Podcast: Conservation, automata, and pet DNA tests

This is a transcript of the 26^th July 2018 edition of the weekly Nature Podcast. Audio files for the current show and archive episodes can be accessed from the Nature Podcast index page , which also contains details on how to subscribe to the Nature Podcast for FREE, and has troubleshooting top-tips. Send us your feedback to podcast@nature.com.

[Jingle]

Host: Benjamin Thompson

Welcome back to the Nature Podcast. This week, we’ll be learning about the problems with genetic testing for pets, and hearing about the history of automata.

Host: Adam Levy

Plus, an ongoing debate about what to do with conservation data. I’m Adam Levy.

Host: Benjamin Thompson

And I’m Benjamin Thompson.

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Host: Benjamin Thompson

First up, Noah Baker has been selflessly volunteering to play with puppies. It was a difficult task, but somebody had to do it. Noah, we salute you. His tireless fieldwork investigates genetic testing in pets. Could it be a useful tool, or a dangerous distraction?

[Puppy noises]

Interviewer: Noah Baker

This is the sound of 11 puppies. They’re just 6 days old and they’re rushing - as much as puppies of that age can rush - to feed from their mum Lola, a tired but proud golden retriever. Lola’s owner is Lily Heywood.

Interviewee: Lily Heywood

So, I’ve had a dog most of my life and occasionally breed and have several, several at home now.

Interviewer: Noah Baker

Before they had puppies, Lily made sure that both Lola and the puppies’ dad, a handsome miniature poodle called Ted, were genetically screened for hereditary diseases.

Interviewee: Lily Heywood

Every time I’ve bought a puppy, I’ve checked that both parents are genetically clear, and if I’ve ever bred a litter, I’ve screened both parents.

Interviewer: Noah Baker

For Lily, the health of her dogs is paramount, but sadly not everyone has the same priorities. The pursuit of desirable physical characteristics has led to inbreeding and with that hereditary disease. The very same diseases that people like Lily are now trying to screen out. It’s a problem that Lisa Moses, a vet and bioethicist based in Massachusetts, knows all too well.

Interviewee: Lisa Moses

We have to sort of confront the legacy of the selective breeding that we’ve done in dogs in particular and all of the associated health concerns that go along with it.

Interviewee: Lily Heywood

I suppose it’s become normality for pedigree dogs to have hereditary problems, so that’s why I wanted to sort of minimise those risks really.

Interviewer: Noah Baker

But this week in Nature, Lisa and her colleagues are arguing that genetic screening in pets may not be all it’s cracked up to be.

Interviewee: Lisa Moses

For most, the vast majority of these tests, we really don’t have any information about whether or not the genetic variant that is tested for is likely to end up causing disease in that individual animal, or whether or not there are other variants that are just as important for us to test for.

Interviewer: Noah Baker

Lisa argues that without more fundamental research to understand the link between genes and disease, there are questions about the usefulness of genetic tests. Even without more research, Lisa doesn’t disapprove of genetic testing per say, but she warns against poor interpretation of the results, in particular when that leads to clinical decisions.

Interviewee: Lisa Moses

I think that there is some validity to using them for guidance in breeding programmes, as long as you understand the context of the specific test. Part of the problem is that our knowledge of whether or not there are other clinically significant genetic variants for individual diseases is limited.

Interviewer: Noah Baker

This is a problem that Lily thinks she may have experienced personally.

Interviewee: Lily Heywood

We’ve had a litter of spaniel-poodle crosses where both lines were genetically tested clear. They we absolutely fine when they were born, but one of the puppies developed deafness and blindness and some neurological issues. They went off to their new homes, and we had two come back with blindness.

Interviewer: Noah Baker

Now, problems in litters can happen - infections, complications in the womb, and so on. But only about a quarter of the puppies were affected in this case, while the others showed no symptoms at all, and that gave Lily pause for thought. She wondered if the problem could be genetic, specifically a common condition called progressive retinal atrophy, or PRA. But both parents had supposedly been genetically cleared for this disease.

