Podcast: An ancient bird trapped in amber, and life beneath the ocean floor

Host: Shamini Bundell

Welcome back to the Nature Podcast. This week, a tiny, ancient bird trapped in amber…

Host: Nick Howe

And evidence of life far beneath the ocean floor. I’m Nick Howe.

Host: Shamini Bundell

And I’m Shamini Bundell.

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Host: Nick Howe

First up on the show, it’s another story for which we’d definitely be playing the Jurassic Park theme tune if we could get the rights. That’s right – it’s time to return to the age of dinosaurs once again. Imagine a small lump of amber held up to the light so that it seems to glow orange and trapped within, a tiny, perfectly preserved bird skull.

Interviewer: Shamini Bundell

Jingmai O’Connor is very excited about her latest find.

Interviewee: Jingmai O’Connor

When I first saw this specimen, I was completely blown away. I was going around showing it to everyone like, ‘Look at this! It’s so cool!’

Interviewer: Shamini Bundell

And with good reason – the tiny bird skull encased in amber is unique and mysterious.

Interviewee: Jingmai O’Connor

It’s so weird. It has this weird combination of morphologies that makes it really difficult to understand how it’s related to other birds, what it was doing, like what was its ecology.

Interviewer: Shamini Bundell

Jingmai is a palaeontologist at the Chinese Academy of Sciences in Beijing. She’s worked on a number of recent specimens of tiny animals that got trapped inside sticky tree resin. These creatures have been perfectly preserved inside the solidified material ever since the time of the dinosaurs.

Interviewee: Jingmai O’Connor

When you have an animal preserved in amber, it looks like it just died yesterday. All the soft tissue in place, trapped in this little window into an ancient time.

Interviewer: Shamini Bundell

This most recent specimen is a skull only 7.1 millimetres long. It’s around the size of the skull of a bee hummingbird, the smallest living bird species. It’s encased in amber that formed 99 million years ago in the Cretaceous period of what is now Myanmar, and it’s been identified as a new species named Oculudentavis khaungraae. Jingmai and her colleagues put the lump of amber into a CT scanner to get a detailed view of the skull inside it.

Interviewee: Jingmai O’Connor

There’s three things about this little specimen that really stand out. One is, of course, it’s size. It’s just so tiny. But then it has all these teeth – that’s the second thing that’s really weird – so you have something that’s really tiny but clearly also a predator, which is just kind of a little bit counterintuitive, and it also has this huge eye. But then if you think about it, some of the birds with the best visual abilities alive today are predatorial birds like owls or falcons. However, there predatorial birds alive today, all their eyes face forward, which gives them binocular vision, which is way better if you’re hunting for prey, but this bird had its eyes facing to the side, so it had zero binocular vision, meaning that the two eyes didn’t overlap with each other. So, there’s nothing alive that has eyes like that so we have no idea really how this bird might have lived.

Interviewer: Shamini Bundell

This tiny, toothy bird lived in the age of dinosaurs, part of a diverse ecosystem that included huge, long-necked sauropods, carnivorous theropods and flying pterosaurs. But while a lot is known about the largest creatures of this period, thanks to huge fossil bones, details on the creatures filling the smallest ecological niches are scarce.

Interviewee: Jingmai O’Connor

These tiny organisms can only be preserved in amber. Even in other places where you have exceptional preservation, small things might have existed but we don’t have any evidence of it. So, if It wasn’t for amber, we wouldn’t know about this minute fauna at all.

Interviewer: Shamini Bundell

Specimens preserved in amber like this help fill in the ecological blanks. They’re also undeniably beautiful, but it takes more than that to impress Henry Gee. Henry is a senior editor here at Nature and the person that papers on this kind of research go to first.

Interviewee: Henry Gee

When the paper arrived on my desk, I have to say I felt a little tired because I get to see quite a lot of papers reporting all sorts of interesting things preserved in amber. But then I had a look at it and to have something preserved that actually is unexpected, to really make you sit up, that’s actually quite rare.

Interviewer: Shamini Bundell

Various features show that this species was a very primitive member of the group we now call birds, though back in the Cretaceous, they were just another kind of dinosaur. And what Henry finds particularly interesting about this animal is its extremely small size compared to other birds and dinosaurs from that time.

