Nature Podcast
Introduction
This is a transcript of the 20th November 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 podcast@nature.com.
Advertisement
The Nature Podcast brought to you by Bio-Rad's 1000-Series Thermal Cycling Platform. When you re-think PCR you think about how easy it can be. See how at http://www.bio-rad.com/1000series.
End Advertisement
Adam Rutherford: Darwin year starts here, that's right, we couldn't wait until 2009. Coming up, in our evolution-tastic show, we have got the mammoth genome, group selection and a simple two-celled eye.
Detlev Arendt: In its basic structure with only these two cells can be compared to what also Darwin considered might have been a proto-eye. So in fact it seems that we can study something that might be very close to something that is very ancient and representative then for an early and first step in eye evolution.
Charlotte Stoddart: And just for all you physicists, have scientists detected the first traces of a dark matter particle?
John Wefel: What we are seeing here is the possible annihilation of two dark matter particles.
Charlotte Stoddart: Find out later in the show. This is the Nature Podcast. I'm Charlotte Stoddart.
Adam Rutherford: And I'm Adam Rutherford. We are all evolving this week marking the anniversary of the publication of the Origin of Species and the beginning of Darwin year. Let's kick off with the latest member of the genome club and the first one to be utterly dead. Yep! This week, Nature publishes the genome of the woolly mammoth. This huge hairy beast has been extinct for thousands of years, but that has not stopped the team led by Stephan Schuster from Penn State University from generating a near complete sequence of the mammoth's genetic code. In a minute, we will be hearing from science writer Henry Nichols on the question that everyone once answered, how do we clone a mammoth, but first I spoke to Stephan earlier this week. Now, science fans will know that we poders like to get behind the research and find out the stories that don't make it into the paper. Now you don't get much better than this. I started by asking Stephan where they got the mammoth tissue from, presumably they spent years digging around the icy permafrost of Siberia. Nature 456, 387–390 (20 November 2008) doi:
Stephan C. Schuster: This story actually is very different from all that. It is almost a modern story that has to do with the internet, because once we realized that there might be the possibility that the hair shaft contained actual DNA, we went out and tried to find sources of DNA that we could reliably step into. And the way I do this, I started searching for them in e-bay and when I immediately found that there is zillion of hairs available, we contacted the seller and then together with authorities of the university, we made sure that there were proper import permits and we also had, palaeontologists and museum curators in Russia to check on the sources of that because we were very worried that some of those hairs and fossils might have illegally being sold outside Russia. And after we verified that all of this was taken care of and there is a clean record, then we started buying hair in a larger supply from that source.
Adam Rutherford: Some of these details aren't mentioned in the method section of the paper. Can I just get you to say that again, you bought these hairs of e-bay, so someone is advertising mammoth hairs on e-bay.
Stephan C. Schuster: Yes, but I think it's very important why I tell this story is it is so easy to find them, but I really want to like to warn people not to just go ahead and buy them, because you might help to generate a very large illegal market and you support it. I really would like people to go through validated sources like sellers that have permits or to go through curators in museums.
Adam Rutherford: What was the successful bid for getting the hairs of e-bay?
Stephan C. Schuster: For a handful of hair, I think it cost me something like 132 bucks.
Adam Rutherford: And that's interesting because we have just done a check on e-bay now and you can get 4 grams for 260 dollars, so quite clearly the market is up for mammoth hairs.
Stephan C. Schuster: People have now realized the value of hairs.
Adam Rutherford: Exactly, but you got in early.
Stephan C. Schuster: We got in earlier. For us the game has totally changed in this regard because museum curators around the world are very supportive for our work and we don't pay for hair any more. So, museums come up to us and say we have this very interesting finds, museum specimen and they would like us to add the genetic genomic data to what they already know about the find and this is why we also say that viz what we do we have invented a new field that we love to call 'museomics', because what we have done on the mammoth's hair also works beautifully on plethora of other species and those papers are also coming out.
Adam Rutherford: The four billion base-pair sequence in his paper reveals not only the position of the mammoth in the elephant evolutionary tree, but also new insights into contemporary conservation.