Interviewee: Lily Heywood

I spoke to a geneticist about that. They were quite sure that it probably wasn’t PRA-related, which is something we questioned. Although, a local veterinary surgeon who’d looked at one of the dogs suggested that it could be a form of PRA that we weren’t testing for.

Interviewer: Noah Baker

Lily never got to the bottom of what the problem was, and this conflicting advice from veterinary professionals can be tricky for dog owners.

Interviewee: Lily Heywood

I think vets’ training, although they’re extremely good at some things, I don’t think they continue their research anywhere near as much when they’re practicing.

Interviewer: Noah Baker

As a practicing vet herself, Lisa agreed with regard to genetics testing, but with one caveat.

Interviewee: Lisa Moses

I really don’t think it’s veterinarians’ fault in most cases. Some of it is that this is a very rapidly developing field and it’s not something that there’s a lot of easily accessible information for most veterinarian professionals.

Interviewer: Noah Baker

Part of the problem, Lisa says, is that unlike in human medicine, there’s little to no regulation for veterinary medicine, at least in the States.

Interviewee: Lisa Moses

The bar is set quite high for genetic variants in human health care to be designated as ones that are really worrisome or likely to cause disease. We have no such system in veterinary medicine. I’m really hoping that within my lifetime, I see the huge benefit that the promise of these tests hold, but we just need more information before we can do that, and we need to adopt some of the standards that they’ve adopted for human healthcare to make sure that we know whether or not we really have to worry about some of these results.

Interviewer: Noah Baker

At least for now, for this litter, Lily can rely on Lola the golden retriever to take care of her puppies as only a dog can, genetic testing or not.

Host: Benjamin Thompson

That was Noah Baker, speaking with Lisa Moses from the MSPCA Angell Animal Medical Center and Harvard Medical School. You also heard from Lily Heywood, a dog owner, and Noah’s friend’s mum. To find out more, you can read Lisa’s Comment at nature.com/news. And if like me, you can’t resist a puppy pic, we’ll tweet some of Lola the golden retriever and her litter. Find that @NaturePodcast.

Interviewer: Adam Levy

Still to come in the Research Highlights: ancient bread and bridging the connections of paralysing injuries. Before that though, it was only last week on the podcast that we brought you a segment about a robotic chemist - a machine that could learn and automatically carry out tens of experiments a day, in the quest for new reactions. This was a new study, but the idea of automatic machines is not a particularly new one. This week in Nature’s Books and Arts section, there’s an essay on humanity’s relationship with these automata throughout history. I went up to the University of Cambridge to meet one of the two authors, Kanta Dihal. She explained to me just how long automatic machines have been a part of human culture.

Interviewee: Kanta Dihal

Automata are actually thousands of years old. So, they were both being actually built by engineers and there were lots of stories about fantastical automata created by the gods that could do even more amazing things than these engineers could. So, in the Iliad which was written roughly 800 BC, Homer describes ideas of the god Hephaestus making robot women, but also automatic tripods to help him in his forge.

Interviewer: Adam Levy

Do you personally, when you look back at, I guess, all these descriptions, do you have a favourite example of one?

Interviewee: Kanta Dihal

So, one I really like is Talos - this was a fictional one. Talos was basically, I would say, the first ‘killer robot’, and he was a bronze, man-shaped robot that could move by itself and walked around the island of Crete, where he would throw boulders at invaders. But the cool thing is that he had limited intelligence, and he was very much programmed to stay around Crete.

Interviewer: Adam Levy

Is this him on the screen here?

Interviewee: Kanta Dihal

Yes, that’s Talos.

Interviewer: Adam Levy

He’s very human though, he’s very, you know, if you hadn’t told me this context, looking at these I would think these were meant to be statues of normal people. I wouldn’t have necessarily thought of an automaton.

Interviewee: Kanta Dihal

Yes, so he looks very human-like, and the only thing that really distinguishes him is that he’s made of bronze.

Interviewer: Adam Levy

So far, for the historical automata, we’ve mostly spoken about the myths of automata. What examples are there of these actually being realised and machines being built?

