Nature Podcast

This is a transcript of the 25th September 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.

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Kerri Smith: Coming up this week, rare stars with incredible magnetic fields.

Alexander Stefanescu: This field is actually so strong that it could rip the flesh off of you, if you were within the 1000 kilometres.

Adam Rutherford: A surprising finding by diabetes researchers.

Alexander V. Chervonsky: Variation in commensal bacteria, the bacteria that normally live in our gut can protect from type-1 diabetes.

Kerri Smith: And McCain and Obama speak for themselves on the big science issues in the last of our special US election segments.

John McCain: I believe that we've to go to green technologies. I believe we can do it. I think we have to eliminate greenhouse gas emissions.

Barack Obama: All of us could get their gas mileage and save oil, just by keeping our tires inflated.

Kerri Smith: This is the Nature Podcast. I'm Kerri Smith.

Adam Rutherford: And I'm Adam Rutherford.

Adam Rutherford: First this week, fish have fins, but tetrapods have fingers or at least digits. The evolutionary move from fins to fingers has been in dispute as some fossils seem to lack an intermediate step. Panderichthys is one of these. A 380-million year old fish that appear to be missing fin radial bones. These are present in such famous specimens as the tetrapod like fish Tiktaalik. In this week's Nature, a team has re-examined Panderichthys using 21st century technology and have determined that actually the digit-like radials are present after all. I spoke to lead author Catherine Boisvert and started by asking her, why the transition from fins to fingers has been such a controversy. Nature 438, 1145–1147 (22 December 2005)

Catherine A. Boisvert: So, we see this 8 fingers that appear in the first tetrapods is Acanthostega, it's the first land animals and then in the fish in Tiktaalik for example, they have branched distal radials and it does tell us that this is probably where finger came from, but did not arrange like the fingers in tetrapods but Panderichthys does have four nice little distal radial that's nicely arranged in array that's very similar to what we find in tetrapods.

Adam Rutherford: So you have gone back to fossils of Panderichthys. How have you done it, what's been the methodology of re-examining these fossils?

Catherine A. Boisvert: So, what we did is that we scanned a fossil that was found in Latvia and stored in Estonia, the Department of Geology at the Tallinn University of Technology. So, we CT scanned it in a medical scanner and because the fossil was very big and heavy in its human size, so it worked well in a CT scanner like this and then from the data we got from the CT scan, we could use a program to reconstruct the fin in 3-dimension with a model that we can happily play with, without disturbing how the fin was actually preserved when the fish died.

Adam Rutherford: And what does the CT scan show, what have you found?

Catherine A. Boisvert: Well, what we see is the whole fin, we have part of the girdle and the whole fin and we have as in our arms humerus, radius, and ulna and then we have ulnar and intermedium which are elements that we as land animals do not have but then you have distal radials, so those small elements that look like finger precursors at the very end of your fin, so we have the whole fin.

Adam Rutherford: And so that indicates that digits are in fact derived from radial bones in fish fins.

Catherine A. Boisvert: Yeah, we believe that in addition to all of the other evidence, Science is like that, everybody knows that it's an addition of all of the evidence around and with all of the genetic evidence that what we now have, with Tiktaalik we now have a very clear picture of where fingers come from.

Adam Rutherford: And in your paper, you mentioned the poster boy of transitional fossils as Tiktaalik, how do the digits on Panderichthys compare to Tiktaaliks?

Catherine A. Boisvert: Well surprisingly enough Tiktaalik is a closer cousin to the first tetrapods and we would expect Tiktaalik to have finger like distal radials much more closer to tetrapods, but in fact Panderichthys surprises us again and the distal radials of Tiktaalik are branched at the very end whereas Panderichthys has four, they are not branched and they are single. So they are much more similar to fingers than what we find in Tiktaalik, although they are the same thing.

Adam Rutherford: Okay, so when you are looking to answer questions like this, you've re-examined some existing data and that's been the key. How much can we gain from going over known specimens, I mean, in your case it has been highly productive.