Stephan C. Schuster: We were very surprised when we did the population genetics on this group of mammoths that we learned that the genetic diversity within each of the two groups was really low and this immediately gave us ideas why don't we look into the situation of modern species that are just at the brink of extinction, for example like the Tasmanian Devil. And so we already looked into the situation of that group of marsupials and the situation is even worse than what we see in the mammoths. We call this biology of extinction where we try to assess not only the population size, but also the genetic diversity that is within that group of organisms and then we hope we can direct, for example through a pedigree selection we can help find the optimal animals to breed with another and then to help increase the genetic diversity and make fitter individuals and then that can be released back into the wild. The first test case for that will be the Tasmanian devil. This is something that we are working on right now.
Adam Rutherford: But the question that will be on everybody's lips is, can we clone a mammoth? Nature asks science writer Henry Nicholls to come up with the recipe for resurrecting the shaggy beast. Now assuming that the sequence is perfect which it isn't and assuming that mammoths have 56 chromosomes like elephants which we don't know, you have to transfer the genome into a donor egg cell, but of what species.
Henry Nicholls: It would make sense really to use something that is closely related to mammoth as you can get and that this paper confirms is the Indian elephant, but you know, an Indian elephant they are diverse, about, I think 6.7 million years ago, relatively close. There is a big problem that is getting the eggs out of an Indian elephant, very very difficult to discover and this is because the ovaries of a female elephant lie so far inside her that you can't visualize them with ultrasound, you can't go in with laparoscopic tools to do sort of surgery on an elephant because it will collapse lungs and she would probably die and there is another problem that the elephants really are only going to be ovulating very rarely. They have a 16-week ovulatory cycle but an adult female elephant is usually either pregnant or lactating. And pregnancy last two years, lactating last another two years and so your elephant you're trying to, you know, collect and harvest whose wonderful eggs to do this is great nuclear transfer is only ovulating once in 4 or 5 years and you know that's a bit of a problem. Thankfully, there is a possible solution. Back in 1998, cryobiologists who decided to work on trying to freeze cells and in particular reproductive cells, cells from ovaries had an opportunity to start to explore the conditions needed to cryopreserve elephant ovarian tissue. There were some elephants being culled in Krueger National Park, they collected, they froze ovarian tissue from some of these females, thawed it out and thought about how they would then, could they use it to harvest eggs. They made what's called a xenotransplantation, so a transplantation with two different species putting tiny slivers of elephant ovarian tissue into, it was mice. So you take out the mouse ovary, you put in a little bit of elephant ovary and it starts to work and they managed to develop and monitor the progression then in a relatively tractable system, a small mouse, you can monitor with a high-resolution ultrasound and you can see the progression of these follicles and they managed to see development of mature follicles, whether they are actually reproductively competent is not known.
Adam Rutherford: Right. So, say you've managed to get a perfect sequence and managed to get into an elephant egg, you still got to get it back in again.
Henry Nicholls: That's difficulty because the ovary is about two and a half meters into the elephant, so no human arm is going to get you that far. They have this extraordinary bit of the reproductive tract called the canalis urogenitalis in humans is just 4 cm, a bit before you get to the hymen and that is 1.3 meters long in an elephant and apparently is an evolutionary adaptation to prevent water getting into the vagina in their aquatic phase. But this obviously makes it rather difficult to do an embryonic transfer, because you got to get through that, then you have got a hymen with a tiny tiny hole in it that you have got to navigate through then a vagina about 30 cm then the uterus and then you want to get right to the top of the uterus near where the fallopian tubes are coming down, it is a distance of 2.5 meters. They have managed to do this. Thomas Hildebrandt, scientist in Berlin have managed to get into the uterus using various contraptions in order to perform artificial insemination using sex-selected sperms. So you can actually get up there and he thinks it would be possible to do an embryonic transfer using this incredibly, I don't know, I would like to see this equipment, it is just you know what is that.
Adam Rutherford: You've managed to get the egg in, you have managed to implant it into the surrogate mother, then you have got the gestation of what?
Henry Nicholls: Almost 2 years.
Adam Rutherford: Almost 2 years and this Asian elephant gives birth to a woolly mammoth.