Interviewee: Kanta Dihal

So, in antiquity you had a lot of machines that worked on steam and water power. So, you had in the Middle Ages, a lot of automata that were particularly used in court to entertain people. I think one of the more brilliant examples that I’ve heard of recently is of someone who made an automaton in the shape of a rabbit, this was 15th century, 16th, I think, a rabbit that could fart fire.

Interviewer: Adam Levy

Okay, and what function could that possibly have?

Interviewee: Kanta Dihal

Clearly, they were used on the one hand to impress people, to show off technical ingenuity, but on the other hand to show off wealth and power.

Interviewer: Adam Levy

So, the idea of automata and actual realisations of automata have been around for hundreds, thousands of years. Have our feelings around them changed in that time? Surely the myths surrounding them have evolved.

Interviewee: Kanta Dihal

Well, perhaps not so much as you might think. It wasn’t until quite a lot later that the fears that are now more common in our stories around AI and robots, you know, killer robots, AI taking over the world, that that really began to come into general discourse.

Interviewer: Adam Levy

Now, whenever we make a video about robots, someone in the comment section on YouTube will immediately mention Terminator and this threat of the robots becoming too powerful, too intelligent. Is that a modern idea?

Interviewee: Kanta Dihal

The idea that robots might become more intelligent than us and that they might therefore try to overthrow us is actually also an idea that has been popping back up throughout the centuries. There was a story of Daedalus. So, Daedalus was a legendary inventor, and he was also said to make automata, which had a will of their own and kept running away so he had to sort of nail them down, if you wanted to keep them under control.

Interviewer: Adam Levy

And I suppose now we are starting to realise maybe a lot of the myths we’ve created about automata - we’re making things which previously were just in stories. Has that itself changed how we view them?

Interviewee: Kanta Dihal

Well, I would say that the stories have changed the way we view science. Because we’ve had such long tradition of telling stories about automata, about robots, about what they could do, that has really influenced our hopes and expectations of real robots. You’ve mentioned The Terminator. The Terminator is probably the biggest distracting factor for everyone because 1) it’s very much something that we’re not trying to do, 2) the stuff that we are doing is nowhere near. But I think, the third reason why The Terminator distracts us is perhaps the most important one, is that if it goes badly wrong, it will not go badly wrong according to the plot of The Terminator. We aren’t building humanoid killer robots, but right now we are deploying autonomous weapons. We are deploying swarms of killer drones and we are deploying machine learning systems in politically sensitive areas. It is not going to look like Arnold Schwarzenegger, it’s going to look more like a flying fidget spinner.

Interviewer: Adam Levy

That was Kanta Dihal of the University of Cambridge. There are many, many more examples of automata throughout the ages. To learn more about them and what they tell us about our relationship with these machines today, check out Kanta’s essay: Ancient dreams of intelligent machines: 3,000 years of robots. Find that at nature.com/news.

Host: Benjamin Thompson

Later in the show: the end of an era of studying the start of the Universe. Plus, plans to fast forward evolution. Both those stories are in the News Chat. Next though, Shamini Bundell is here with some bite-sized science stories in this week’s Research Highlights.

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Interviewer: Shamini Bundell

Do you love the smell of freshly baked bread? Well, our ancient ancestors did too. Archaeologists found breadcrumbs at an archaeological site in northeastern Jordan. The site is in the same region that farming developed, but this bread dates back 4,000 years before agriculture began. The remains were uncovered beside stone fireplaces, and probably came from flatbreads. The bakers most likely used a hot stone or fireplace ashes to bake their bread, rather than an oven, and the breads contain a tasty combo of wheat, barley and a type of wild tuber. The effort it would have taken to bake this bread means it was probably a delicacy. Read that tasty study in the Proceedings of the National Academy of Science.

[Jingle]Interviewer: Shamini Bundell

Researchers are working on a new way to treat spinal injuries. These injuries often break connections between the brain and spinal cord, causing paralysis. But the shorter circuits communicating between spinal segments can stay intact. Researchers tried to take advantage of this remaining circuitry in paralysed mice. They used a molecule to reduce the activity of neurons near the damaged spinal tissue. This shifted the currents to the local connections and 80% of the mice were then able to take steps with this treatment. Read more in Cell.

