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Interviewer: Benjamin Thompson
Welcome back to the Nature Podcast. This week we’re looking at squishy sea creatures and the evolutionary forces acting on words.
Interviewer: Adam Levy
Plus, the ambitious project that’s sequencing the Earth’s microbiome. This is the Nature Podcastfor November the 2nd2017. I’m Adam Levy.
Interviewer: Benjamin Thompson
And I’m Benjamin Thompson.
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Interviewer: Benjamin Thompson
First up, we've taken a tip off from Nature's Books and Arts section about two new books on ocean invertebrates: one about jellyfish by science writer Julie Berwald; and one about cephalopods by marine Scientist Danna Staaf. Invertebrate researcher Lisa Gershwin has reviewed the books so our reporter Geoff Marsh gave her a call.
Interviewer: Geoff Marsh
Now on the face of it jellies and cephalopods are very different animals aren’t they? Jellies lacking a heart, blood, brain – nonchalantly floating their way through evolution – and then we’ve got the highly intelligent cephalopods. They seem like such different animals but you love them both?
Interviewee: Lisa Gershwin
You’re right. They couldn’t be further apart; the jellies, as I’m so fond of saying are spineless and brainless with have no visible means of support. The cephalopods on the other hand, they are like little Houdinis. They’re fast and they’re fearsome predators – completely different.
Interviewer: Geoff Marsh
Let’s tackles the jellyfish first then. If I were to play extreme devil’s advocate I might say to you that jellyfish are perhaps the most boring animal evolution has ever given us.
Interviewee: Lisa Gershwin
Ah that’s unfair.
Interviewer: Geoff Marsh
Tell me why it’s unfair.
Interviewee: Lisa Gershwin
Well, they’re not boring at all. I mean, for one thing being these incredibly primitive creatures – they’ve been around for at least half a billion years and they haven’t changed a bit. They are the master-survivors.
Interviewer: Geoff Marsh
What’s their secret then behind their evolutionary staying power?
Interviewee: Lisa Gershwin
You know, they can clone in 13 different ways. Cloning itself is cool but they can clone in 13 different ways. They can grow really fast and opportunistically when conditions change favorably for them. They can de-grow when there’s no food available. They don’t need to see to eat. They just use tactile feel to find food. Several species are truly biologically immortal.
Interviewer: Geoff Marsh
Lisa, I take it back. You’re slowly convincing me. You mention there that they don’t need vision to see but I have actually heard about one type of jellyfish that has remarkable vision.
Interviewee: Lisa Gershwin
The box jellies are the ones that really fascinate me. They’ve got 24 eyes; 8 of these eyes have lenses and retinas and corneas just like our eyes and they can see like we see. They can actually see except they don’t have a brain to interpret what they’re seeing. I don’t know – that kind of makes me… like my head just goes… [makes nonsense noise].
Interviewer: Geoff Marsh
And not only do they have this remarkable vision but it might be the only – I suppose because of their radial-symmetry – it might be the only example of sort of 360 degree vision that we see in the animal kingdom.
Interviewee: Lisa Gershwin
Oh yeah but it’s even cooler than that. It’s like the inverse of 360 degrees. So the eyes on the left side are actually seeing past the right side to see what’s over there.
Interviewer: Geoff Marsh
We could talk forever about jellyfish but I guess we’ve got to talk about cephalopods as well because that’s what the other book’s about. These must be YouTube’s most famous invertebrate group – everyone’s seen these mimic octopus and giant squid and colour switching cuttlefish.
Interviewee: Lisa Gershwin
Some of the most fantastic ones I’ve ever seen are in what’s called the mid-water which is way, way out and way, way down. So, it’s definitely the domain of thee squids – no question about that. One of them that’s my favourite is one called histioteuthisand it’s got these spots all over it when you see it. One of the eyes faces up and catches the down-welling light and the other eye faces down and then they can mimic the light. Those spots are actually photophores – they’re light organs.
Interviewer: Geoff Marsh
So a photophore as opposed to a chromatophore: this actually emits light.