Catherine A. Boisvert: Yes, well in this case it is actually a different specimen than the one that had been originally described. I did go back to the original material to confirm that what we had seen in the new specimen was really not an anomaly of this specimen, but really what was going on there. I think there is a fair amount that can be gained with CT scanning in this new computer tomography and that's what many many researchers are doing at the moment. They are scanning specimens. They can look at the cranial cavities of dead fish. They can do all sorts of things, so this gives us more information without destroying any fossil. You do not need to remove any bone to be able to get to the cranial cavity of a fossil. So you can just leave the specimen intact and you get your data. So it's wonderful.

Kerri Smith: That was Catherine Boisvert of Uppsala University. Coming up later in the show, how scientists are getting to grips with the genome of our gut bacteria and how these friendly bugs could help prevent diabetes.

Adam Rutherford: First though, here's Geoff Brumfiel with some rather rare but very flashy dead stars.

Geoff Brumfiel: When big old stars die, they explode but they leave behind a tiny dead core made mainly of neutrons. These neutron stars are small as a city as dense as the sun and they are almost completely dark, I say almost because two papers in this week's Nature have seen some flashes in the sky that they believe came from a type of neutron star called a Magnetar. As Alex Stefanescu of the Max Planck Institute for Extraterrestrial Physics explained to me the magnetic field on these Magnetars is so strong that you wouldn't want to get too close. Nature 455, 503–505 (25 September 2008)

Alexander Stefanescu: This field is actually so strong that, for example, it could rip the flesh off of you if you were within the 1000 kilometres. So it's really extremely strong. It's so strong that us physicists get very excited about it because all sorts of weird things start to happen that you usually don't see. The exact details of how it works in the inner are not yet really well understood because in the lab, we can't produce such things. So we can only look at what happens around these objects in astronomy. Now what we saw was a star that flashed very brightly.

Geoff Brumfiel: So, now when you say it flashed brightly, I mean, a lot of us would have seen a star twinkle or something like that but when you say flash, I mean what are you actually talking about, how big a flash are we looking at?

Alexander Stefanescu: You can imagine a star that is just barely physical on the sky becoming as bright as the brightest stars you can see in the sky within something like 4 seconds. In the brightest phase it was bright enough so that you could see it with a good amateur telescope.

Geoff Brumfiel: I guess, you know, if you got this incredibly dense object, this producing an enormous magnetic field that still doesn't explain why you are seeing flashes of light. Where's that coming from?

Alexander Stefanescu: So, what we think was happening in the object that we saw prove us that the magnetic field of a Magnetar is not really stable in the beginning, so it's a very violent object and sometimes the strings of the force that it exerts on the crust of a Magnetar is so strong that the crust can actually break and if this happens, a lot of energy that is trapped within the crust is released in a sudden outburst. What can also happen is that the magnetic field is changing and is spun up and this puts tension on the magnetic field like on a spring basically and sometimes the spring breaks, what happens then is the magnetic field all of a sudden reconfigures itself in a less spun up configuration and this releases a lot of the energy that was put into spinning it up in the first place. What you usually see is flash and high energy radiation that is x-ray radiation or gamma radiation. What we saw though was not this extremely violent behaviour in high energy regime but then extremely violent behaviour in an optical regime which is much lower in energy. Up to now most of the observations of these violent things happening has actually been in the high energy regime and not in the optical regime, so this is a completely new thing that was very very unexpected.

Geoff Brumfiel: So, what could be making this thing release light in the optical wavelength?

Alexander Stefanescu: So we went to the literature and tried to find ideas of what could be happening here and we found a couple of intriguing ideas though and the idea that could explain what we saw here was that there's a lot of electrons and ions in the magnetosphere of a Magnetar that are ripped out of the surface of the neutron star and these particles, these ions they spiral along the magnetic field line and they absorb energy in one height above the surface of the Magnetar and then re-emits this energy that they soaked up in a different height where the frequency is an another one, so that we can see energy transferred from one energy range into another energy range and we have observed it in the optical where it was produced sort of by this process.

Geoff Brumfiel: So, it sounds kind of like Northern lights run amok or something.

Alexander Stefanescu: Right, right exactly, it is a little bit similar to what's you would have seen in Northern lights.

Geoff Brumfiel: And so I guess what comes next for you guys. Are you going to keep looking at this Magnetar or it is quiet down out for a while.