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Interviewer: Benjamin Thompson

When it comes to conservation, knowing what animal or plant is where is super important. Making good policy or management decisions without good data is difficult. For example, if you want to create a nature reserve to protect a particular species, you need to make sure you’re putting it in the right place. But important conservation data isn’t just related to where a species is or isn’t, it also includes things like the locations of nests, breeding sites and sources of food. And once the data is collected, what should you do with it? There are a variety of places where data can be stored and shared – journals, online repositories and citizen science programmes. However, having these data available can be a double-edged sword, as Ayesha Tulloch from the University of Sydney explains.

Interviewee: Ayesha Tulloch

The problem for conservation is that we have this trade-off between wanting more information to inform where we do and how we do conservation, but having a risk that the more information that is out there, the more that species are at risk of exploitation.

Interviewer: Benjamin Thompson

And this risk is real. For example, after the whereabouts of a population of Chinese cave geckos living in Vietnam was published, they were swiftly poached for the pet trade. So, perhaps this kind of data shouldn’t be shared?

Interviewee: Ayesha Tulloch

The balance is important, because if we spend too much time thinking about only the risks to species of data being out there, then we become very risk-averse in the way that we manage our species. We try to lock our information away from people. The problem with that is there are a lot of organisations and individuals out there who have very positive motivations and those organisations - if they don’t have the correct data - are at risk of making the wrong decisions for conservation.

Interviewer: Benjamin Thompson

Ayesha and her colleagues have written a Perspective in this week’s Nature Ecology and Evolution, in which they’ve developed a system to help researchers find a balance between risk and benefit when thinking about publishing biodiversity data.

Interviewee: Ayesha Tulloch

There’s been quite a lot of disagreement in the literature over the recent years about should we publish data, shouldn’t we publish data and there’s some very vocal and very good arguments on both sides. So, what we wanted to do is progress some useful guidance or advice for the research community. So, the solution we sort of proposed to this ongoing debate is a decision tree protocol.

Interviewer: Benjamin Thompson

You may have seen a decision tree before. It starts at the top of a page with a question that has a yes/no answer. If you answer yes, you follow one path, and if you answer no, you follow the other. Then you get to another question, and this again has a yes/no answer, and you keep following the branches until you get to a result. In this case, the decision tree helps researchers who are thinking about releasing data to consider the different pressures on a species and any conservation or policy efforts that are already in place. To test it, the authors put the tree through its paces.

Interviewee: Ayesha Tulloch

One of the examples we move through is actually a giant rat that was recently discovered in the Solomon Islands. We want that information to be out there, but we first need to think about well, what are the risks if we put the information about where it’s been discovered in the public domain?

Interviewer: Benjamin Thompson

So, the team worked through the decision tree, answering questions like ‘Is the wildlife trade the primary threat to the species’?

Interviewee: Ayesha Tulloch

For a giant kind of hairy rat in the Solomon Islands in the Pacific Ocean, it’s not very valuable to the wildlife trade.

Interviewer: Benjamin Thompson

So, that’s a no. But could the species be threatened by human disturbances? For example, would lots of wildlife spotters travel to the Solomon Islands to tick the rat off their list?

Interviewee: Ayesha Tulloch

From the point of view of the Vangunu giant rat, that’s also a no. It’s not something like a prized exotic bird.

Interviewer: Benjamin Thompson

Okay. Well, is the species threatened by humans because they’re considered to be a nuisance?

Interviewee: Ayesha Tulloch

Again, for the giant rat, that was also a no.

Interviewer: Benjamin Thompson

So, a lot of ‘no’s there, suggesting that releasing location data about the rat wouldn’t be too detrimental. In fact, making the data public could be beneficial to an animal that researchers suggest is likely to be classified as critically endangered.

Interviewee: Ayesha Tulloch

We found that yes, that information is really useful in a policy sphere because at the moment, most of the habitat for that giant rat is at threat of being logged on the island where it occurs. And by information being out there about where that information occurs, conservation organisations can use that to inform where to place nature reserves, and where to ensure that logging doesn’t affect the habitat of that species in a negative way.