Interviewee: Henry Gee

We knew that dinosaurs on the bird line, as it were, were getting quite small, but this is absolutely extreme and like nothing we had ever seen before. Nobody had any idea that dinosaurs were that small, that early. What it does is underscore the fact that the dinosaurs really were dominant in the Earth ecosystem. They really filled all the holes that are now filled by mammals, reptiles and, of course, birds, so if there was an ecological niche to fill, you can bet there’d be some dinosaur that would fill it. So, there were dinosaurs as big as buses and there were dinosaurs as small as or smaller than hummingbirds.

Interviewer: Shamini Bundell

Amber provides an amazing window into these tiny ecological niches, but palaeontologists need to be careful when looking to amber for answers.

Interviewee: Henry Gee

Amber from Myanmar is mined commercially and there have been concerns raised about the ethics of the mining operations, both in relation to the conditions in which it’s mined and the activities that selling the amber goes to fund. So, we have asked the authors to provide a statement saying that their fossil was obtained above board, as it were, and that’s something that I think we would do for most amber fossils.

Interviewer: Shamini Bundell

With more and more fossils being found in amber, particularly in Myanmar, this is something that will be an ongoing concern. Jingmai, however, is still excited about what the next set of amber fossils will reveal.

Interviewee: Jingmai O’Connor

Right now, we’re only in the very beginning of the study of these specimens, of what information we can glean from this material. But I’m hoping in the next ten years that we’re going to develop techniques that are going to allow us to access the biochemistry of the soft tissues that are preserved in there to be able to look for melanosomes in the feathers, in order to determine colour. But also, I actually am sitting on quite a few amazing specimens that I haven’t had time to study yet, but there’s a lot of very cool things that we still have on the backburner that we’ll be studying very soon, so stay tuned. There’s a lot more cool stuff out there.

Interviewer: Shamini Bundell

That was Jingmai O’Connor of the Chinese Academy of Sciences and Henry Gee, senior editor here at Nature. You can find the paper online now at nature.com, but if you want a 360-degree view of the specimen and to hear more from Jingmai, head over to youtube.com/NatureVideoChannel, where we’ve got a short film exploring the new find.

Host: Nick Howe

Coming up in the News Chat, we’ll talk about the problem of peer review in predatory journals. Right now, though, it’s time for the Research Highlights, read this week by Dan Fox.

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Dan Fox

Imagine an ancient Norse Viking. Are you picturing an intrepid explorer? A fearsome warrior? A skilled seaman? Well, you can probably add another feature to your mental image – a terrible toothache. A team of dentists and ancient historians have investigated the prevalence of dental cavities in the remains of 18 individuals buried in a 10^th-century graveyard on the Swedish island of Gotland. They found that 14 were suffering from the signs of tooth decay and several had lost whole teeth before they died. The researchers hope that this study can offer some new insight into Viking life on the island, where they think that a diet rich in sugary foods like berries, fruit or the honey-based alcoholic drink mead, might be a cause for the high number of cavities. However, despite the lack of modern dentistry, the team found that the Vikings had, on average, fewer cavities than modern humans. Sink your teeth into that research at International Journal Osteoarchaeology.

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Dan Fox

Every year, 1.3 million Serengeti wildebeest migrate through the Mara River basin in Kenya and Tanzania. Thousands drown trying to cross the river and now, researchers have learnt how their bones go on to feed one of the world’s most famous ecosystems. Scientists from the University of Florida in the US staked bags of fresh bones to the riverbed, and measured the bone nutrients before and after 216 days in the water. They found that nitrogen quickly leached out of the bones, whereas phosphorus was released much more slowly into the environment. These nutrients fed sticky collections of bacteria called biofilms that grew on the bones and, these biofilms, in turn, fed fish and other river creatures. Read that research in full at Frontiers in Ecology and Evolution.

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Host: Nick Howe

The cliché goes that we know more about the surface of the Moon than we do about the bottom of the oceans, and those murky depths are where we’re headed for our next story on this week’s podcast. Despite being an inhospitable environment, researchers have found whole communities of microorganisms living in the often incredibly thick layer of sediment at the bottom of the Earth’s oceans. Microbes have even been found in the layer of rock beneath – the so-called upper oceanic crust. But what about the layer of rock below that – the lower oceanic crust? In a paper in this week’s Nature, a team of researchers have taken to the waves to look for life hundreds of metres below the bottom of the sea. One of these researchers is Ginny Edgcomb from the Woods Hole Oceanographic Institution in the US. Benjamin Thompson gave her a call to talk about her search, and he began their chat by asking her what was known about microbes in the lower oceanic crust.

