COVID, 2020 and a year of lost research

Host: Benjamin Thompson

Welcome back to the Nature Podcast. This week, how the pandemic could widen existing disparities in science.

Host: Nick Petrić Howe

And a symbiotic relationship to rival the mitochondrion. I’m Nick Petrić Howe.

Host: Benjamin Thompson

And I’m Benjamin Thompson.

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Interviewer: Benjamin Thompson

The COVID-19 pandemic has of course changed the world in many ways, including the world of science. In some cases, this has given a kind of turbo boost to research. Think of the speed with which the current vaccines were developed for instance. But the pandemic has also fundamentally disrupted the scientific enterprise in other ways, and this disruption has taken an unequal toll on researchers, worsening existing disparities and leading to some members of the community bearing much more of a burden than others. To find out more, I called up our colleague Holly Else who told me how the world of scientific publishing was altered in 2020.

Interviewee: Holly Else

So, what we saw last year at least was a massive boom in the number of papers that researchers were submitting to journals for publication, and there’s several sort of reasons why that might be. It might be because they are at home and less likely to be doing wet lab-type research, so perhaps they’ve got time to write up papers that have been sitting needing work for many months. So, yeah, I mean, last year there was probably 100,000 papers just on COVID published.

Interviewer: Benjamin Thompson

Yeah, you would imagine that you could see that sort of health and medicine papers would increase, but it wasn’t, it was sort of across the board we saw in 2020.

Interviewee: Holly Else

Yeah, across the board, all subjects. And also, publishing changed quite a lot during the pandemic. So, in order to accommodate the fast research that was going on into vaccines and the virus itself, peer-review structures were tweaked and maybe there was a fast-track system set up which helped papers get published quicker. Preprints – so those are the papers that are uploaded before peer review – they also saw a huge rise in submissions or uploads too.

Interviewer: Benjamin Thompson

On one hand, you can say well, that’s really, really good. It gives us a lot more things to talk about. But, Holly, you and I have talked a lot on the podcast in the past about, well, the significant and persistent disparities that exist in science and in academia – I guess, what, just 30% of researchers are female, for example – and sadly, we’re seeing these disparities really coming through within this sort of submission boom.

Interviewee: Holly Else

Yeah, we are. So, across all career stages and genders and all subjects, submissions for research papers are increasing, but this massive increase has not been equal between men and women. So, the growth of submissions by men has increased a lot more than the growth in submissions by women, and we particularly see this at the senior level, so those who are professors or more. So, the rate of growth between typically a professor in the life sciences might be 10 percentage points higher for men than for women. We see a similar effect in physical sciences but it’s about a 5 percentage point increase for men versus women.

Interviewer: Benjamin Thompson

Well, what do we know about the potential reasons behind this disparity then?

Interviewee: Holly Else

Well, we don’t know too much to be honest. Obviously, if you’re at home trying to do your job while home schooling or looking after people, you probably have some idea what the issues might be, but in terms of systematic evidence we don’t have much yet. And one of the main arguments put forward is that in a lot of societies, women are still the main caregiver in a family and we sort of see that borne out in the data in that it’s the more senior women who are seeing the biggest effects, and they are more likely to have caring responsibilities, perhaps children to home school, than those at the start of their careers. There was one sort of early survey that looked at how much time academics had to do their research in the pandemic, and this particular survey found that in terms of how many hours scientists are dedicating to the research part of their job, they found that women with dependent children, so younger children, had a significantly reduced time available to do research as compared to with men.

Interviewer: Benjamin Thompson

And of course, this could have some quite serious knock-ons, Holly. I mean, I know in science the phrase ‘publish or perish’ is used a lot, which means you need to kind of get your papers and your data out there to be able to apply for tenure or promotions or what have you. So, this could have some quite serious, long-term consequences.

Interviewee: Holly Else

Yeah, this could potentially be a lost year for some researchers, and given the competitive nature of science, like you said, Ben, with the promotion criteria needing publications and outputs and evidence of all these things you’ve done, losing a year on your way to becoming tenure track, for example, could have quite a big implication longer term. So, now, we’re sort of settled into this new working environment, those are the conversations that are now starting to be had amongst funders and those who evaluate research. How can they take into consideration what’s happened in this year and how they need to be mindful of the fact that it’s not everybody who’s been affected in the same way.