Interviewer: Benjamin Thompson

Making data public, as in the case of this giant rat, is only one outcome of the decision tree. At the other end of the scale the outcome might be that data on a species and its location are totally restricted if that organism is especially threatened. In some instances, the outcome of the tree could be somewhere between the two, for example suggesting that it’s ok to release data on what a species is, but not precisely where it is – a strategy that’s been used in conservation efforts in the past.

Interviewee: Ayesha Tulloch

A decision like that was actually taken recently when an animal called the night parrot in Australia was recently rediscovered. And the government and the recovery team decided to release information that the bird had been found - it’s a pretty amazing discovery - but hide the exact location of where that species was, and that just protected that parrot until conservation mechanisms are in place. Now, that parrot is protected by reserve and by quite big vines if someone enters that reserve, so we can share that information now and make it public.

Interviewer: Benjamin Thompson

This week’s Perspective article is the latest chapter in the ongoing debate about what to do with sensitive conservation data. Ayesha says that there are a lot of valuable existing protocols for assessing the risk associated with data sharing, but she hopes that the new decision tree will help open up discussions about the potential benefits of data being shared.

Interviewee: Ayesha Tulloch

We’re definitely not proposing that this is a sort of a one-size-fits-all solution. We’re really hoping that both researchers and governments engage with us about this decision tree, about how we can implement it into policy, or how we can adapt it to different contexts and different situations. We step through our tree with a very particular objective of conserving threatened species populations, but there’s other objectives about why you might share data - things like community engagement, so how might sharing information on the locations of animals and plants actually build a rapport with communities and help us get better outcomes for conservation.

Interviewer: Benjamin Thompson

That was Ayesha Tullock. You can read her Perspective over at Nature Ecology and Evolution, that’s at nature.com/nee. There’s also an Editorial on the issue of conservation data sharing, and you can find that at nature.com/opinion.

Interviewer: Adam Levy

Finally this week, it’s time for the News Chat, and Nature Briefing editor Flora Graham joins us in the studio. Hello Flora.

Interviewee: Flora Graham

Hello.

Interviewer: Adam Levy

Our first story for this week’s News Chat is our second story of conservation in Australia, and here researchers have been trying to give natural selection a helping hand.

Interviewee: Flora Graham

That’s right. Australia has a lot of very endangered marsupials, as we know. One of them is called the quoll - this little marsupial, it’s like a cute, little, kind of long-nosed rat, and unfortunately it has a taste for invasive cane toads which are poisonous. Now, when invasive cane toads come to a quoll habitat, unfortunately the quolls have fun eating them up and they tend to get wiped out pretty quickly.

Interviewer: Adam Levy

So, when did the cane toads first actually arrive in Australia?

Interviewee: Flora Graham

Well, about 80 years ago they were purposely introduced to Australia in order to control a sugar cane-eating beetle, but like a lot of these things, it didn’t work out in the long haul.

Interviewer: Adam Levy

So, what researchers have been doing, they’ve been kind of trying to turbo-charge natural selection. But what is the natural selection process that’s been taking place in the first place?

Interviewee: Flora Graham

Well, the researchers did spot that some populations of these quoll marsupials did seem to develop an aversion to cane toads. And in the lab, when they took these toad-averse quolls and match-made them with quolls that like cane toads, they found that the offspring did tend to be averse to toads. So, they did seem to have evolved this aversion to toads, and it seemed to be able to be passed onto the offspring.

Interviewer: Adam Levy

So, this is important, right, because otherwise it might just be something that parent quolls are teaching their offspring rather than some kind of, I suppose, genetic thing.

Interviewee: Flora Graham

Exactly. The key thing here is that this behaviour is heritable. And what they’re doing now is introducing these two populations - the toad-lovers and toad-haters - onto an island, and seeing whether they can in the wild reproduce what they found in the lab, which is that they end up with a population of quolls that will not eat toads. And hopefully this means that this technique can be used for all kinds of endangered animals to give them a little helping hand, so this isn’t CRISPR, this isn’t genetic engineering, this is simply putting two populations together in order to promote the passing on of certain traits.

