A lab assistant uses a pipette to prepare Coronavirus RNA for sequencing at the Wellcome Sanger Institute that is operated by Genome Research in Cambridge, Thursday, March 4, 2021.
( Frank Augstein
JOSH SOMMER Every single person eventually is going to be a patient. Like none of us escapes disease, and so it behooves all of us to get the rapid flow of information in research right.
ROXANNE KHAMSI The coronavirus opened the floodgates by bringing down paywalls. What will happen next? From WNYC in New York, this is On the Media, I'm Roxanne Khamsi. Also on this week's show, how one unconventional database is taking on the traditional science world.
MERIDITH WADMAN Here you have this one man controlling access to what's just become a vital database for researchers the world over.
ROXANNE KHAMSI Plus, the language of mental health. Are you burnt out, breaking down? Perhaps you're languishing.
ADAM GRANT When you're languishing, it's not depression because you still have a sense of hope. It's not burnout, you still have energy. You just feel a little bit joyless and aimless.
ROXANNE KHAMSI How to describe a pandemic state of mind. Coming up after this.
BROOKE GLADSTONE From WNYC in New York, this is On the Media, I'm Brooke Gladstone. So, the show's finding a new rhythm this summer, and that begins this week for two pressing reasons. The first, of course, is Bob's departure. The second less dramatic is that I long ago made plans to see my daughter in L.A. after 15 long months, and I'm going. So I'm handing off the episode to the first of several incredible new voices who'll host with me or like this week, host alone.
[Price is Right Music Plays]
BROOKE GLADSTONE Roxanne Khamsi, come on down!
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BROOKE GLADSTONE Welcome to our world.
ROXANNE KHAMSI Thank you, Brooke. I am a long time listener, first time guest host-er, and I am so excited to be here. In my regular life. I'm a science journalist and I write for places like The New York Times and Wired.
BROOKE GLADSTONE You couldn't be coming at a better time because you've been doing so much reporting on the pandemic.
ROXANNE KHAMSI Yeah, it's been keeping myself and a lot of us science journalists really busy, and it's a thrill to be part of the show because I think that people don't always think about science journalism as deeply influenced by the larger forces in media and politics, but I think there's a lot that we need to talk about there.
BROOKE GLADSTONE I can't wait to hear the show.
ROXANNE KHAMSI Thank you, Brooke. So, as I told Brooke, I'm a science journalist, and I've been on the beat for many years. On this week's show, I want to open a window into how scientists do their work and share it with the wider world. So in the next couple segments, I'm going to introduce you to some of these mechanisms that keep the scientific world spinning. OK, here we go!
Variants, our versions of the coronavirus or any virus that have evolved slight genetic tweaks. In order to understand how the virus is mutating, scientists share genetic sequences. Those sequences are a window into how an organism works, how it's created, and how it's changed from its predecessors. When a researcher identifies the genetic sequence for a variant of the coronavirus, the easiest way to share it is through an online database, but not all databases operate the same way. One key difference – credit. In traditional databases run by governments and NGOs, researchers can access data and use it for their own analysis without having to say where or whom it came from. That's led to a problem. Many researchers in the global south argue the Western world is far too comfortable receiving data without giving any attribution in return. In 2008, though, the global Initiative on aharing all influenza data, known as GISAID, decided to try and level the field. Meredith Wadman is a staff writer for Science magazine, and she explains how glissade, having become one of the biggest databases of its kind, is unlike the others. And it's not just because it was founded by a former media executive.
MERIDITH WADMAN ....Named Peter Bogner, who established it back in 2008 in a bid to make influenza sequences really readily available to far more scientists than they were. And also, he wanted scientists in non wealthy countries when they deposited sequences into the GISAID database to be credited when those sequences were used in publications, for instance. And he wanted any scientist using those sequences to reach out to the scientists who deposited them and try to collaborate with them so that they become a coauthor, for instance, on such a paper. This isn't typically how, well I'll call the legacy databases, the big ones like the US's has GenBank or like the European Nucleotide Archive, work. They work with completely anonymous access to the database and anonymous use of any material in it. And so that's quite a different model to what GISAID established.
ROXANNE KHAMSI What's happened to get said during the pandemic? Has it grown?
MERIDITH WADMAN Oh my God, yes. It really has become the worldwide database that scientists are putting their coronavirus genome sequences in, and give you just a flavor of how quickly it's growing, when I wrote a piece for Science about GISAID that was published in early March, there were about 700,000 sequences in it. Today, May 25th, there are 1.7 million and growing. And the more that goes into it, the more people want to deposit there, because they know that that's where everyone is going to be turning to find coronavirus sequences of interest for study.