Interviewer: Benjamin Thompson

Well, of course, yeah. I mean, here in the UK, we’ve got the REF, the Research Excellence Framework, going on, which is this kind of national academic evaluation exercise. That’s in full swing now and is ongoing. How is this going to account for the issues that you’ve raised?

Interviewee: Holly Else

Yeah, so academics in the UK were preparing for the REF, which is this massive assessment exercise that doesn’t happen very often and when it does it’s very stressful for universities, and that’s when the pandemic hit. So, what’s happened is that the people who administer the REF have extended the deadlines slightly, but they’ve also made some changes in terms of what you can submit. So, for example, if you were writing a book and you were expecting it to be published and actually you haven’t managed to do that because of the pandemic, you can now submit the digital copy or what work you have done. Another thing that’s been affected is where researchers have to show that their work has had an impact in the real world, and lots of researchers might be holding events or conferences or going out into the community and that work forms part of their impact submission, and obviously we haven’t had public gatherings so, in response, the evaluators have increased the window of opportunity that you could show the impact of you work.

Interviewer: Benjamin Thompson

Well, if that’s maybe a positive step then that’s going on in the UK to maybe take into account all that’s gone on over the past year or so, is this part of a broader trend we’re seeing in other countries? And what about independent research funders as well, how are they looking at what’s been going on and how it might be affecting people?

Interviewee: Holly Else

Well, another country that has a big research assessment activity similar to the UK is in Italy, and their timescale is slightly different from ours. So, they have a few more years yet really to figure out exactly how they’re going to take into account what has gone on, but those conversations are very much starting now. And when you talk about independent research funders who are not evaluating, per se, specific research, they might get a grant application, see somebody’s publication history, a lot of that is around working out whether the person who has applied for this grant is the right person to do the work, and the people that we’ve been speaking to feel maybe that they might be slightly less affected because it’s more of a perspective thing. They’re looking for the future whereas the research evaluators are looking back to see what you’ve actually done and how well you did it. But that’s not to say that research funding for grants won’t be affected by this because obviously people’s publication histories and promotion statistics, all that kind of stuff is taken into account when funders are awarding grants.

Interviewer: Benjamin Thompson

Well, finally, Holly, we don’t know if there’s going to be one year, two years, ten years before we kind of really get a sense of the knock-on effects of what’s happened in this particularly strange sort of period of time we’ve had here. But in an ideal world, I mean, where could science go? How do you think the scientific enterprise could improve and could learn from what’s happened?

Interviewee: Holly Else

For me, one of the biggest things science could learn is actually to look back on itself and collect the data, find out what is actually happening. I mean, what is going on? Why is it happening and how can we prevent it from happening in the future? And once we know that, the relevant people can sit around the table to thrash out some way to make sure that allowances are made so that things like this don’t continue to be a problem.

Interviewer: Benjamin Thompson

That was Nature’s Holly Else. This week, Nature has an editorial on how research evaluation efforts need to take into account some of the things we’ve talked about today. You can find a link to that in the show notes.

Host: Nick Petrić Howe

Coming up, we’ll hear how a microscopic protist swallowing a bacterium led to a whole new way of thriving without oxygen. Before that though, Dan Fox is here with this week’s Research Highlights.

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Dan Fox

If having a parasitic worm take up residence in your gut didn’t sound bad enough, scientists have discovered that they may also make viral infections more deadly. Researchers studying mice infected with an intestinal roundworm and West Nile virus found that rodents were more likely to die when infected with both pathogens than when infected by just one. The team found that sensory cells called tuft cells lining the rodents’ intestines activate a cycle to attempt to clear the parasites. But this process could ultimately damage the intestines’ protective inner layer and impair the ability of immune cells to destroy virus-infected cells. The virus can then more readily infect the central nervous system and other tissues. These findings suggest that roundworms can make their hosts more susceptible to infection by viruses that target the intestines. Read that research in full in Cell.