Henry Nicholls: Mmm..... Surprising day for her, when imagined.
Jingle
Charlotte Stoddart: That was Henry Nicholls on the implausibility of cloning a mammoth. Now to something that you definitely can't buy on e-bay, but is almost as difficult to achieve. Here's Geoff Brumfiel on that elusive stuff dark matter.
Geoff Brumfiel: If it doesn't shine, astronomers don't see it and they know for a fact that there is a lot they can't see. I am not just talking about planets and asteroids. According to observations, about 85% of the matter in the universe is dark matter, meaning it only interacts with regular matter through the force of gravity. Just what exactly this dark matter could be is the subject of great speculation among physicists and astronomers alike, but a high-altitude balloon experiment over Antarctica may be offering a tantalizing clue. The advanced thin ionization calorimeter or ATIC has seen an unusual number of high-energy electrons that could be the by-product of a dark matter interaction. It's the second such signal in recent months. Earlier this year an experiment called PAMELA saw something similar, I called John Wefel who is head of ATIC at Louisiana State University to learn more about what the experiment has seen and what it might mean for physics. Nature 456, 362–365 (20 November 2008) doi:
John P. Wefel: What we are seeing here is the possible annihilation of two dark matter particles where they annihilate just like matter and antimatter does and they annihilate into standard particles. In this case, what we see is a signature that would be going into electron positron pairs but what we measure is actually total electrons, we cannot separate the electrons from the positrons. Now the difficulty has always been that there is a galactic background of electrons that are accelerated in super nova remnants and possibly in pulsars and various other kinds of galactic sources and that background has always been too large to in fact observe any other component. However at a very high energy that background is way down and is out there that you may have a chance of seeing one of these near by sources.
Geoff Brumfiel: Where do you go to see these high-energy electrons?
John P. Wefel: Well, they are very rare first of all, if you want to look at the spectrum, so you need to have an instrument that can be as big as possible and can fly as long as possible and it would be nice if you could ground in the space but we couldn't do that, so we had to use long duration balloon technology and there you get the longest flights at very high altitude from the Antarctic continent.
Geoff Brumfiel: So, how high up are these balloons? Where are they?
John P. Wefel: The balloons are roughly 35 km, we are above 99.5% of the Earth's atmosphere which is the reason why we can see these instant particles and if we were lower of course the atmosphere would absorb them.
Geoff Brumfiel: So, you have seen some particles now and tell me what you guys saw?
John P. Wefel: Well, what we finally have seen by putting together the results from a couple of flights is a spectrum of electrons that follows the spectrum expected from the combination of supernovas and all the other galactic acceleration processes until you get up to into the hundreds of GeV region where in fact the electrons that we measured go up rather than continuing to fall as these spectrum would predict. So we see an excess which is a feature or a bump if you will sitting on top of the expected normal galactic background spectrum.
Geoff Brumfiel: I don't think the podcast probably has a lot of dark matter geeks listening to it but I am a dark matter geek and I know that there is been another satellite, a satellite I guess not a balloon machine but someone else has seen an excess of high-energy positrons, these are anti-electrons recently. How does your result fit with PAMELA, I mean, have you guys seen the same thing, do you think.
John P. Wefel: Well okay, actually your question is that there is apparently very nice consistency between the two results. That's in the dark matter world that can also be consistent if you are seeing the results of some nearby source like a bare pulsar or something like that where we are seeing the effect of a pulsar sticking above the background spectrum at high energies and PAMELA is seeing it in a different light by looking at only the positrons whose background is very very low compared to the overall electron background. So in several respects the two measurements complement each other.
Geoff Brumfiel: So, would you say a bare pulsar that's a different and much less exciting astronomical object although pulsars are still exciting in their own right.
John P. Wefel: Yeah, exactly. So I mean there is a possibility that each one was observing actually some kind of not unknown but some kind of nearby object that hasn't yet been observed by people using the x-ray and gamma ray telescopes or the optical telescopes if you will and it's sort of sitting out there and spitting out particles out if you will, which is again a kind of, an exciting thing to contemplate. So, it could go either way.
Geoff Brumfiel: And what's your hunch on it. Do you think it's dark matter?