ROXANNE KHAMSI I get the sense that different scientists have different perspectives on what kind of database works best and that the sticking point does seem to be this credit question. How does credit work when scientists do use each other's data, and why is this so important?
MERIDITH WADMAN Well, papers and publications are the lifeblood of a scientific career. If you deposit data and are not given a chance to collaborate, that doesn't help your advancement. And while GenBank, the US government sequenced database and others like it do require you to say, "I used GenBank sequence E4892 in this paper". And while a curious reader and a determined one could go back and use E4892 to find out who deposited it in GenBank, that person will in no way receive credit for that deposition and will remain obscure. So GISAID and GenBank, in terms of that crediting process, are very different.
ROXANNE KHAMSI There's clearly research done all over the world and there are these legacy databases. As I understand, there was kind of a letter that was written with some signatories. What were they looking for?
MERIDITH WADMAN Oh, my gosh. So this was like the powers that be in the genome sequencing world. There's more than 700 people, almost all of them Europeans, some North American who signed this letter that was published in Nature back, I believe, in February. Singing, without naming, GISAID that all sequence data should be freely and anonymously accessible with no constraints. Any scientist should be able to go into a database and just get what they need and have no one control how they use that. It went through in Canada, and there we're fewer than 20 signatories from the global south on that letter. This was a first world effort to say we think our model is better and we really hope you'll deposit to our databases, which don't have constraints on how you use and share the data.
ROXANNE KHAMSI I guess that's what confuses me a little bit, is what are those constraints beyond just credit the folks who are uploading the sequences? It seems like they're really doing important work. What is so difficult about acknowledging people?
MERIDITH WADMAN What the Western letter writers were objecting to wasn't that if I look at sequence in GISAID and use it in my work, I need to reach out to the depositor of that sequence and try to collaborate with them. That's another issue. Their issue is some of the constraints that GISAID imposes around how, as a scientist, I can then further share the data once I've gotten it from GISAID. So let's say I want to create a website that is for my community. I'm a good scientist and I think I could do a pretty good variant tracker and I want to just put this out for free use. So people in the eastern U.S. can see how various variants are moving between states here, for example. GISAID won't let you just use the data in a public service way like that, not without going through explicit approvals that are sometimes given and sometimes not.
ROXANNE KHAMSI So even though these legacy databases are putting up a fight, is there any real chance the tide will turn against GISAID?
MERIDITH WADMAN I think that's hugely unlikely just because the momentum now is so strong for deposition and to GISAID. It's not to say that certain researchers aren't depositing both into GISAID and into the legacy databases. No reason not to do that, although Peter Bogner doesn't like it when they do. He is all about GISAID only, but why are you going to deposit if you want your material used to a government database with at most several hundred thousand samples when you've got just a widely relevant database with sequences from so many countries and with 1.7 million samples and growing, you know, it's probably grown by dozens, just as we've been talking.
ROXANNE KHAMSI Could GISAID's size and power have unexpected consequences for the scientific community?
MERIDITH WADMAN Yeah, I mean, the scientific community in the West, at least in some ways, just doesn't know how to deal. Because they're used to these governmental agencies and international aid groups or non-profits working together, or the World Health Organization in a very establishment way running these databases. And here you have this one man who's kind of judge and jury on the whole thing, controlling access to what's just become a vital database for researchers, the world over.
ROXANNE KHAMSI So all of this is very scientific sounding and almost a little abstract. For all of us living through this pandemic, is there an example of an instance where this data, in GISAID really helped us somehow understand the coronavirus or what to do about it?
MERIDITH WADMAN Oh, I think there's probably a myriad of examples. One that comes to mind for me is when South African researchers in December published a paper defining for the first time the important variant and concerning variant that arose in South Africa, they were able to use GISAID data to establish that this was a new, very concerning variant with several worrisome mutations that was driving this wildfire outbreak in the Eastern Cape and later the Western Cape. And GISAID data made that paper possible.
ROXANNE KHAMSI Thank you so much, Meredith.
MERIDITH WADMAN Oh, it's been a pleasure.
ROXANNE KHAMSI Meredith Waldman is a staff writer for Science magazine and the author of The Vaccine Race: Science, Politics and the Human Costs of Defeating Disease. We reached out to GISAID for comment, and Peter Bogner himself called us back. He said that scientists who wish to use GISAID must identify themselves, and when creating a website with GISAID data, they must state what they want to do. He said that typically anybody that makes an application for a website gets a green light.
Coming up, a 355 year old business model is under pressure to change. This is On the Media.
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