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Dan Fox

Satellite observations have revealed an unprecedented space hurricane in Earth’s upper atmosphere. Previously, the existence of space hurricanes – hurricane-like circulation patterns in planets’ upper atmospheres – has been uncertain. Now, researchers have used satellite data to identify a space hurricane over Earth’s northern magnetic pole, and this hurricane wasn’t a whirling pattern of air but of plasma – ionised gas. Like a regular hurricane, the space hurricane featured a quiet centre, multiple spiral arms and widespread circulation. It also features precipitation, not of rain but of energetic electrons. And like a regular hurricane, space hurricanes could be disruptive as they drag energy from solar wind into Earth’s atmosphere, potentially causing disturbances in radio communications and satellite navigation systems. See if that research blows you away at Nature Communications.

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Interviewer: Nick Petrić Howe

Symbiosis – two different organisms coexisting, in many cases to the mutual benefit of both. These relationships are a crucial element of biology. Part of the reason that complex organisms exist at all is down to a symbiosis. Some time in the distant past, an ancient cell swallowed up a smaller cell and the symbiosis between mitochondria and eukaryotes was born. Mitochondria are organelles that allow eukaryotic cells to create energy in the form of ATP using oxygen. But some eukaryotes live in areas where oxygen isn’t present. They survive primarily using fermentation, which produces energy but not as efficiently as mitochondria. But now, researchers have discovered an organism with a brand new way of thriving without oxygen. A paper in this week’s Nature describes a single-celled organism discovered in a lake in Switzerland that rather than using oxygen or fermentation can produce energy from nitrogen oxides, and it does it by creating a symbiosis with a bacterium, much like the ancestor of eukaryotic cells did with the ancestral mitochondrion. I called up one of the researchers, Jana Milucka, to find out more about their discovery.

Interviewee: Jana Milucka

Well, what we found was we believe we understand the mechanisms by which anaerobic eukaryotes can also respire under an aerobic conditions, so they live without oxygen but they have reverted to respiring a different electron acceptor under these conditions, and the mechanisms by which they accomplish this respiration is that they have entered a symbiosis with a bacterium which performs this process for them. And this sort of respiratory symbiosis or energy symbiosis, if you will, is really unusual and as far as we know, a similar type is only known from the original symbiosis between the mitochondria predecessor and the original archaea.

Interviewer: Nick Petrić Howe

Tell me about this symbiosis. What cells are involved in this and is it sort of an endosymbiosis where one is inside the other or is it a different sort of relationship?

Interviewee: Jana Milucka

Yeah, so the host is an anaerobic unicell or ciliate and the endosymbiont is an obligately endosymbiotically living anaerobic bacterium that has the capacity to perform denitrification, so anaerobic respiration.

Interviewer: Nick Petrić Howe

So, it’s a way for these organisms to use, as you said, nitrate as an electron acceptor, so use them to create energy. Were you surprised when you saw this?

Interviewee: Jana Milucka

Yes, very much so. I must say, this is not something that really we in anyway anticipated to find. What we first found was the genome of the endosymbiont and already from the properties of the genome we could tell that we were looking at something that is not a free-living organism, but it is something that has been living together with a host for a long, long time, and we could tell that from the fact that the genome was very small and it had specific features that are very typical among obligate endosymbionts. However, the obligate endosymbionts known to date that have genomes with these sorts of properties, they occur in insects, for example, and they primarily serve the function that they provide that host with nutrition, for example with essential vitamins or other nutrients, or maybe they provide defence mechanisms for the host. But when we looked at the genes that were encoded in the endosymbiont genome, we saw that the metabolic capacity to provide to synthesise any sort of vitamins were nearly absent from the genome, so clearly the function of these organisms was not to synthesise something. On the other hand, the capacity to encode enzymes for the respiratory pathway for the export of ATP and any genes related to respiration and energy metabolism were abundantly present in the genome and were also highly transcribed, pointing to the role that this organism plays a role in respiration and in energy metabolism.

Interviewer: Nick Petrić Howe

And so you said you found this basically through doing some sort of sequencing. Were you able to test experimentally what was going on here? Were you able to show what exactly the processes these things are undergoing in the lab?