Interviewee: Ginny Edgcomb

A previous team had sampled the lower crust in a completely different location, and they had used DNA-based approaches to recover the signatures of microbes from that site, and so we thought that there was a pretty good likelihood that we would find more evidence for microbial activities and that we would be able to culture microbes from the lower crust.

Interviewer: Benjamin Thompson

And what sort of depths were you looking at in this study?

Interviewee: Ginny Edgcomb

We were on a ship in the Indian Ocean at a site that’s east of Madagascar, and this site is called Atlantis Bank. There was only about 700 metres of water above the seafloor because the lower ocean crust is exposed directly at the seafloor of this spot due to plate tectonics, which makes it easier for the drill ship to drill further into the lower crust. We drilled to about 780 metres below the sea floor, so we’re looking at around 1,500 metres depth.

Interviewer: Benjamin Thompson

And what were you looking for specifically in these drill samples from the lower crust?

Interviewee: Ginny Edgcomb

Well, as the drill advanced and as the samples came up to the ship, we selected samples from each 10-metre-depth fraction that showed the most evidence of rock-water interaction and the most evidence of fractures and veins in the rocks because we posited that if microorganisms are to be found there, we’d most likely encounter them in regions where fluids could pass through the rocks that could deliver much needed nutrients to that realm.

Interviewer: Benjamin Thompson

And I guess the $64,000 question – how deep did you find evidence of life underneath the seafloor?

Interviewee: Ginny Edgcomb

The deepest sample that we have analysed is from about 750 metres into the lower crust, and we found evidence of active microorganisms there.

Interviewer: Benjamin Thompson

And how did you show that these microbes were active?

Interviewee: Ginny Edgcomb

For each of our samples, we took material and we extracted different types of biomarkers, for instance, lipid biomarkers, which are indicative of viable intact cells. We extracted messenger RNA, which tells us that the cells, at least, were taking the first steps towards protein synthesis, and we cultured bacteria and microbial fungi from our samples.

Interviewer: Benjamin Thompson

That was my next question. What did these results show? What sorts of things did you find?

Interviewee: Ginny Edgcomb

The analyses of the bacterial enrichments are still in progress, but we have established a collection of around 200 unique fungal isolates, and these are really fascinating to us because we have recovered fungi from deep subsurface sediments in previous studies, so it’s exciting to us to find them also in the lower ocean crust.

Interviewer: Benjamin Thompson

How are these microorganisms surviving at such depths?

Interviewee: Ginny Edgcomb

The ones that are active are probably very resourceful at recycling organic carbon. They are expressing genes involved in the metabolism of amino acids and of lipids, so they’re basically eating the cells of their dead neighbours, and they’re able to recycle pools of organic carbon within their own cells. They also appear to be able to store carbon in the form of a molecule called polyhydroxyalkanoate. This has only been demonstrated using laboratory cultures to date.

Interviewer: Benjamin Thompson

So, were you surprised or delighted to find microorganisms at this depth?

Interviewee: Ginny Edgcomb

I was more delighted than surprised because I thought that we would find living organisms, and I just hoped that we would drill through zones where there was fracturing and fluid flow and we were lucky that we did.

Interviewer: Benjamin Thompson

Well, finally, Ginny, if we can zoom out a bit and take a look at your expedition as a whole, what’s it like to be a microbiologist on the ocean waves?

Interviewee: Ginny Edgcomb

These are three-month expeditions, and so the ship works 24 hours a day. The science party is divided into two ships, and so there’s always a microbiologist processing samples 24/7.

Interviewer: Benjamin Thompson

Is that hard to do? I’ve been on maybe a ferry or something when my family go on holiday, and I don’t really have my sea legs and if my pipet was shaking around underneath me, that might make things difficult. What is it like trying to microbiology when your lab is sort of shifting from side to side?

Interviewee: Ginny Edgcomb

The JOIDES is very stable so on 9/10 of the days, this is not a problem. You get your sea legs fairly quickly and you get into your sleep and work routine. You show up for work. You have your breakfast at whatever hour that is and start working in the lab. You spend a lot of time running up to the deck where the cores are brought on to the ship, and then running down to the microbiology lab to process the samples before the next one comes up on deck.

Interviewer: Benjamin Thompson

You’ve said something there that I need to pick you up on. You said, ‘9/10 of the time this isn’t a problem’, which suggests to me that there’s something else going on in the 1/10 time. Ginny, what would you explain that to be?

Interviewee: Ginny Edgcomb

Well, the weather is not always perfect and we do encounter rough weather sometimes. We sailed through a few fairly significant storms in the Indian Ocean on our way to the sampling site, so that was pretty exciting and people spent a lot of time sleeping in their bunks.