John P. Wefel: It is sure it's an attractive explanation, but again as one of the reviewers of our Nature paper said you don't have the smoking gun and that is certainly true.
Charlotte Stoddart: John Wefel there and you can find out more about the hunt for a dark matter particle in our documentary series, that's 'Missions in Space-Time' and is available at http://www.nature.com/video/lindau.
Adam Rutherford: Okay, after that physics interlude it's back to evolution. Coming up how do simple proto-eyes of the kind predicted by Charles Darwin actually work. Kerry has been looking into them, but first Natasha Gilbert has been finding out about the controversial resurrection of group selection.
Natasha Gilbert: It's been a black listed theory among biologists since the 1960s, the group selection, the idea that traits damaging to individuals can flourish if they benefit the group seems to be making a come back. Proponents point to experiments in viruses which keep their hosts alive longer to seemingly benefit the group. Opponents say looking at phenomena like virus behaviour as group selection adds nothing to understanding of natural selection. So I asked Marek Kohn, author of a feature for Nature to explain the debate. Published online 19 November 2008 Nature 456, 296–299 (2008) doi:
Marek Kohn: Originally Darwin saw a problem, he saw that the interests of a group and the interest of the individual need not necessarily to be one and the same and this was initially that was never really worked through. So by the 1950s and 1960s, he had a lot of people in biology and naturalists who had come to assume that things did work out for the good of the group or the good of the species and in the early 60s Vero Wynne-Edwards, the naturalist published a book in which he took these arguments from being assumptions to being explicit claims, since that provoked a reaction from a relatively small number of naturalists and biologists, who had been thinking, "look this really can't be right," and they picked up on a new theory that had been proposed by then young biologist called W.D. Hamilton. He worked out that the apparent contradiction could be resolved if benefits were given according to the degree of relativeness of beneficiaries. This idea was labelled 'kin selection' and that wasn't Hamilton's turn but it became if you like the spearhead of the challenge to this to what the critics regarded as woolly good of the group and it was very very successful though not immediately and then in the early 70s the whole thing is cemented into place by Richard Dawkins who takes up these ideas and puts them in a very very forceful and persuasive way in his book 'selfish-gene'.
Natasha Gilbert: But now the idea of group selection seems to be reviving, it's coming back.
Marek Kohn: That's right, yep in a sense it didn't really go away, in that way Edwards talked to his guns till the end of his life and in the 1970s David Sloan Wilson in the States took up the course of group selection but then you get another factor coming in and that's what's been the major transition in evolution and this is the idea that you can't just take living organization for granted. You can't just take the cells and societies and colonies and the self structures that we see in the living world around us have given. At some stage, you need to start looking how they themselves evolved and to address those problems, you have to try and work out how you get from a bunch of individuals, say, the bacteria that combine to form nuclear cells with mitochondria. You have to work out why was reproductive interests of those individual organisms to cement their will as it were to a larger group. How was the conflicts of interest suppress efficiently for this to happen and when you get into that kind of area you are thinking about, first this adaptation is happening around the level of the group, so you are actually coming around to looking at the idea of selection upon groups.
Natasha Gilbert: Where do you see this debate going? Do you think it is going to catch on in the wider scientific community?
Marek Kohn: It's difficult to say what way the debate will go and it is difficult enough for an outsider to get a grips of it all. The conceptual disagreement seemed to be very very hard to resolve among the theorists themselves. It really is philosophy of biology and that's where the philosopher Sameer Akasha comes in and you really need to think about the concepts before you can actually resolve what the debate is about. One of the areas where group selection ideas do seem to be quite keenly applied is such as microbial evolution, bacteria and viruses and it is certainly possible that if we do experimental findings that make us a stronger case for the existence and importance of group selection, so that could be well be the kind of organisms that these experiments focus on.
Natasha Gilbert: Why is it so much of interest to us?
Marek Kohn: I think ultimately the reason that we are interested in this is that it's about us. People intuitively recognize that we are a very, very groupish species. Now whether that comes from heredity or from the unique human phenomenon of culture is an open and interesting question, but the bottom-line is that we care about group selection because it seems to add off in some ways to understand how we the human society even perhaps how we could go about organizing our society rather better than we do at the present.