Interviewee: Lisa Gershwin
That’s exactly right. So, in shallow water cephalopods use the chromatophores to mimic the colours that they’re on so that they go invisible but in the deep sea there is no colour. It’s just the faintest twilight sort of light.
Interviewer: Geoff Marsh
I’ve often thought that evolution dealt the cephalopods a bit of a tough hand by making them so delicious. Do humans pose a serious threat to the cephalopods to the same extent as we do to slow-growing fish like cod and what-not?
Interviewee: Lisa Gershwin
Well, that’s a really interesting question. On the one hand we are certainly harvesting a lot of cephalopods but on the other hand they’re growing so fast and when you look at some of these disturbed areas around the world what we’re seeing is jellyfish and cephalopods doing really, really well in these disturbed systems while fish and of course marine mammals and sea birds and things like that aren’t doing so well and so the communities in these disturbed areas are changing and becoming less crunchy and fishy and more squishy and chewy.
Interviewer: Geoff Marsh
What do we know about the evolution of jellyfish and cephalopods because I imagine that they’re hidden from the fossil records owing to their fleshy reluctance to fossilize?
Interviewee: Lisa Gershwin
They actually do fossilize and some of the fossils are just splendid. They leave a footprint rather than a chunky thing but they be just amazingly detailed.
Interviewer: Geoff Marsh
Okay, finally then I’m sure you’ve piqued a lot of people’s interest in these fantastic invertebrates. Would you recommend these books?
Interviewee: Lisa Gershwin
Look, I really love these books. I really think anybody who loves invertebrates, anybody who loves fossils, anybody who loves a good nature story is going to love these books.
Interviewer: Benjamin Thompson
That was marine biologist Lisa Gershwin there who’s based in Tasmania, Australia. And if the two books discussed here don’t satisfy your appetite, Lisa has published a couple of her own on Jellyfish which you can find links to on her website.
Interviewer: Adam Levy
Still to come in the highlights: targeting malaria proteins and the evolution of the wild horse. Now though… in 2010, a group of researchers set out on an ambitious endeavour. Their goal: to understand microbial life on our planet. Now, seven years later the first phase of this 'Earth Microbiome Project' is being published, and it catalogues tens of thousands of samples. I called up Janet Jansson – one of the researchers who coordinated the study – to find out exactly what the Earth Microbiome Project was setting out to do.
Interviewee: Janet Jansson
We live on a microbial planet, basically. So there are microorganisms on every single habitat on earth including soil, water and our own bodies. So this we already knew. The challenge was we didn’t know who they were for the majority anyhow or what they were doing.
Interviewer: Adam Levy
So, back in 2010 when this project was conceived, you knew you had the sequencing technology to sequence samples from all around the world but I suppose how do you get samples from all around the world in the first place?
Interviewee: Janet Jansson
That’s the hardest part – is to get the samples from different countries. It turned out at the end of this particular study, we had over 300 researchers involved from 43 different countries, over 27,000 environmental samples and the only way that that was possible was by crowd sourcing. We would solicit samples from different scientists that had interesting projects that were sampling different areas around the globe.
Interviewer: Adam Levy
And there were three of you coordinating these efforts and each of you was in charge of a different category of samples.
Interviewee: Janet Jansson
Rob mainly got human samples and samples from different kinds of animals: everything from ants to iguanas and Jack Gilbert, he mainly got the samples from aquatic environments and this included lakes and ocean samples. I mainly got samples from soil and that included everything from soil from deserts and permafrost in Alaska. So in that way we were able to really get quite a unique and very interesting collection of samples.
Interviewer: Adam Levy
What’s having this catalogue actually useful for in terms of research?
Interviewee: Janet Jansson
The thing that’s very useful about this particular catalogue is because all of the samples were processed in a standardized way, they are comparable across sample types and that allows you to answer fundamental questions such as what is the composition and distribution of life on earth and are there global patterns of microbial-diversity and without having that standardized approach, the way that it was done previously, it wasn’t possible to compare between different studies.
Interviewer: Adam Levy
How representative do you think the sample you’ve got is of the level of variety we see on our planet?
