Nature Podcast

This is a transcript of the 31st May 2012 edition of the weekly Nature Podcast. Audio files for the current show and archive episodes can be accessed from the Nature Podcast index page (http://www.nature.com/nature/podcast), which also contains details on how to subscribe to the Nature Podcast for FREE, and has troubleshooting top-tips. Send us your feedback to mailto:podcast@nature.com.

Kerri Smith: This week, extreme conservation

Henry Nicholls: We've got to such a critical point they say, well either you do nothing and the species goes we try and do as much as we can.

Geoff Marsh: And why birds have baby dinosaur heads?

Bart-Anjan Bhullar: Birds actually show a number of features that are common across all vertebrates that are due now.

Kerri Smith: Plus scientists embrace their artistic side and paint a molecular canvas. This is the Nature Podcast. I'm Kerri Smith.

Geoff Marsh: And I'm Geoff Marsh.

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Geoff Marsh: First off this week, look out the window and try and find the bird, or if you can't do that try to summon one into your mind's eye, now tell me what you see, was that baby dinosaur, correct.

Kerri Smith: You may have also noticed before but birds' skulls show a striking similarity to those of juvenile dinos, it might not be just coincidence. The idea that a species sometimes looks like a juvenile of its ancestors, it's called pedomorphosis and it could explain several of the major evolutionary transitions on the way to modern birds. Nature's Natasha Gilbert called Bhart-Anjan Bhullar, at Harvard University to hear more. Nature (2012)

Bhart-Anjan Bhullar: Birds are therapod dinosaurs which means that they are part of the group of predatory dinosaurs, the dinosaurs never went extinct, most of the big ones, all the big ones, went extinct and the ends of the Mesozoic which is the time of the dinosaurs, but a number of the very small ones and the ones that looked rather like the juveniles of their ancestors actually made it through and they're now actually the most specious or the most number of species of any of the land vertebrate groups.

Natasha Gilbert: So given that relationship then you would expect to see some similarities in structure but why the skull and can you describe what it looks like?

Bhart-Anjan Bhullar: The head is really, I think, most will agree the most kind of complex part of the vertebrate body, it contains the senses, it contains the parts that are used for feeding, which of course is very important to a living organism and so it often really heavily bears the signatures of evolution.

Natasha Gilbert: And so can you describe some of the similarities between the birds' skulls and the juvenile dinosaur skulls.

Bhart-Anjan Bhullar: Yeah, birds actually show a number of features that are common across all vertebrates that are juveniles. So, you can imagine this just as well with a puppy, if you think about a puppy, you think of the typical kind of cute animal baby characters like they're very large eyes and the large size of the eyes reflects actually the relatively large size of all of the sensory organs and the large size of the brain relative to the head again and then they also have very short faces. Birds in particular early birds like archaeopteryx show kind of, all these major signature features. In fact modern birds are even more embryonic or juvenile-like than these early birds. We think they have very long faces because we look at them and we see the beak, but the beak is actually a one bone called the pre-maxilla which is just drastically enlarged and kind of a different trajectory of the rest. The remainder of the face is really cordoned in.

Natasha Gilbert: So what is it about these juvenile features, I mean, why is there a relationship there?

Bhart-Anjan Bhullar: The principle that seems to be operating here is something called paedomorphosis. It is basically where the descendants look like the babies or the juveniles of their ancestors. So in some animals where it has been studied, it looks like the basic pattern of the body or the head or whatever part it's pedamorphic hasn't really changed. So, it's more like the growth is just truncated and growth is generally enacted by kind of hormonal pathways and so it can actually be a relatively simple switch and the babies really sort of became the reproducing unit.

Natasha Gilbert: Does it have any evolutionary advantage?

Bhart-Anjan Bhullar: There is this idea that as things change shape with age more and more they become kind of more and more specialized and we do tend to see that these really specialized features get kind of added on later in development. So there is this idea that perhaps if you kind of rewind then you have given yourself a bit of more of a clean slate, there is more kind of variation adaptation that is possible and the other thing is just the size. If you abruptly kind of truncate your development and you become mature as a baby, you're then able to potentially exploit all these kind of ecological roles that also seems to be what happened actually with modern amphibians, their ancestors as far as we know were actually relatively large and heavily built animals and the modern amphibian radiation is a radiation also of pedamorphic or you know juvenile-like animals. There is the idea that humans are somewhat pedamorphic with respect to our more chimpanzee like ancestors. Although we are large in body size and we have long lifespans which suggests it's somewhat different kind of paedomorphosis., we show a lot of these signature features. We show a relatively large brain and also in sort of the persistence of the period of neuroplasticity that we have, it seems like we ourselves may be a product of this process.