Adam Rutherford: Science writer Marek Kohn there and for more from him on evolution have a look at his latest book, 'A Reason for Everything: Natural Selection and the English Imagination'.
Charlotte Stoddart: Now for our final Darwin tribute piece, well for now at least. Kerri has been looking into the evolution of the eye.
Kerri Smith: The eye is such a complex structure that its existence is sometimes considered by creationists to be an argument against evolution. They argue that its intermediate stages would be useless and so it couldn't have evolved in steps. Nature takes a close look at the eye this week. Science writer Simon Ings has put together the feature. He dropped by the pod to tell me what Darwin thought of the eye. Published online 19 November 2008 Nature 456, 304–309 (2008)
Simon Ings: Charles Darwin was as well as a visionary and brilliant and observing scientist, a very very good writer and his work is full of rhetorical devices and one of his favourites was to steal the thunder of opposing views by stating how ludicrous the theory of evolution as he saw it was to a first glance and the eye at first seems ludicrous, it's far too complicated, to be put together stage by stage or at least so it seems. Now it's worth remembering when he uses his devices and he says it's beyond comprehension that this thing could be created but I believe it and I believe it for this and that reason, is that he uses this rhetorical technique throughout the book because at that time that he is writing he has no evidence of the animal life prior to what we now call the Cambrian explosion. He has actually creating a theory which is not supported by the fossil evidence and wasn't supported by the fossil evidence until living memory.
Kerri Smith: Darwin even wrote that to suppose that the eye have evolved seems absurd in the highest possible degree before going on to argue that it was indeed a product of natural selection. He suggested that there should exist a proto-eye the first eye to appear in evolution and Nature paper this week has found out how such an eye works. It's known that zooplankton, tiny sea dwelling creatures with eye spots made of just two cells could steer themselves towards light but how they do this has not been clear. I spoke to Detlev Arendt and Gáspár Jékely from the European Molecular Biology Lab in Heidelberg in Germany about their work. Here's Detlev. Nature 456, 395–399 (20 November 2008)
Detlev Arendt: In this work we unravelled how zooplanktons are small animal larvae that swim in billions in the ocean in every litre of ocean water, how they steer themselves towards the light and it is of course well established that they do so and it's also clear that this is of high ecological significance but in fact we didn't have the slightest idea before how this actually works. The eyes are as simple as you can imagine. In fact these eyes only consist of two cells, one cell that is detecting the light the photoreceptor and one cell that is covering the shielding pigment and when you compare to the human eye or to other eyes of invertebrate animals, this is really much simpler and in its basic structure with only these two cells can be compared to what also Darwin considered might have been a proto-eye. So in fact by looking at the Platynereis eyes, it seems that we can study something that might be very close in its structure with only these two cells to something that is very ancient and representative then for an early and first step in eye evolution.
Kerri Smith: But how do these eyes sense light. First author Gáspár Jékely.
Gáspár Jékely: So first what we have to understand is how these eyes connect to the rest of the larva cell. All eyes usually extend axons into the brain to the visual centres and we wanted to find out where these eyes are projecting their axons. So we tried to find this out by different methods. One was by electromicroscopy, so Harald Hausen actually a collaborator was slicing up a tiny larva into very very slim slices and he could follow the morphology of the whole photoreceptor cell and found an axon in the neuronal process which was coming out of the photoreceptor and was going towards the cilia, these are propelling the larva. So this is the first eye that does not send its wires or axons into the middle of the brain as all eyes do but it sends its axons directly to the motor of the larva.
Kerri Smith: So the mechanism proved to be bit of a no brainer. But these larvae do have a rudimentary brain. Finding out what it does is the team's next challenge.
Detlev Arendt: Of course these eyes are also connected to a simple larva brain, also for brain evolution our model species has a brain that is very interesting to study because it is very simple on the one hand and on the other hand has a lot of cell types in common with the brains of, say more complex organisms. So, how at the end these two-celled eyes more or less on their own are able to steer phototaxis. So the exciting question the next step to take is how they are then connected to the brain, what is the brain control over phototaxis and how is this all connected, so this is certainly something we are going to try to find out next.