Interviewee: Janet Jansson
So this is only a sub-sample of course of all of the microbial habitats that there are on our planet and what we really aim to do was to get a broad geographic distribution of sample types that we could be able to see. You know if there was some pattern that emerged. We are just scratching the surface.
Interviewer: Adam Levy
Where will this project go? Is there a way it could be completed? Is there a point when you can say right, we’re done, we’ve sequenced the earth. Or does it just keep going and going?
Interviewee: Janet Jansson
So, one thing that we’re finding is that for some kinds of samples, for example the human gut, with the accumulated sequences it starts to level off so that might indicate that okay, we probably have a good enough idea. If you contrast that to something like soil or sediment there’s no leveling off at all so every new sequence data set provides new sequence information. So that indicates that the amount of diversity in those kinds of habitats is just enormous and so to your question, when will we accomplish the feat of understanding all of the diversity in those kinds of samples, I wouldn’t say it wouldn’t be possible but it’s going to be still a big challenge for many years.
Interviewer: Adam Levy
It seems like you’ve got a lot of work left to do then. Do you find that daunting?
Interviewee: Janet Jansson
I find it incredibly fascinating. It is daunting but I’ve been working for a microbiologist for about 30 years and it’s so gratifying to finally be at the stage where we’re getting some answers to these questions that were not possible to achieve 10 years ago.
Interviewer: Adam Levy
That was Janet Jansson who's based at Pacific Northwest National Laboratory in Washington State, USA. To find out more about the Earth Microbiome Project the paper plus a News & Views are available on nature.com/nature.
Interviewer: Benjamin Thompson
The News Chat is still to come, and we’ll be taking a taking a look at evolution’s role in mental illness. Now though, it’s time for two quick hits of new research as Shamini Bundell brings us this week’s Research Highlights.
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Interviewer: Shamini Bundell
The deadliest form of malaria – Plasmodium falciparum – could be stopped in its tracks by multi-tasking medication. In Southeast Asia, the pernicious parasite has already developed resistance to one of the top antimalarial drugs. But researchers have now pinpointed a protein that helps the parasite infect red blood cells and another one that helps it spread. A separate team have found a group of enzymes that targets both of these proteins. In mice with the malaria-like disease the compound cleared the infection in less than 2 weeks and stopped it spreading. That pair of papers can be found in Science.
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Interviewer: Shamini Bundell
Prehistoric horses may have galloped off the plains for a sheltered life in the forests. A team analyzed DNA from the ancient wild horses that hoofed around Europe thousands of years ago. The genes reveal that over a 12000 year period the main coat colour changed from a bright reddish-brown to black. A model of ancient equine habitats suggests that the feral horses left the plains and headed into the forests where dark coats would have helped them hide among the trees. These woodland wanderers survived in Europe and Asia until the 1900s and seemed to have evaded that mass-extinction that wiped out their cousins cantering across America’s open plains. Trot over to Nature Ecology and Evolutionfor more.
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Interviewer: Benjamin Thompson
Language changes all the time and words are always coming in or going out of fashion. But they don’t just appear or disappear. They also evolve. A new paper in Natureis looking at how verb endings change using evolutionary biology methods. To find out more about the processes involved, the researchers from the University of Pennsylvania behind the work needed to study an enormous amount of text. I asked Mitchell Newberry, the lead author of the paper, where they got hold of such a large body of work, also known as a corpus.
Interviewee: Mitchell Newberry
One of the corpora that we used is the Corpus of Historical American English which involves 200 years of magazine articles, news articles, books that is curated to represent the speech that was used at a given time.
Interviewer: Benjamin Thompson
The Corpus of Historical American English contains of four million words from over 100,000 books. These books are helpfully tagged to identify different parts of speech – verbs, nouns, adjectives and soon. The team focused on past tense verbs and how their usage have changed over the years.
Interviewee: Mitchell Newberry
So we isolated instances where both a regular and an irregular form of a past tense verb were circulating in the population. Now, we call these polymorphic verbs because there are multiple forms available for speakers to learn.