Interviewee: Jana Milucka

We thought that was absolutely crucial because the predictions from the genome were so unbelievable that we really wanted to make sure that this is indeed what is happening in situ. But we don’t have cultures of these organisms, so all the experiments that we did we had to perform with ciliates that were hand-picked into the experiment vials. Indeed, we did test for the process of denitrification, so we picked the individual ciliates and we measured whether they were capable of respiring nitrate, and we do see that this is what is going on.

Interviewer: Nick Petrić Howe

Does this endosymbiont that you’ve found, this relationship, does this give us any clues as to how this might have happened with the mitochondrion?

Interviewee: Jana Milucka

So, the mitochondria and this symbiont, they have a completely different independent evolutionary origin. The predecessor of our symbiont and the predecessor of mitochondria do not share common origin. But it appears that the path they took down the line, the evolutionary path, seems to be very similar. So obviously, mitochondria much further than our symbiont because they had much longer to evolve and they have also lost more genes in that process, but when we look at where our symbiont is now, it’s intriguing that it has maintained such a strikingly similar set of functions and genes to those that mitochondria have retained. So, yes, I think it tells us something about the evolution of these kinds of respiratory symbiosis and to date, we thought that this is an event that happened once and it’s something that cannot be repeated, but I think based on this discovery we should rethink whether this sort of symbiosis and these sorts of evolutionary trajectories of symbiosis might happen more often.

Interviewer: Nick Petrić Howe

That’s a really interesting proposal. So, what are your sort of next steps with this? Where is this research going next?

Interviewee: Jana Milucka

The biggest question I think is really how and where this symbiosis evolved, and for that we will have to look in a different setting than the lake that we studied because the lake in Switzerland we looked at is a post-glacial lake and this lake only originated roughly 10,000 years ago. But we know that the symbiosis that we are looking at is hundreds of millions of years old, so the question is where did it start? Is there maybe a freshwater system that is old enough to have been the cradle for this symbiosis or did this symbiosis evolve from the marine system and adapted to freshwater afterwards? I think these are all exciting questions.

Interviewer: Nick Petrić Howe

That was Jana Milucka from the Max Planck Institute for Marine Microbiology in Germany. To find out more about this endosymbiosis then be sure to check out the show notes where there’ll be a link to Jana’s paper and an accompanying News and Views article.

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. Nick, what’s your Briefing highlight this time?

Host: Nick Petrić Howe

Well, I’ve been reading an article in The Guardian all about the Atlantic Meridional Overturning Circulation – a system that underpins the Gulf Stream in the Atlantic – and it seems like it’s at the weakest it’s been for a millennium.

Host: Benjamin Thompson

Well, Nick, I’ve heard about the Gulf Stream certainly – that’s what sometimes brings half-decent summer weather to the southwest of the UK – but the other thing you said there, I must confess I am less familiar with it.

Host: Nick Petrić Howe

Yeah, and I’d emphasise the ‘half-decent’ weather to the south of the UK. But yes, the Atlantic Meridional Overturning Circulation – let’s just call it AMOC for short – is basically a system of currents that underpins the Gulf Stream, and it’s essentially what brings warm water from the Gulf of Mexico up all the way to Iceland where it gets cooler and saltier and continues to pull more warm water from the Gulf of Mexico, and it’s responsible for kind of making things sort of mild and a bit wet here in the UK and having sort of a warming effect overall on western Europe and making things a bit more mild. And that’s the thing that appears to be affected according to this article in The Guardian, and researchers have basically been looking at ice cores and other data that can give us information about the weather from the past millennium and have said that it looks like it’s at its weakest point that it’s been for a thousand years, and climate change is the probable cause.

Host: Benjamin Thompson

I mean, it seems that on our Briefing chats it often is a probable cause, Nick, and I’m guessing that this is probably not good news then.

Host: Nick Petrić Howe

No, so, as I said, this AMOC brings nice weather, essentially mild weather, to the UK and Europe, so its disruption isn’t particularly great, and potentially this could lead to more uncertain weather in Europe. It could lead to more hurricanes in the UK, it could lead to more heatwaves, and even on the east coast of the US it could lead to higher sea levels, so not great all around. So, the AMOC has slowed by around 15% and by the end of this century it could go as much as 45% slowing down, and if it gets to that point then researchers are worried that we’ll reach some sort of tipping point where we can see some of these more disastrous effects.

