Nature Podcast

This is a transcript of the 19th March 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

Geoff Brumfiel: This week, realizing the potential of molecular machines.

David A. Leigh: In stark contrast to biology, none of mankind's fantastic myriad of today's technology exploits molecular machines in any way at all and nature hasn't evolved to do that over four billion years for no reason.

Kerri Smith: And investigating heat in the Earth's crust using this cool set up.

Alan G. Whittington: She has this big scary-looking piece of equipment that fires a laser at a very thin slice of rock. The laser hits the bottom side and that heats it up.

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

Geoff Brumfiel: And I'm Geoff Brumfiel. First up how to do miniature mechanics. There is no instruction book, so Katharine Sanderson talked to the leader of a team who has been busy making machines on the micro scale.

Katharine Sanderson: Molecules are traditionally held together with bonds between atoms, or at least that's what we are all taught at school, but some chemists have spend the past few years making molecules that are held together mechanically using spindles and wheels. So far most of these so called rotaxane molecules have been made out of carbon, but far more useful would be to include metal-based parts with their more interesting electrical, magnetic or catalytic capabilities. David Leigh at the University of Edinburgh has made rotaxane systems with both carbon based and metal based parts connected together to form a molecular shuttle. I spoke to David to find out where all these difficult chemistry might lead. Nature 458, 314–318 (19 March 2009)

David A. Leigh: My group is interested in trying to construct synthetic versions of molecular machines and perhaps the best way to appreciate the technological potential of molecular machines is to realize that nature uses this solution in all biological processes in stark contrast of biology none of mankind's fantastic may be added today's technology exploits molecular machines in any way at all and nature hasn't evolved to do that over four billion years for no reason and when mankind had to construct molecular machines, I am sure it's going to revolutionalize all aspects of functional molecule and materials design.

Katharine Sanderson: So we are talking about molecules that actually sort of behave as mechanical parts.

David A. Leigh: Yes, very much, just like mechano and the moving parts that you get in mechanical machines in the microscopic world. We are talking about doing the same sort of thing with molecular level systems.

Katharine Sanderson: So tell us about the paper that you have got coming out in Nature. What have you done here and what's the advance?

David A. Leigh: The new thing about the paper that we are publishing in Nature this week is that we find a way to combine organic chemistry and inorganic chemistry, so that's the chemistry of elements other than carbon in single molecules by linking them together mechanically at the molecular level and the reason that this is, perhaps significant is that organic chemistry is traditionally very different to inorganic chemistry and they have very different traits and characteristics. And being able to combine those building blocks, inorganic and organic building blocks in the same molecule, could give a stability to combine the two chemistries in potentially interesting ways.

Katharine Sanderson: So you've made what you call a molecular shuttle, so this is basically one sort of molecule that forms an axis and one that forms a ring that can sort of shoot up and down the axis, is that right?

David A. Leigh: Yes, so we've got a metal-based ring that fits on to an organic or a carbon-based axle and the metal ring is able to shuttle up and down, move up and down this organic axle and that's a typical characteristic of organic molecules having this sort of dynamics associated with it, but the metal-based ring brings with it all the properties of metal such as magnetic properties and potentially catalytic properties and so we are able to bring those sorts of aspects now to the chemistry of organic compounds by combining those in the same molecule.

Katharine Sanderson: How do you get the wheel to move up and down the axle?

David A. Leigh: That works just through the background thermal noise or Brownian motion. The actual getting the ring on to the axle is the potentially tricky bait, but we use a process called self-assembly where all the different components actually assemble together through programmed hydrogen bonding, hydrogen bonding that's programmed into the molecular design and then once the wheel is on the axle it actually just is able to move up and down the thread just by random thermal motion.

Katharine Sanderson: Is that controllable at all?

David A. Leigh: Yes, well that's going to be the next stage. So in these early systems we've just demonstrated that the motion occurs and the next step is to be able to control the motion.

Katharine Sanderson: Can you tell us a bit about the metals that you used to form the rings, and why these are interesting to you?

David A. Leigh: The metals that are incorporated into the ring are chromium and Cobalt although we can also use other kinds of metals. There is also nickel, iron and copper. They've got magnetic properties, which is normally quite difficult to introduce into organic systems and in particular these inorganic wheels that we are using have possibly got some applications in quantum computing. The classical computing uses bits which store information as these are on 0 or 1 that sounds a bit like a light switch; the bit can either be ON or OFF. In a quantum computer, the information is stored in what's called the qubits where the strange rules of quantum mechanics allow the information to be present as both a zero and a one and their pre-positioning between. The inorganic rings that we made in this paper have got the necessary requisites to be good qubits. Now, sort of the major challenge is to learn how to bring them together to build a device that could do calculations and how to read from and write to the qubits.

Katharine Sanderson: So that kind of answers my next question, which is now you've got these molecular shuttles and you're trying to control them, what would you use them for? Is there any other application apart from this qubits?

David A. Leigh: Yes, so there could be other sorts of applications that might come from combining properties of one chemistry with another chemistry so interesting magnetic properties are one perhaps in switchable systems or even in conventional computers as well. It's just 30 days at the moment. We've just found the ways of connecting these units together and now we need to find out about how combining these chemistries in single molecule systems enables us to do new kinds of things.