Interviewer: Benjamin Thompson

Are you pleased to be going back to the dry land lab when you have to analyse these samples?

Interviewee: Ginny Edgcomb

Yeah, I think by the end of three months everybody – even though it’s wonderful interacting with the other scientists and the science party – is ready to go home.

Host: Shamini Bundell

That was Ginny Edgcomb talking with Benjamin Thompson. You can read her paper over at nature.com.

Interviewer: Nick Howe

Finally on the show, it’s time for the News Chat, and I’m joined in the studio by Nisha Gaind, Nature’s European Bureau Chief and Richard Van Noorden, features editor here at Nature. Hi, both.

Interviewee: Nisha Gaind

Hello.

Interviewee: Richard Van Noorden

Hi.

Interviewer: Nick Howe

So, first up, it’s of course time to talk about coronavirus again and the usual caveat applies – this is recorded on a Tuesday morning and things may have changed quite a bit since we’ve left the studio. So, Nisha, since you were down here last week, what’s changed?

Interviewee: Nisha Gaind

Rather a lot has changed. I think the whole tenure if this outbreak seems to be on a kind of inflection point, or that might just be because it seems it’s coming rather closer to home for many of us in Europe and in the United States. In the past week, cases have been growing enormously. The virus seems to have reached more than 100 countries around the world and we’ve now topped 100,000 cases worldwide. Deaths are at around 4,000. But from our perspective, we have continued to focus on the science and we’ve been looking at things, including the role of children in the outbreak, which has been one of the major questions that researchers have been trying to answer.

Interviewer: Nick Howe

So, what do we know about this then?

Interviewee: Nisha Gaind

It seems that children don’t seem to become as infected or that they don’t seem to show symptoms as much, and that’s based on either some quite quick analyses or anecdotal evidence. But what we’ve seen this week is an analysis out of Shenzhen in China, and it’s a really detailed analysis on the spread of the virus, and it shows that children are just as likely to be infected with the virus as adults are.

Interviewer: Nick Howe

So, that sounds quite concerning.

Interviewee: Nisha Gaind

Yeah, the reason that children are so interesting is that we know from other viruses like flu that they seem to be very important links in these transmission chains, and naturally, children gather every day at school, so research on this question is something that’s quite important and could influence these measures known as social distancing measures. These are the things that many governments around the world are talking about at the moment – whether to close schools for long periods of time. Italy – the whole country has gone on lockdown, as of this week – so that’s something that happened there, but many other nations will also be considering whether to put in place these measures. So, it’s quite crucial that there is this research on this question of what role children might play in this outbreak.

Interviewer: Nick Howe

So, obviously, things are stepping up in a number of countries, and to try and combat this, money is obviously an important factor. What’s been the financial response?

Interviewee: Nisha Gaind

There’s been a large amount of money in the past week approved by the US government to fight coronavirus. Their congress approved about US$8 billion for the response. It’s not quite clear how much of that will be for research itself, and we’re also seeing other pledges from governments and institutions around the world. Some of these are more directed towards research. There are drug and vaccine efforts that are being funded by individual governments. So, as this outbreak escalates, and it really now is escalating to become a global crisis, governments and financial institutions are pledging billions and billions of dollars. But there is, of course, calls to say that what has been promised already isn’t enough, and one analysis by a group co-convened by the World Health Organisation and the World Bank Group said that at least US$8 billion more is needed to address the most pressing threats of this outbreak.

Interviewer: Nick Howe

And one of the ways this money will be spent and what some researchers are doing is turning towards animal models. What can you tell me about this?

Interviewee: Nisha Gaind

Yeah, this is another question that we have been looking at this week, and this is more to do on the basic research side rather than the public health response, but this is how researchers are investigating the virus in the lab, and the natural thing to do is to study the course of this infection in various different animal models, and these include mice and primates and also ferrets for this particular disease.

Interviewer: Nick Howe

And what have these models been able to tell us thus far?

Interviewee: Nisha Gaind

So, we’re getting some very initial findings from these studies, which have just started infected animals with the virus that causes the disease. One of the interesting things that researchers have seen is that both in mice and monkeys, the virus seems to cause quite a mild illness, and it hasn’t yet replicated the severe illness that we have seen in many people and many of the people that go on to die. But nonetheless, it’s interesting to see from these mild illnesses in these animals that this replicates quite similarly what happens in humans. There are signs of pneumonia in monkeys as we have seen in humans, and the researchers doing this work hope that they can use these models to start testing preliminary drug candidates and vaccines, but they also say they will have to start developing different animal models that more closely replicate these severe illnesses that we see in people.