Alexander Stefanescu: It is quiet down. So what usually happens is that these things flash light or flash radiation for sometime in a intermittent and very bright manner and then they quiet down again and at some point, they might recur but you cannot predict when it is going to come again, so we do keep an eye on this source but we don't expect it to go off anytime soon again. The fact alone that we seen this leaves us to believe that these sort of things might not be that rare, so it might be that we are going to be lucky enough in our further observation campaign and see something similar somewhere else in the sky.

Adam Rutherford: Alexander Stefanescu talking to Geoff. Next up the final instalment of our special US election packages. Here's Kerri.

Kerri Smith: This week's issue of Nature features an election special which our Washington DC based News Editor Alex Witze has been coordinating. No long to go the election now. Nature 455, 442–445 (2008)

Alexandra Witze: That's right, coming up faster than you think.

Kerri Smith: We are hearing a lot about the election in general in the media but in terms of science issues what have we got in store in the magazine.

Alexandra Witze: What we have done is taken a look at how science might change in the new administration. You've to remember of course that for the last 8 years, we've had Bush administration about which the scientists have had a lot to say. There has been everything from discussions of potential interference and scientific integrity and the advisory process to the federal government. So a lot of scientists are wondering how things might change with the new President. We have to remember too it's not just a new President but we will have a new Presidential Science Advisor and the heads of all the major agencies, you know, NASA, the NIH, the Environmental Protection Agency are likely to change too and with that will come, sort of, major changes in how science has done across these various agencies. What we've done in our print special is taken a look at some of these agencies, what the key issues are, for instance where the Space Policy might go under a new President, whether that President, whether he is McCain or Obama might take forward Bush's plan to send astronauts to the Moon and on to Mars. Also in this issue, we talked to the scientists right now who are advising both Obama and McCain on science and technology issues to get a sense of who is really listening to them, who is the most influential and what things that they might be saying to other candidate.

Kerri Smith: There has been quite a lot of talk about having a decent Science Advisor, I guess, McCain and Obama themselves, not a great deal of scientific background, how much can that really affect their policies on science.

Alexandra Witze: Right, so one big issue that a lot of people are talking about in Washington now is the importance of the Presidential Science Advisor. Specifically when Bush started, it took him a number of months to appoint his Science Advisor John Marburger and there has been a lot of discussion about how that kind of lessened the influence of the position over time. So right now, pretty much every scientist who come to Washington who is talking about politics these days is speculating about how soon we can get a Presidential Science Advisor and who will be, and how close and near to the President they have. In fact our columnist David Goldstein has a piece in this issue too about the role of the Presidential Science Advisor.

Kerri Smith: And I suppose may be scientific issues will take less of a back seat if the Scientific Advisor is one that everyone is happy with.

Alexandra Witze: Well, I am not sure everyone is always happy with the Presidential Science Advisor. The question is how influential are they in getting science taken into account at these bigger policy questions. There has been a lot of discussion about whether the Science Advisor is a cheerleader for science which I think is probably the wrong role for it.

Kerri Smith: What about voters. Is scientific issue a priority for them?

Alexandra Witze: Poll after poll suggests no. American voters are more worried about issues like the economy, the war in Iraq. The closest thing you might get to a science issue is the cost of oil and the cost of gas, which gets them to start thinking about energy policies and climate policies a bit more than they might otherwise.

Kerri Smith: All right, great stuff. Alex thanks for joining me.

Alexandra Witze: Thank you.

Kerri Smith: And to access Nature's full coverage of the US Presidential elections together with that series of special podcasts, go to http://www.nature.com/news/specials.

Adam Rutherford: Next up why just study one genome when you could look at a whole bucketful. Natasha Gilbert finds out about metagenomics.