Interviewer: Adam Levy

And you mentioned there that their doing this real-world experiment, introducing quolls to an island. So far, how’s that been going?

Interviewee: Flora Graham

So, they’ve been doing this since May of last year. They released 54 quolls on the island, and the island already had these poisonous cane toads on it, and it’s been a bit of a mixed bag. So, unfortunately, far fewer quolls survived than they’d hoped. Just 16 quolls were alive at the end of this experiment in April of this year, but most of them did seem to be toad-averse, so the good news is that the ones that are surviving are holding onto this really beneficial trait.

Interviewer: Adam Levy

That’s something I guess we’ll have to keep watching to see if those only 16 quolls can survive and help populate this island.

Interviewee: Flora Graham

Exactly, so the researchers are heading back next year and they’re going to see what the state of play is then.

Interviewer: Adam Levy

For our last story in this week’s show, let’s turn to the end of era for Planck. Planck is a satellite that many physicists may know, but can you give us a little refresher on what Planck was doing?

Interviewee: Flora Graham

Absolutely. So, Planck was looking at the cosmic microwave background - this is this very faint glow from the absolute earliest moments of the Universe that can reveal a lot of things about how the Universe initially was born and how it developed in its early stages.

Interviewer: Adam Levy

But this wasn’t the first satellite that was making observations of the Big Bang’s afterglow?

Interviewee: Flora Graham

Absolutely. There’s been 3 major space telescopes, including COBE, you might have heard of, there’s been ground-based, balloon-based experiments. But the thing about Planck is that it collected data for such a long time, at such incredible detail, that a lot of researchers have been able to base whole careers on this data so far, and it’s just released its last analysis.

Interviewer: Adam Levy

So, why is this the last analysis? Why’s it coming to an end?

Interviewee: Flora Graham

Well, Planck has really done all that it can do. I think some of the researchers that we spoke to for our article talked about the great discoveries that have come from it, but actually the data has kind of served its purpose. So, I think everyone is now looking forward to think where are we going to get our next insight into the evolution of the Universe.

Interviewer: Adam Levy

But there isn’t a replacement for Planck actually planned at the moment.

Interviewee: Flora Graham

That’s right. A lot of physicists feel that the next thing to look at is the polarisation of the cosmic microwave background, and because that hasn’t really been observed in other experiments, not a lot of governments are really willing to invest the huge amounts of money necessary to put up another satellite for something that just might not be there.

Interviewer: Adam Levy

If we get clues of that then would that potentially lead to a satellite being launched?

Interviewee: Flora Graham

I think that’s the hopes. There was a very well-publicised experiment called BICEP2 that said that it had found evidence of this, but then it was actually Planck data that revealed it was actually dust in the end, it wasn’t the observation that they had hoped it was. So right now, this is really a big question mark hanging over it.

Interviewer: Adam Levy

So, at the moment, without any further information, are we done with the cosmic microwave background radiation?

Interviewee: Flora Graham

I can’t see that we could be done with it, because it’s such a great kind of time machine back to the beginning of the Universe, and especially with inflation being one of the biggest topics in cosmology at the moment, did the Universe expand very, very quickly at the beginning? How did it do that and how did that contribute to way the Universe is today? I think we’re bound to hear more from the CMB.

Interviewer: Adam Levy

Flora Graham, thank you for joining us. For more on those two news stories and others of course, head to nature.com/news.

Host: Benjamin Thompson

Well listeners, that’s it for this week’s show. But before we go, I’d just like to say that we always like to hear from you, so don’t forget that you can get in touch on Twitter, we’re @NaturePodcast, or on email: podcast@nature.com.

Host: Adam Levy

And make sure to check our latest video at youtube.com/NatureVideoChannel. It features lizards and leaf blowers, evolution and extreme weather. Trust me, it will blow you away. I’m Adam Levy.

Host: Benjamin Thompson

And I’m Benjamin Thompson. Thanks for listening.

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