Interviewer: Nick Howe

Well, listeners, as always, go to the website nature.com/news for all the latest on the coronavirus outbreak. For our second story though, we’re looking at peer review in predatory journals, and Richard, before we get into that, what exactly is a predatory journal?

Interviewee: Richard Van Noorden

So, predatory journals are journals that basically publish any manuscript you send to them because they want to collect the author fees, and they don’t provide quality checks. They may not provide long-term archiving. In other words, they’re preying on academia. That’s a very informal term, and actually defining whether a journal is predatory or merely under resourced and low quality is extremely difficult, but the key thing is that the predatory journal is usually quite deceptive or non-transparent about what it’s doing.

Interviewer: Nick Howe

So, as you say, they’re not always conducting these quality checks, so it seems almost surprising that there is an amount of peer review that’s going on here.

Interviewee: Richard Van Noorden

Apparently, there is, and this story is about hundreds of academics who say that they are doing peer reviews for predatory journals, and this was discovered by people looking at a website called Publons, where a scientist can post records of their peer review. And this may sound surprising because why would a predatory journal even ask for peer review in the first place? Well, one suggestion is that this might be a kind of fig leaf, that they’re kind of doing it to pretend that they’re doing review. Another suggestion is that perhaps these predatory journals where review is taking place might be misclassified, and here we get to the question of what is such a journal? This study looked at journals called ‘predatory’ on a blacklist made by a firm called Cabells, and Cabells says that it calls journals ‘predatory’ for a whole list of deceptive practices, like not being transparent about who the editors are and things like that. So, it’s just possible that a journal could be doing peer review but still be called ‘predatory’ on this list, and in fact, 10% at least of the journals on this list do appear to be doing peer review, according to what’s being said on this website, at least.

Interviewer: Nick Howe

So, what might be the harm then in these journals conducting this sort of peer review?

Interviewee: Richard Van Noorden

Well, the potential harm is really a huge waste of time for the scientists who are presumably doing these reviews. Now, it should be said that we don’t know very much about what’s going on here because these reviews are all totted up by an algorithm that was working off this list of journals, looking at the website and counting up reviews being claimed for these journals. But the study doesn’t talk about which journals they are, it doesn’t talk about who the individuals are, so we don’t know for sure the contents of the reviews or whether the individuals spent much time on these reviews or even whether the reviews happened, although Publons says it does verify that claimed reviews did actually happen, usually asking for emails from authors or from editors. Now, I actually looked at the Publons site and I actually emailed some of these people who said that they were doing reviews, and I did get some replies back. One researcher in Germany said, ‘Yes, I did review for a predatory journal and they completely ignored my review,’ but then he said, ‘well, that does happen sometimes with established journals as well, to be fair.’ Another person in Cambridge, UK, said, ‘I thought I was going to improve the quality of the papers because I saw these papers were not very good, but again, everything I said was ignored so now I’m not going to do anymore.’ So, there is a kind of question about are these academics being tricked, or what actually was found about these academics is that many of them are inexperienced, they haven’t published much, they’re younger and they are often from countries in Africa or the Middle East, according to the study. So, another suggestion is that these academics think that just by reviewing for as many titles as possible will bolster their academic credentials because you can point to your record of peer-reviewing activity and say I’ve reviewed for loads of journals. So, until they actually look at the reviews themselves or they contact the academics one by one, it’s not entirely clear what’s going on. But the study authors do say this is a colossal waste of time, and funders and institutes should tell people, ‘Don’t just think about not publishing in predatory journals, also think about not reviewing for them as well.’

Interviewer: Nick Howe

Well, listeners, to read more about this, head over to nature.com/news, and that’s where you’ll find all the latest on coronavirus as well. So, all that’s left is to thank both of my guests, Nisha and Richard. Thank you both.

Interviewee: Richard Van Noorden

Thanks.

Interviewee: Nisha Gaind

Thank you very much.

Host: Shamini Bundell

And that’s a wrap for another show. But if you’re interested to see as well as hear more about that tiny bird trapped in amber, then don’t forget to check out the video, made by yours truly, over at youtube.com/NatureVideoChannel. I’m Shamini Bundell.

Interviewer: Nick Howe

And I’m Nick Howe. See you next time.