Katharine Sanderson: I was hoping you might say that you wanted to make a little tiny car.

David A. Leigh: We want to make a little tiny car. We don't want to make a little tiny car that will be great if it were possible, but it isn't and we wouldn't/t want to make a car like that anyway because where would you want to go.

Geoff Brumfiel: David Leigh squashing Katharine's dreams of mini Formula-1.


Kerri Smith: Coming up shortly two types of meltdown. One in science journalism and one in the Antarctic ice. But first an experiment that rocks. Here's Natasha Gilbert.

Natasha Gilbert: Scientists' don't have too many ways of measuring temperatures deep inside the Earth's crust. So Alan Whittington and his colleagues from the Universities of Missouri and Washington in the United States recreated the conditions in a lab. They fired lasers at superheated rocks to discover how fast heat diffuses through them. I called Alan to learn more. Nature 458, 319–321 (19 March 2009)

Alan G. Whittington: Basically what we did was we experimentally measured the thermal diffusivity of some rocks. Thermal diffusivity controls how fast heat flows through material. So if you've got something hot how fast does the heat diffuse away? And how fast can it cool down? And we measured these rocks up to quite high temperatures; temperatures that you might find at the base of continental crusts, perhaps 30 km deep in the Earth. And what we found is that the thermal diffusivity decreases rapidly with increasing temperature. So what that means is as you heat rocks up, it's harder and harder for them to cool down and that's quite important for continental crust, especially continental crust that is doing something exciting like being squashed and thickened for example in the hemilayer.

Natasha Gilbert: And you did this by shooting lasers at them?

Alan G. Whittington: Yeah, that's right. Yes, so this is in the lab of Anne Hofmeister who is one of the authors on the paper at Washington University in St. Louis and yes she has this big scary-looking piece of equipment that fires a laser at a very thin slice of rock. The laser hits the bottom side and that heats it up and then it takes sometime for that heat to diffuse, for that heat energy to diffuse through the sample and there's a detector mounted above the sample that just watches to see how long it takes for the topside to heat up.

Natasha Gilbert: So you found that hot rocks are better thermal insulators than cool rocks.

Alan G. Whittington: That's right.

Natasha Gilbert: And why would we want to know about them.

Alan G. Whittington: Yeah, that's a good question. So if you're interested in temperatures inside the Earth, we don't have too many ways of directly measuring temperature inside the Earth and there's a few places where deep bore holes have been drilled; but no one has ever drilled a hole to the base of continental crust and so a lot of what we think we know about temperature inside the crust comes from a variety of measurements on how much heat energy is flowing through the crust and some assumed properties of the crust. And for heat flow the most important property is the thermal diffusivity.

Natasha Gilbert: So how could we apply this model?

Alan G. Whittington: The example that we did some thermal modelling of would be a case like the hemilayer whereas continental crust gets thickened in a collision in that case between India and Eurasia. The crust gets thicker, so parts of the crust get pushed deeper into the Earth and they heat up. As they are doing this, they are also deforming because they are being squashed and that produces what's called strain heating and what happens is that the heat energy is produced and the rocks heat up. The thermal diffusivity goes down and they tend to hang on to that heat. So what can happen is that you can actually drive those rocks all the way up to the point at which they start to melt. What's important I think is one of the more important findings of the paper is that the strain heating alone is sufficient to produce melting of the crust in mountain belts, whereas most previous models have relied on having a loss of radioactive elements producing heat which is not always there.

Natasha Gilbert: And would this have an implication for, I don't know volcanoes or something like that or is it just more understanding of what's happening at the Earth's core?

Alan G. Whittington: Certainly we do make the argument that it is important for magmatism and volcanoes which is probably more exciting because magma is much more fun to look out when it comes out of the ground then when you find it millions of years later. A lot of places on Earth, volcanoes such as Yellowstone for example, the magma there, is produced by hot basaltic magma coming up from the mantle and intruding into the Earth's crust. It then sits there and this is a large amount of hot magma and that heat is transferred to the crust and partially melts it. With the new thermal diffusivity data mean is that you don't need as much basaltic magma to produce the observed amount of magma produced in the big eruptions at Yellowstone for example.

Natasha Gilbert: And what's your next step. Where are you going to go now with this?

Alan G. Whittington: We have several ideas. This paper is focused on the crust. I would say that the next big thing is looking at melting in the mantle.

Kerri Smith: That was Alan Whittington.

Geoff Brumfiel: Coming up in just a moment the state of science communication, but before that what warming oceans could do to Antarctic ice sheets. Here's Rieko Kawabata.