Interviewer: Benjamin Thompson
Polymorphic verbs include words like burn; burn’s past tense could be ‘burnt’ or is could be ‘burned’. And the same with learn which becomes either ‘learnt’ or ‘learned’. Mitchell and his colleagues studied 36 of these verbs to see how their usage evolved over time. Now, theories suggest that in general, verbs become more regular. In other words, it becomes more likely that they’ll end up with a typical ‘ed’ ending for the past tense: ‘Ben walked into the studio’ is one such example. But Mitchell and his colleagues found four examples of verbs with selection pressure towards the irregular and in one case at least have put forward a reason why.
Interviewee: Mitchell Newberry
One example where we might have an explanation for is the word ‘dived’ and dove’. Now ‘dived’ is the ancestral form and it has been recently ‘irregularising’ to ‘dove’ in America and one conjecture that might explain that is the increase of the irregular verb ‘drive’ and ‘drove’. Now, ‘drive’ and ‘drove’ is always irregular. No-one says ‘drived’ and that word has been increasing in frequency perhaps because of the invention of cars. But we think that maybe an increase in use in drove makes the rhyming of ‘dive’ and ‘dove’ feel normal to speakers and given the option of saying ‘dove’ and ‘dived’ when ‘dove’ is acceptable, speakers might prefer to say ‘dove’.
Interviewer: Benjamin Thompson
So in this instance, the tendency to rhyme has resulted in the selection of ‘dove’. Selective pressure is a big driver for evolution but what about its cousin, genetic drift? Unlike natural selection’s survival of the fittest, genetic drift describes random changes that don’t result in an organism becoming fitter. Drift is apparent for words too, and here’s an example… take two sets of parents – one who use ‘spilt’ while the other use ‘spilled’. If the ‘spilt’ parents have one child but the ‘spilled’ parents have two, and these offspring learn these words off their parents, ‘spilled’ has become more common in the population even though neither word is fitter. The team behind this work showed that ‘drift’ is stronger for rare verbs and that the strength of that drift depends on the frequency that the word is used. So the more that a verb is uttered, the more its past tense stays the same in future generations. Repetition is key and this repetition keeps regular verbs regular and irregular verbs irregular. But what does it all mean for the words we use today? Mitchell explains that understanding how words are evolving might give us a clue to the pace of their change.
Interviewee: Mitchell Newberry
I think where we find selection we expect one form to eventually replace the other. It depends on the magnitudes of selection and drift. Under strong selection a verb might change quite rapidly over the course of 100 years. Under drift it might take much longer for one form to replace another just because people eventually forget one or the other forms.
Interviewer: Benjamin Thompson
That was Mitchell Newbury, the first author of Detecting Evolutionary Forces in Language Change, which you can find on Nature.com/nature.
Interviewer: Adam Levy
Time now for this week’s News Chat and biomedical and policy reporter Sara Reardon joins us on the line from Washington DC. Hi Sara.
Interviewee: Sara Reardon
Hey Adam.
Interviewer: Adam Levy
Now first up you’ve written a story about the evolution of mental illness. Now this is something I hadn’t really thought that much about before. Why is it a difficult topic for researchers to grapple with?
Interviewee: Sara Reardon
Well mental illness in general is a difficult topic – trying to figure out the genetics that underlie it because there are so many interacting genetic and environmental influences that lead to things like depression and autism and schizophrenia. It’s very hard to tease those apart and if you just look at the genetics there are hundreds or thousands of either genes or other little points in people’s genomes that differ that might contribute a little bit. So if you are trying to look at the evolution of that, instead of just being able to track one gene for some trait that differs from our ancestors, you’re going to be looking at hundreds of thousands of places. So you really have to have massive, massive numbers of genomes in a database to really even be able to start looking at how these could have shown up.
Interviewer: Adam Levy
And this new work that’s been looking into the origins of mental illness… how have they been approaching the problem and what have they uncovered?