Natasha Gilbert: So how do you know that this was a definite evolutionary process rather than just some sorts of superficial accident that they look, you know, similar?

Bhart-Anjan Bhullar: Fortunately we have microscopic data from fossil dinosaur bones as well as data from living animals that shows proximally how long in absolute time they took to become mature and what you also see again corroborated that this sudden size reduction is a really dramatic reduction in times of maturity. So you go from something like 10 to 12 years with more primitive dinosaurs and with things like alligators to a couple of years in these early bird relatives and down to from anywhere to a couple of months to a year in modern birds and each of these reductions also sort of corresponds to aid more and more juvenile looking shape of the head.

Kerri Smith: That was Bhart-Anjan Bhullar talking to Natasha.

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Kerri Smith: In just a jiffy Corie Lok has the highlights from the world outside of Nature. First though a trip to the Nano gallery.

Geoff Marsh: Scientists have been using DNA to make very small shapes and patterns for around three decades. Most recently these nanotechnologists have used a technique called DNA origami which uses lots of short DNA strands called staples to hold together a longer scaffold strand in a complex shape. Now researchers at Harvard Medical School have revisited an older idea of painting a tiny molecular canvas using lots of short pieces of DNA, whilst in theory this method should be much simpler, assembling large number of short strand has always been thought near impossible. The researchers' success remains a bit of a mystery but does open a door to much more rapid design of DNA nanostructures. Ebbe Sloth Andersen from Aarhus University in Denmark has written a news and views article about the paper and I gave him a call to hear more. Nature 485, 623-626 (31 May 2012) Nature 485, 584-585 (31 May 2012)

Ebbe Sloth Andersen: DNA is a very nice material, because we understand its structure and its assembly properties so it makes it really a reliable material for constructing shapes at the nano scale.

Geoff Marsh: And listeners might remember that there has been a lot of buzz over recent years about one particular type of DNA technology called DNA origami.

Ebbe Sloth Andersen: Yes, that was introduced in 2006 and was basically a big step forward to mix several hundreds of DNA strands and see that they actually can assemble into predefined shapes.

Geoff Marsh: Okay and this DNA origami has essentially one long bit of DNA being scaffolded together by hundreds of little shorter strands called staples. But you have written a news and views article this week about a new technique which seems to be taking a step back to a kind of molecular canvas, painting a molecular canvas.

Ebbe Sloth Andersen: And so the single strand of tiles works by having specific sequences that are complementary to neighbouring strands and these strands are laid out on a molecular canvas, that could be like 300 of those and you would then pick out on the canvas the shape you want by picking out like the pixels of the canvas and which relates to picking out the individual strands and then in the end you don't have the shape that you originally painted on the canvas.

Geoff Marsh: It strikes me that origami seems to be a sort of 3D phenomenon whereas a molecular canvas sounds very 2D, is this a step backwards?

Ebbe Sloth Andersen: It's not a step backwards at all, so the strength of the new technique is that it has modularity of shape, so basically you can come up given such of stable strands or small DNA strands, you can create any shape by just picking out the strands, it could be a 3D canvas so to say and I would expect that to be a further development in the future.

Geoff Marsh: Now this sort of tiling technique was actually first formally described 12 years ago, why has it been revisited now?

Ebbe Sloth Andersen: Whilst the DNA origami technique and molecular canvas technique really violates the prevailing wisdom about what works and essentially the new technique and the main problem here is that when you have individual tiles coming together you would expect them to form like fragments of a puzzle that wouldn't fit together but what's really fascinating about the June study is that they actually come together to form a real world shape that was designed and yes it's going to be really interesting to kick out exactly how this self assembly works and the one idea is that if two strands try and switch other and start growing a structure then they form a kind of a seat that will make the structure form rapidly and fully before any other strands could come in and inhibit this assembly of the perfect shape.