Host: Benjamin Thompson

I mean, that really doesn’t sound good then. I mean, is there anything the researchers think can be done to try and obviously avoid this scenario?

Host: Nick Petrić Howe

I mean, it’s a similar story with a lot of climate change work, and that is we need to produce less greenhouse gas emissions and we need to work more quickly towards a world where we are either carbon neutral or actively reducing the carbon in the atmosphere. So, we know what to do, like we’ve known what to do for a long time now, it’s just doing it and this is just another bit of information that will show one of the potential impacts for not doing enough when it comes to climate change.

Host: Benjamin Thompson

Well, Nick, I’ve got a story that’s certainly kind of related to climate change, I guess, and it’s to do with a new satellite that was successfully launched a few days ago, and it’s a story that I read about in Science.

Host: Nick Petrić Howe

Oh, okay, and will this satellite give us more data to understand the impacts of climate change or past climate change?

Host: Benjamin Thompson

Well, it certainly will give more data, and actually it’s kind of an achievement for Brazil because it’s the first time they have sort of designed and made a satellite in its entirety, and it’s now up in orbit, going around. And what it’s doing is it’s having a good look at the Amazon rainforest, so it’s called Amazonia-1, and it’s going to be part of a three-satellite series, and it’s really getting sort of eyes on what’s going on there in terms of things like deforestation.

Host: Nick Petrić Howe

Yeah, and the Amazon is something we hear a lot about and in terms of how it’s being depleted and fires and all sorts. It’s not really that much good news. But what will this new satellite, this Amazonia-1, tell us about what we don’t know about the Amazon rainforest?

Host: Benjamin Thompson

Well, this satellite, which was developed by Brazil’s National Institute for Space Research, it’s got these kind of cameras on it and it’s got a bunch of tech that will let it see any areas of deforestation I think larger than 4 football pitches or 4 soccer fields, I guess, that have been deforested. Now, the imaging that it provides isn’t actually better than satellites that are already sort of going around and looking at the Amazon rainforest, but what this satellite does, it means that the time between images being taken is much shorter. It’s only a couple of days before when a satellite goes over to have a look, I think, at this point, and so it can almost give essentially more real-time data that can be used by law enforcement agencies to stop logging where it shouldn’t be done, for example, and also give data on things like the forest fires that you mentioned to researchers.

Host: Nick Petrić Howe

Well, we’ve been a bit dour on this week on this week’s Briefing chat, but this actually sounds like a bit of good news.

Host: Benjamin Thompson

Well, Nick, good and bad news, I’m afraid, with this story. Scientists are obviously eager to get their hands on this data, but there are concerns that the data on deforestation may be of limited use, and that’s in part because, for example, Brazil’s president back in 2019, he said that the sort of data that had been collected on deforestation was false, for example, and there are also concerns about how science will be funded in Brazil and in terms of how the mission can continue. And also, researchers are saying, ‘Well this is great, we’ve got this satellite, but we’re going to need a lot more to be able to see over a much wider area to really get a handle on what’s going on in the rainforest in as close to real time as we can.’

Host: Nick Petrić Howe

Well, more data can only be a good thing as long as it’s accessible and used well. So, thanks for telling me about that, Ben. And listeners, if you’re interested in more stories like this but instead as an email then make sure you check out the Nature Briefing. We’ll put a link in the show notes where you can sign up.

Host: Benjamin Thompson

Before we go, just time to tell you that we’ve got a new video on our YouTube channel. It’s about how scientists are trying to build a quantum internet and to do so, they need to develop these things called quantum repeaters, and you can find out what they are in the video, and we’ll put a link to that in the show notes.

Host: Nick Petrić Howe

That’s all for this week. As always, if you want to reach out then we’re on Twitter. We’re @NaturePodcast. Or if you prefer email then we’re podcast@nature.com. I’m Nick Petrić Howe.

Host: Benjamin Thompson

And I’m Benjamin Thompson. See you next time.