Interviewee: Sara Reardon
One of the studies I saw – it took hundreds of thousands of genomes that are all in this big database and she used a new statistical method that lets people look for very recent changes in the genome over the last 2000 years. What she found was that various brain regions have evolved over time seeming to become smarter and also that there was some selection, though not very strong selection, for genes and gene variants that might be protecting us against schizophrenia and that’s really interesting because there has been work before this that’s proposed that schizophrenia in particular is tied to the evolution of language. People who have schizophrenia hear voices – auditory hallucination and also have jumbled speech patterns. It goes back to that theory that once we started developing language and all of these very complex genetic and brain traits, that anything that goes wrong would manifest itself as something that we recognize as a mental illness.
Interviewer: Adam Levy
Do we have a good understanding of just how much these genetic factors play into mental illness in the first place? What influence they have compared to, say, environmental factors.
Interviewee: Sara Reardon
It depends on the particular mental illness and there have been some genes that have been pretty strongly linked to things like schizophrenia, autism in particular, but it’s all just very difficult to tease apart and the only way people are going to be able to get to it is through these big massive databases where they are actually able to have people’s genomes along with a lot of other information about their medical history and environmental exposures, family histories and things like that.
Interviewer: Adam Levy
Let’s move onto our second story and it’s now six months since the March for Science in Washington DC. Now, what was the March for Science all about in case people have forgotten?
Interviewee: Sara Reardon
Well it depends on who you speak with. The March for Science itself – I could say that it was not politically motivated, necessarily. They were marching in support of science which they feel is not valued in American society the way that it should be. There are also many people who have interpreted it as a march against President Trump and the people in congress right now who have been taking action, talking in ways that suggest they don’t think science is important. The Trump administration proposed huge, huge cuts to government agencies including the NIH which historically Presidents have really loved – our biomedical research enterprise – and Trump proposed huge cuts to that. So a lot of scientists and people who support science and think science is important came out in mass.
Interviewer: Adam Levy
But now half a year on from the march, the management of the March for Science are facing complaints from volunteers who were involved.
Interviewee: Sara Reardon
Yes so this is something that’s come up in the last couple of weeks here. Some of the people who were initially involved in organizing it have written a letter protesting that there’s been a lack of transparency amongst some of the organizers and people who took over the management of this march for science and the continuing organisation that it’s trying to be. And so when you have a new organisation it’s going to need directors, management and they hired people allegedly without conducting an actual search. They just kind of started paying someone to be their director. They made payments to other people who were theoretically volunteers. They had some of their initial organizers sign non-disclosure agreements so that we don’t really know what’s going on behind the scenes. People are saying well, they were being so secretive here and that makes it really difficult for minority groups and women, historically marginalized populations, to really have their voices heard.
Interviewer: Adam Levy
Are any groups actually distancing themselves or kind of leaving the organisation?
Interviewee: Sara Reardon
Well, at least the New York group that made the satellite march that happened in New York City, they decided they don’t want to be involved with the politics of the central March for Science group in DC and so they’ve been trying to distance themselves. The initial three organizers who came up with the idea have also resigned from the board but they’ve also signed non-disclosure agreements so they can’t really say what’s been going on from their perspective.
Interviewer: Adam Levy
What’s been the response from the management now then – from the interim director?
Interviewee: Sara Reardon
I think they think these accusations are unfair, that people should recognize that any new organisation has to go through certain growing pains, so to speak, and there’s a level of management that has to be in place. People have been spending their time and their effort and there’s a lot of work that goes into putting something like this together and yeah, they feel like there should be the ability to be compensated for that. Interviewer: Adam Levy
Thanks for the update Sara. For all the latest science news, head on over to nature.com/news.
Interviewer: Benjamin Thompson
That’s it for this week. But if you haven’t heard enough of us just yet, make sure to follow us on twitter. I’m @JacquesHughes.
Interviewer: Adam Levy
And you can find my stream of consciousness @ClimateAdam: no spelling necessary. Or follow the podcast @NaturePodcast. I’m Adam Levy.
Interviewer: Benjamin Thompson
And I’m Benjamin Thompson. Thanks for listening. See you all next time.
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