Kerri Smith: Detlev Arendt and before him Gáspár Jékely. Where exactly does this new result fit into our picture of eye evolution then. Simon Ings again.
Simon Ings: I think that it makes a very important bridge between the phototaxis of single-celled algae like Chlamydomonas and our own eyes or any kind of multicellular complex eye. This is exciting because it is an actual demonstration, an actual investigation into how a multicellular eye of a very simple sort works.
Charlotte Stoddart: Simon Ings, ending that eye-catching report by Kerri, who will be back in the pod next week with news from the Society for Neuroscience Conference.
Adam Rutherford: But here now with a healthy dollop of science news is Nature's Dan Cressey. Welcome back Dan.
Daniel Cressey: Hi Adam.
Adam Rutherford: So, it seems that the monster that is Google is now contributing to healthcare predictions.
Daniel Cressey: That's right a team in States have discovered that the number of people searching for the term flu is actually a very good predictor of the annual flu epidemics that occur and even more surprisingly this actually appears to be better than the indicators which are currently used which is either cultures from people who apparently have flu or deaths from flu and looking at just the terms people are searching for they can predict a week before these other indicators when this epidemic is coming.
Adam Rutherford: And this is actually going to be a paper in Nature next week although it is released already.
Daniel Cressey: That's right.
Adam Rutherford: Okay, so is this sort of technique going to be useful for searching for other terms other than of course Britney Spears and Harry Potter?
Daniel Cressey: Well, it certainly looks like that and basically this is really the start of using these massive data sets that companies like Google and Yahoo do collect of what people are searching for and it's possible as a whole wealth of information now which we could extract reasonably quickly and reasonably cheaply.
Adam Rutherford: Okay and sticking with health issues, it seems that stem cell biology has fused with transplantation.
Daniel Cressey: That's right, a 30-year-old woman in Spain has had a new windpipe transplanted into her and the important thing here is this windpipe has been constructed of her own stem cells.
Adam Rutherford: And so the problems with doing that sort of operation before would be what?
Daniel Cressey: Well, before hand the problem would be that you would need to take immunosuppressive drugs or your body would reject the implant and what the research team did here was they took a donor windpipe wash pretty much everything except the collagen out of that with a number of chemicals and then seeded this windpipe with the woman's own stem cells and they can then implant that into her and there are apparently no antibodies in this woman's body to this implant despite the fact that she has taken no immunosuppressive drugs at all.
Adam Rutherford: And how is she doing now?
Daniel Cressey: She is apparently fine.
Adam Rutherford: Okay and then finally, we have got our first images of planets outside the Solar system.
Daniel Cressey: That's right, we are always hearing that there are extrasolar planets and then new extra solar planet has been discovered but these are normally detected indirectly, so either by looking for a slight blink when they pass in front of a star or by looking at the way a star wobbles as they orbit. And now two teams are claiming that they have actually taken the first images of extrasolar planets.
Adam Rutherford: And these images do they give us any new information about what the planets actually might be like.
Daniel Cressey: Well, at the moment it's not entirely clear that these are planets. They are extremely large objects, one was found by the Hubble Space Telescope which is 3 times the mass of Jupiter and there are three other objects found with some ground based telescopes in Hawaii which are between 5 and 13 times the mass of Jupiter and it is possible that these are failed stars that are orbiting another star.
Adam Rutherford: So, why do we think that these are planets and not failed stars then?
Daniel Cressey: Well, in the case of the three objects going around one star, we have never before seen three failed stars orbiting around another sun.
Adam Rutherford: And that's all happening in a galaxy far far away. Okay, thanks Dan. Those images and those three stories are available on http://www.nature.com/news.
Charlotte Stoddart: You have been listening to the Nature podcast. I'm Charlotte Stoddart.
Adam Rutherford: And I'm Adam Rutherford. You keep evolving science fans.
Advertisement
The Nature Podcast is sponsored by Bio-Rad, at the centre of scientific discovery for over 50 years. On the web at http://discover.bio-rad.com.
End Advertisement
