly washing over the Earth. So, what they found is some surprises. There are these little, high speed spikes in the solar wind, so sometimes when the spacecraft is flying through, suddenly the solar wind gets twice as fast. It’s like a little burst and it’s very energetic. The magnetism in these little bursts sort of flips around the direction of its magnetic field. I guess if you were going up the waterfall, you’d be hitting really rough patches, and nobody had seen that before and that may have implications for solar storms here on Earth.

Interviewer: Benjamin Thompson

My goodness, a lot going on then. Were the scientists surprised by this? Were they excited by it?

Interviewee: Alex Witze

They’re both surprised and excited. There’s some puzzling things they’ve found in the data. The solar wind also kind of rotates around with the Sun and that’s moving at a different speed than they’d expected. So, there’s all this weird stuff happening and when I asked the scientists if they were surprised, some of them were like yeah, we had no idea this was going on, and others were like, look, this is the first time we’re been to a new frontier. We’ve never been this close to the Sun before. We figured there was going to be weird stuff going on and yeah, it is really weird.

Interviewer: Benjamin Thompson

Well, what are the next steps then for researchers as they continue to paddle up their metaphorical waterfall?

Interviewee: Alex Witze

The one thing that they’re really waiting for in this mission is there’s a boundary at a certain distance from the Sun and they’re waiting for the probe to cross that boundary and they don’t really know where that boundary is. It’s like we’re almost to the edge of the ‘here be dragons’ scenario but we’re not quite there yet. They think that maybe on this next pass by the Sun, which is going to come in January, if we’re lucky we might cross that boundary and all sorts of things might change with the magnetic energy coming from the Sun. You might have particles flowing in different directions, you might have magnetic fields doing strange things, so everyone’s just hoping that we’re going to cross this boundary really soon. We could do it as soon as January.

Interviewer: Benjamin Thompson

My goodness, and what will that mean for astronomy and astrophysics here on Earth?

Interviewee: Alex Witze

Yeah, it’s interesting because the Sun, of course, is just one star among many – I mean, think about the Milky Way, how many stars we have there – so the things that we’re learning from our own Sun, from building this really tough spacecraft and hurling it at our star and measuring all our energy and particles and plasma coming off it, that could help us better understand other stars as well too. The Sun is a very basic star. It’s not anything really special. It’s kind of your ordinary, middle-aged, regular star. So, as we learn more about what causes our Sun to do its thing, it can tell us more about other stars as well too.

Interviewer: Benjamin Thompson

Well, lastly then, Alex, on this one. It seems like we’re getting a lot of data, a lot of exciting results back from this probe. Is this kind of it? Is our interest in the Sun kind of extinguished as a result?

Interviewee: Alex Witze

Oh, there’s lots more to come. There are a couple of other spacecraft now that are looking at the Sun from further away, but we’ve got some really cool stuff coming up in solar physics in the next couple of years. So, as early as February, there’s a European mission called Solar Orbiter. That’s going to launch and be sort of further away from the Sun than Parker is. It’ll be kind of orbiting out there and watching Parker as Parker dive bombs the Sun again and again. And then also next year, in Hawaii, the world’s biggest solar telescope on the ground is going to get going – that’s a US project – and they’ll be taking images of the solar corona every single day. So, they’ll get a really good sense about what the Sun is doing all the time. And then of course, the Sun goes through an 11-year cycle of activity. It has more sun spots, more solar flares, more activity. We’re kind of at the bottom of that right now. The Sun’s kind of in its doldrums. But in the next couple of years, scientists expect that activity to ramp up, so the Sun will start to get much more active and exciting, so all these spacecraft, all these telescopes are going to have an awful lot to look at.

Interviewer: Benjamin Thompson

So, plenty more for us to talk about then in the near future. Alex, thank you so much for joining me today.

Interviewee: Alex Witze

Thanks for having me.

Interviewer: Benjamin Thompson

Listeners, head over to nature.com/news to read even more of the latest science updates.

Host: Shamini Bundell

That’s all for this week. Once again, if you get a chance, it would be amazing if you can fill out our survey. You can find it over at go.nature.com/podsurvey19 or just look for a link on the podcast page over at nature.com/podcast. I’m Shamini Bundell.

Host: Benjamin Thompson

And I’m Benjamin Thompson. Thanks for listening.