Natasha Gilbert: Microbial communities are everywhere and scientists are interested in knowing more about their genomes to understand their function and processes, but most micro organisms can't be grown in the lab. Because not enough is understood about their nutritional and growth requirements. This has led scientists able to study any tiny fraction of the microbial world. Metagenomics changed all that by enabling scientists to analyze DNA from samples taken directly from the environment, from a bucket of sea water or a spade full of soil. The term metagenomics was coined 10 years ago. I asked Philip Hugenholtz who has written a question and answer paper in the topic for Nature. How important the technique is being revolutionizing microbiology and where it might take the field over the next 10 years. Nature 455, 481–483 (25 September 2008)

Philip Hugenholtz: The current sequencing technology produces sequences in small lengths and so it becomes like a giant jigsaw puzzle. So in the case of the human genome you have just the one picture on the box and you put it back together and you get the human genome. In metagenomics is if you go out to the environment and you got a handful of soil or a litre of sea water and you extract all the DNA from that sample and then sequence that so what you are doing is you are sequencing a community of organisms, every organism that inhabits that environmental sample get sequenced and then what you have is a jigsaw puzzle, not one jigsaw puzzle, but many jigsaw puzzles and you don't have all the pieces to all the jigsaw puzzles.

Natasha Gilbert: Why is metagenomics important?

Philip Hugenholtz: The reason this is important is because most micro organisms cannot be grown on a agar plate which is the way that we have come to know them over the last 150 years. So our knowledge of microbiology is very skewed, so metagenomics is great in that it gives us a direct window into all of those organisms that can't be cultured.

Natasha Gilbert: This could tell us then more about the microbes in humans.

Philip Hugenholtz: So the figure that's always bandied about that's always a nice one is that we are in fact only 1/10th human, so if you count the number of cells on and in us we are actually 9/10th microbial. We've got the human genome, so now we want to know, what are all these micro organisms on us and in us doing? I mean, they are not just there for fun. They are interacting with us and so some of the gut ones are providing vitamins that we can't synthesize for instance and so by sequencing all of these organisms that are associated with us will get a better understanding of their cells.

Natasha Gilbert: So before we had metagenomics did we just not know any thing about these micro organisms?

Philip Hugenholtz: We had some idea from cultivation, so some of the organisms that stay in our gut can be cultivated in fact they may now in 10 to 20% of the organisms that are present there are from cultivation studies, but we lacked the overall ecological perspective.

Natasha Gilbert: And how could you apply this other than you know this being, kind of, an intellectual curiosity, does this have any sort of useful applications?

Philip Hugenholtz: Yes, sure, so one of the early targets with the human microbiome project has been looking at what's the difference between a normal gut microbiome that's in a healthy human and the microbiome that's present in say somebody with Crohn's disease or some other nasty disease like that, with the idea that we can work out if those organisms are responsible for it or a product of it or if a diagnostic of the disease for instance.

Natasha Gilbert: How important has metagenomics being in revolutionizing the field of microbiology?

Philip Hugenholtz: In my opinion, huge, because up until now, we have had this really narrow view of the microbial world based on what we can cultivate and so this really throws open the doors that we suddenly get to see the genomes of all of these organisms that cannot be cultured, so we can start to get really important insights into metabolism, all these unknown metabolism of organisms that have been grown and into the evolution of these organisms as well because each sequence that you are getting back is coming from an individual, so you are essentially getting a composite picture of the population and from that composite picture you can then learn about how the population is evolving, what's pushing it forward.

Natasha Gilbert: Where do you think metagenomics will go over the next 10 years or where do you think that it will take our understanding?

Philip Hugenholtz: That's going to be really hard to predict. It's going to be exciting whatever happens, the technology is shifting very fast now. This is a new sequencing; the next generation sequencing. You're producing sequence data for hundreds at the cost of the more traditional dye-terminator sequencing. So you can just generate a huge amount of new data. The other thing is that techniques are now available; at least you can look at expression of those genes. So metagenomics strictly speaking only tells you the potential of an organism or of the community of organisms by looking at the genes, you can work out what they may be able to do. That if you can actually sequence the messenger RNAs or you sequence the proteins that are translated from the messenger RNAs, you can see what they are actually doing. Then there have been a number of studies in the last few years showing both at the transcript level and at the protein level. So I think we are going to have really unprecedented view of how microbial communities function and evolve.

Adam Rutherford: That was Phil Hugenholtz of the US Department of Energy's Joint Genome Institute in California.

Kerri Smith: One thing metagenomics is proving useful for is investigating our own gut-based microbial communities. Another paper this week looks at how some of these bacteria might play a protective role against a nasty disease. Here's Charlotte Stoddart with more.