Geoff Marsh: And I suppose the other astonishing thing about this research is just the speed of which it happened.

Ebbe Sloth Andersen: Yes the researchers could make one shape in one hour and that basically means that pipette around a 1000 DNA strands and they sped up the process even further by using a robot to pipette out the strands, I mean this way they could mass produce many different structures.

Geoff Marsh: And finally I have seen lots of examples of this work with DNA nanotechnology from miniature dolphins and smiley faces and different emoticons, is it all just a bit gimmicky or, you know, what are the other real world applications of this technology.

Ebbe Sloth Andersen: Yeah I know it looks fun with all these emoticons and so on but already we have seen lots of very nice applications, for example for organizing carbon nanotubes to make small transistors and also a new example of a clam-shell DNA structure that can be programmed to respond to a specific cancer types popping open and revealing therapeutic pay load. So that's another application possible and what we are doing with the fun structures which is mainly testing what we can do in the art of shaping DNA at our will.

Geoff Marsh: Ebbe Sloth Andersen there and if you would like to find the paper, the research was carried out by Bryan Wei at the Harvard Medical School and his colleagues.

Kerri Smith: Stay tuned for the news chat coming up at the end of the show, now though it's the highlights. Over to Corie Lok in Boston.

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Corie Lok: Does vitamin D boost your ability to fight infections? It's been a subject of much debate. Some studies say yes, others can't seem to find a link but a new study provides a possible explanation for why it's been so hard to answer this question. It turns out that vitamin D can boost immunity but it doesn't work alone. Researchers have found that in human skin cells that vitamin D is to partner up with one or two hormones to increase the production of an antimicrobial molecule. In mice the hormones compensate for low levels of vitamin D which could explain why some studies have failed to find a link between the vitamin and infection rates. This paper was published in the Journal Science Translational Medicine. Nature 485, 551 (31 May 2012)Here's another paper we liked looking at what's probably one of the most famous human proteins, the tumour suppressing p53. Mutations in the p53 gene are at the heart of many types of cancer. Now researchers in New Jersey have identified a compound that can reverse the effects of a common p53 mutation. In cancer cells with this mutant protein the chemical triggers programmed cell death which is what normal p53 usually does. The chemical also slowed down the growth of tumours with this mutation in mice. How does the compound work? It seems to restore the shape of the mutated proteins so that it functions properly. This chemical could be a candidate for drug development. You can find the study in the Journal Cancer Cell. Nature 485, 550 (31 May 2012)

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Kerri Smith: Now for a story on the extreme lengths conservationists go to save species on the brink, here's Geoff.

Geoff Marsh: Earlier this year a crack team of German Vets flew out to Malaysian Borneo to perform an operation on Puntung or Stumpy a three legged Sumatran rhino who formed a basis of a very ambitious conservation effort, hot on their tails was freelance journalist Henry Nicholls who covered the story for a feature in Nature this week. And now he is here to tell us all about it. Hi Henry.

Henry Nicholls: Hello.

Geoff Marsh: So first off why is this animal called Stumpy.

Henry Nicholls: Well, in about 2007 people out there in a field they spotted these bizarre tracks in the rain forests, a three legged animal of some kind. So that was years before they even saw this animal that she was known as Stumpy. They think she must have lost her front left foot to a poacher snare when she was a baby.

Geoff Marsh: Right and that's not her only ailment is it?

Henry Nicholls: She has a very trouble uterus. So the hope was that she would be brought into captivity be paired up with this male that has been in captivity since 2008 and there was great excitement over that but when the vets got to do the examination in February, they found that she is basically infertile. She seems to have had pregnancy in the wild quite remarkably for her handicap and it probably didn't work out and the baby died and seriously damaged the lining.

Geoff Marsh: This has been an adventurous effort from the beginning though right, she was brought into captivity via a helicopter.

Henry Nicholls: Yeah extra ordinary , I mean it took 20 months to capture a three legged rhino but of course that was miles away from any access and they have to rent this helicopter to airlift her into this captive compound. The whole operation to capture over 20 months probably cost quarter of a million dollars.

Geoff Marsh: That sounds like extraordinary measures for one individual. I mean what's the state of her species?

Henry Nicholls: In Sabah in Malaysian Borneo, there are probably only 20 animals left, possibly fewer, and quite a lot of them could be carrying high levels of infertility. Their species does exist more widely historically on peninsular Malaysia though it is probably already extinct there and there are more of them on Sumatra which belongs to Indonesia then maybe 150, 200 there.

Geoff Marsh: Okay so some of the advocates of these more extreme measures are saying now that to ensure their survival they should bring them all in.

Henry Nicholls: We have got to such a critical point they say while either you do nothing and the species goes. Or we try and do as much as we can and we've got to the point where as much as you can is exactly that it's total captivity now for as many animals as you can get.

Geoff Marsh: But presumably not everyone agrees with going to these lengths to save a seemingly doomed species.

Henry Nicholls: It's sort of quite quickly opens up the bigger question about how these spends goes conservation funding. Is this the best way to spend it and there is sort of triage model of conservation where actually you would need to prioritize all those species differently. So there are some species where funding would be most efficiently spent where it can go the furthest and spending large amounts on a large mammal whose biology we don't know very much about may not be the most efficient, that's the argument.

Geoff Marsh: I suppose the other option is to focus all that money, time and effort on the ultimate cause of the species problems which is the habitat loss.

Henry Nicholls: That has already happened, that's gone, so we're now at a position where there is no point in spending any on habitat conservation they argue. There are so few animals and there is enough habitat for those remaining animals. So, there are no longer in fact habitat losses, the immediate issue, either we do something to save these last individuals or they are gone.

Geoff Marsh: You have actually met this remarkable animal and it must be hard to stay neutral, where do you sit on this?

Henry Nicholls: Slightly on the fence, she was remarkable to meet as an individual animal, you know so if you are that close and seen and met this animal and you know you can do something then I guess that's the position all these people close to her are in.

Geoff Marsh: So this team of German vets went out specifically to operate on Stumpy, how did that operation go? Is she ready for reproduction?

Henry Nicholls: They struggled to get into the uterus. So the cervix was incredibly tight, it required a massive physical effort for the vets themselves down there for half an hour and sweating and physically exhausted, so the operation didn't go to plan, the cysts are still there and they have sort of now thinking about the next stage which may be using a chemical to strip away the lining of the uterus.

Geoff Marsh: So, it's not necessarily the end of the road for Stumpy just yet.

Henry Nicholls: It's not. There are lots of options, you know you could even try and collect eggs from her ovaries and then try and do some very cunning IVF procedure but that's way beyond what has been achieved so far in these big mammals.

Geoff Marsh: Okay, well thank you for coming in Henry and I should mention that you've also managed to capture Stumpy's ordeal on video which listeners can go and watch in the usual place on our Nature video channel on YouTube.

Kerri Smith: Finally this week it's time for the news chat with Richard Van Noorden. Hi Richard.

Richard Van Noorden: Hi Kerri.

Kerri Smith: Now first off we're off to Italy for what is actually rather a worrying story.

Richard Van Noorden: So on 7th of May there was a shooting of a Nuclear Engineering Executive Roberto Adinolfi and he is okay, he got shot in the leg but subsequently an anarchists group calling itself the Olga Cell of the Informal Anarchist Federation-International Revolutionary Front claimed responsibility for this shooting. Now we've looked in to this and we find that the same group sent a letter bomb to a Swiss pro-nuclear lobby group last year and attempted to bomb IBM's nanotech lab in Switzerland in 2010 and has ties with another anarchists group which is responsible for at least four bomb attacks on nanotech facilities in Mexico. When we talked to security authorities in Italy and Switzerland where the IBM lab was, they say that these essentially the sort of eco- anarchists groups are forging stronger links.

Kerri Smith: What's their beef exactly with the industry?

Richard Van Noorden: Well, essentially they don't really have a direct beef with the nuclear industry or with the nano tech industry, they just feel that basically technology or really civilization is responsible for the world's ills and scientists who are further in technology are sort of as it where the hand maidens of capitalism and if you see the letter that this Cell wrote to the Italian Newspaper Corriere della Sera, when they claimed responsibility for shooting out the executive they called him a sorcerer of the atom and said he knew it was only a matter of time before European Fukushima kills in our continent.