Charlotte Stoddart: Our body's immune system isn't faultless. Sometimes, it actually causes disease by attacking our own cells. This is what happens in type-1 diabetes when the insulin producing part of the pancreas is destroyed by our T-cells. Alexander Chervonsky of the University of Chicago and team, have been looking into the development of this autoimmune disease in mice. And I called Alexander to hear about their results. Nature advance online publication (21 September 2008)

Alexander V. Chervonsky: We have found that variation in commensal bacteria, the bacteria that normally live in our gut can protect from type-1 diabetes.

Charlotte Stoddart: Now that sounds quite surprising to me that these gut bacteria might offer some protection against diabetes. What made you think that bacteria might have an influence on type-1 diabetes?

Alexander V. Chervonsky: It has been known for a while that if you take a mouse that can develop diabetes spontaneously so called NOD mouse and house it in a different facilities, the efficiency of diabetes development differs quite widely, suggesting that environmental cues can be involved in development of type-1 diabetes.

Charlotte Stoddart: So what did you do to look a bit further into this?

Alexander V. Chervonsky: Well, we start with removing a protein called MyD88 which is an adapter of many many so called innate receptors that is required for response to pathogens and normal bacteria. And it turns out that NOD mice is lacking this receptor no longer develop type-1 diabetes and that was quite a puzzle which we pursued further.

Charlotte Stoddart: So how did you come up with this conclusion that bacteria in the gut of the mice you were testing actually were having an influence on whether or not they developed diabetes?

Alexander V. Chervonsky: That was quite simple, when we found that MyD88 deficient animals stopped developing type-1 diabetes, we asked what happens to their T-cells that normally in NOD mice destroy pancreatic islets and we found that in fact these T-cells were still in place in every lymphoid organ except the pancreatic lymph nodes and what's special about these lymph nodes is that they drain both the gut and the pancreas, so contents of the gut can get into the lymph nodes and pancreatic proteins can also get there. So the T-cells that destroy pancreas are usually activated in this pancreatic lymph nodes and in MyD88 knockout animals were found that T-cells in this node were tolerant. And now, they did not respond to pancreatic antigens. So that suggested that the gut is involved and then it is only one step to consider that bacteria involved.

Charlotte Stoddart: Do you have any idea why it is that these gut bacteria seem to offer some protection against type-1 diabetes?

Alexander V. Chervonsky: Well what I think they are doing, this bacteria, they are trying to protect themselves from immune response and as a result they also tolerize against pancreatic antigens. So organism does not react anymore to the pancreatic antigens.

Charlotte Stoddart: I see, so this is just a, sort of, happy consequence of the bacteria's own self-defence mechanism.

Alexander V. Chervonsky: Yes.

Charlotte Stoddart: And could these friendly gut bacteria then be used as a treatment for people with type-1 diabetes.

Alexander V. Chervonsky: That's what we hope at the end, but I think that first it can be used for prevention of type-1 diabetes. If the friendly bacteria can be provided to people with high-risk of development of type-1 diabetes that will be the first step that we will be looking at.

Charlotte Stoddart: Would this be in the form of, sort of, yogurts with friendly gut bacteria? Or would this be more, perhaps an injection of these gut bacteria?

Alexander V. Chervonsky: Well it could be the yogurt type of treatment, however, the immune system tends to eliminate this bacteria and you have to keep going with that all the time; it could be a pill at the end which contains the bacterial products that can replace the actual bacteria; that will be ideal.

Charlotte Stoddart: And what your next step is then towards developing this preventative medicine.

Alexander V. Chervonsky: There are few steps. One is to look into what particular bacteria, what kind of bacteria can be protective. So we will spend the next few years in doing that and then we will try to identify bacterial products that can be used instead of bacteria and in parallel we would like to know what signalling pathways are used by these bacteria to cause immune tolerance.

Adam Rutherford: The University of Chicago's Alexander Chervonsky talking to Charlotte.

Adam Rutherford: That's all from us this week. Don't forget, you can find all the research and news from the pod online at http://www.nature.com/nature including the rest of the all singing, all dancing election special at http://www.nature.com/news/specials.

Kerri Smith: We will be back same time next week with among other things a special report on HIV research and the tale of two fish species sharing Lake Victoria. I'm Kerri Smith.

Adam Rutherford: And I'm Adam Rutherford which is nice.

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