Kerri Smith: So, in the face of what turns out to be quite an organized or more organized plan than we thought to sabotage of these industries, people are ramping up securities, is there anything else that can be done?

Richard Van Noorden: Well, there is not necessarily much else that can be done, so the Swiss Federal Intelligent Service looked into this after the IBM attempted attack and they said that they saw signs of an increasing degree of international networking between perpetrators, but Simon Johner who is their spokesman said well we can only make you aware of the dangers, it's up to institutions and it's up to scientists to take preventative actions. For the moment it seems to be fringe activity but slightly worrying science as it already seems to be a luddite movement gaining some organization.

Kerri Smith: All right well, we're going on from Italy and the anarchists now to the long running saga of where to put the world's largest radio telescope.

Richard Van Noorden: Finally the square kilometre array which has got 3015 metre dishes and many more than that antenna a decision has been made where it is going to be. It's going to be a 2 billion dollar telescope and it will be the world's most powerful telescope and it's going to be built by about 2024 and it's going to be built in two places.

Kerri Smith: The two places that was squabbling over it. Right?

Richard Van Noorden: Yes, South Africa and Australia and there's been a awful lot of politicking about why one site is better than the other over the last years and months but essentially it seems out of political expediency and to please everyone the Board of the square kilometre arrays decided that the telescope will be in two places. South Africa will have most of the dishes and Australia will have the antennas, the antennas are kind of pickup general signals from everywhere and the dishes are a bit more focussed. Ultimately this means the cost is going to go up. People we talked say about by 30% - it's already at 2 billion of course. You remember that other enormous projects like ITER the fusion reactor in France or CERN you know the cost go up because so many people and governments were involved.

Kerri Smith: What kinds of things that people are hoping it's going to be doing once it's up and running?

Richard Van Noorden: Well, it's going to be powerful enough to image the universe at the time when the first stars and galaxies began to form a few hundred million years after the big bang and it's sensitive enough to spot a TV signal from a planet orbiting a nearby star can pickup signals from 50 light years away. So if any aliens are broadcasting you should be able to hear that. It's also going to look how gravity is affected near black holes. So, really it's dozens of times more powerful than any previous radio telescope.

Kerri Smith: Now the last story is about scientists' names?

Richard Van Noorden: Right well, K Smith, I'd like to know how many papers you published last year and…..

Kerri Smith: It's very prolific.

Richard Van Noorden: 466 papers from K Smith last year, filing more than one a day it's very impressive but you were eclipsed by the most prolific author last year, Y Wang, 3926 publications.

Kerri Smith: Now of course what that disguises is the fact that there is more than one K. Smith and definitely more than one Y. Wang.

Richard Van Noorden: Exactly that's this very kind of confusing problem that if you're looking up stats on who publishes what and where scientists publish, most databases record names and not numbers. So there is a new system called ORCID, the Open Researcher and Contributor ID, its essentially an ID system that will give scientists their own machine-readable 16 digit unique number.

Kerri Smith: Their little scientist barcode basically.

Richard Van Noorden: Their little scientist bar code, exactly. Now this simple idea could actually revolutionize research management, so we talked to the guy who looked at the biblio matrix and count at the stats and they say that they're really excited and solving this problem is a massive deal in the science of science.

Kerri Smith: So, when does this all roll out then?

Richard Van Noorden: Well, this was originally going to roll out this summer but it's been pushed to autumn and the question really for this system is although it seems so obvious that we would need it, it needs wide support than it's got. So 280 organizations have signed up but some researchers have never heard of this which is why I am talking about it on the podcast and you know who knows whether it's going to be as widely adopted as say the DOI, the digital object identifier which now is attached to every scientific paper. So we're going to have to see it's seems like a very good idea to me.

Kerri Smith: Thank you very much Richard, for bringing that in; it's been just as much of interest. We are not very competitive here on the Nature Podcast but how many papers did G. Marsh publish.

Richard Van Noorden: G. Marsh published 8 papers last year. So he's obviously slacking.

Kerri Smith: Sorry Geoff, pipped you to the post there. Alright more on all of those stories at http://www.nature.com/news as always.

Geoff Marsh: Join us next week for looking forward to the upcoming climate meeting in Rio. I am Geoff Marsh

Kerri Smith: And I am Kerri Smith.