Rieko Kawabata: Two papers in Nature this week take a close look at the links between climate change and rapidly retreating ice sheets in the Antarctic. One is by Tim Naish at the Institute of Geological and Nuclear Sciences in New Zealand who has studied how ice sheets are affected by changes in the earth's axial tilt. The other by David Pollard at Pennsylvania State University examines the way the ice sheets grow and collapse. I spoke to David Pollard who began by telling me why the West Antarctic ice sheet is vulnerable to collapse. Nature 458, 329–332 (19 March 2009)

David Pollard: The West Antarctic Ice Sheet is just one part of the whole Antarctic ice sheet and it's thought to be particularly vulnerable to very fast retreat and in the future it is vulnerable to global warming and warming in the ocean surrounding Antarctica. And the reason it's vulnerable is because it's base, is resting on bedrock that's far below sea level 500 to 1000 meters below sea level compared to the rest of Antarctica which is called the East Antarctica ice sheet which is quite a bit larger and that's resting on land that's mostly above sea level or would quickly rise above sea level if the ice started to retreat.

Rieko Kawabata: So your paper looks at the way that ice sheets retreat and I think you mentioned that they collapse. Can you talk me through the process of growth and collapse?

David Pollard: Sure, it collapses a bit of a misnomer, I mean, it's just one word that captures a rapid retreat, but there is no literal sudden vertical avalanche into the ocean or anything it's just the word we used to mean rapid retreat. In our model it takes about a 1000 to 2000 years.

Rieko Kawabata: Right, so that's the time scale that we are looking at, is it. Is it thousands of years, millions of years?

David Pollard: Yes it's thousands. And that's actually a fairly new result from our model. It's not hundreds and it's not tens of thousands. It's just one or two thousand years, at least in our model.

Rieko Kawabata: And how did you actually go about modelling this collapse?

David Pollard: We started off with a three-dimensional numerical code model and to simulate both the West Antarctic and the East Antarctic ice sheet, we included the numerical model representation both for terrestrial ice sheets sitting on land and also the floe in the floating ice shelves. And the one thing that we did that's new is that we coupled those together using a new parameterization by a researcher called Christian Schoof, who looked at the boundary layer essentially, where those two meet. The floating and the grounded ice, they meet in a strip called the grounding line and we used his new results to better capture the migration of the grounding line.

Rieko Kawabata: What triggers this collapse?

David Pollard: The collapse can be triggered either by increases in ocean temperature which melt the ice, the floating ice from below or directly from sea level rise. In the past 2 million years or so, sea level rise has been a big factor because the north hemispheric ice sheets have been coming and going at the same time and they have actually dominated sea level and caused it to rise and fall by 100 meters or so and that has a big effect on the West Antarctic ice sheet too. In the future though the main dominant forcing for the next 1000 years will likely be increases in ocean temperature right off shore and under the ice shelves. And now our model is concentrating on the two really big West Antarctic ice shelves, the big, big floating tongues. And there's two really, really much, much bigger by an order of magnitude once when most of it flows out, one is called the Ross Ice Shelf on the edge of which the Naish et al's core was drilled, the data that we're really comparing to.

Rieko Kawabata: So can you tell me a bit more about the connections between your work and Tim Naish's paper?

David Pollard: There are two sort of real connections with the model and the data paper. One is that we ran our model over the same period that they are analyzing their data for and we do get nice agreement between the frequencies of amplitude of change that they see in their core with our model. We looked at the conditions at the closest grid point to their site at the ANDRILL core site, just off of Ross island in the McMurdo Shelf and we see a sequenced change very much like they see. And the other thing what we did is then we can then show that the data that they see right at just that one site really does represent and correlate in time with long term changes of the whole West Antarctic ice sheet, so I think those are the connections between the two papers.

Rieko Kawabata: And will you be collaborating in the future?

David Pollard: Yes, the ANDRILL is a big international project and it continues with the analysis of another core that they drilled recently and hopefully the funding will allow at least one more core in the future.

Geoff Brumfiel: U Penn's David Pollard talking to Rieko Kawabata.


Kerri Smith: Finally this week the news chat is all about science news itself. A feature in Nature looks at the future of communicating science and as it happens the reporter who has been investigating is our very own Geoff Brumfiel.

Kerri Smith: Geoff why did you decide to look into this topic now?

Geoff Brumfiel: Well, I think the reason that we decided to look into it now is that basically at the moment there is a crisis in mainstream media. Especially in America newspapers are having more and more trouble keeping their staff and keeping their budgets because advertising revenues are declining and their credit crunch only made this worse you know, circulations are dropping. The whole thing is sort of snow balling. So in the US papers are closing their science sections. The Boston Globe has just announced its folding Science and Health into its main sort of newspaper section and won't have their special section name. In Europe we are finding that that there isn't as much in terms of layoffs but people are being asked to give more with less.

Kerri Smith: Do you get a sense that science is being particularly badly hit by the crisis in the mainstream media as a whole?

Geoff Brumfiel: Well, I don't think that science is necessarily being singled out per se, but I think what you have as a situation where when newsrooms have to make cutbacks they are choosing the stuff that isn't essential. So basically anything that isn't business reporting or sports reporting or just general news in politics, so what you are finding is that science sections in the US never really were very big money makers for the papers, in fact they often lost money, so they are one of the first sections to go. But you know we are seeing the same thing in the arts, we are seeing the same thing in other sections of the newspapers.

Kerri Smith: So I mean what's filling this hole. Is science reporting just disappearing completely and is there is no science information reaching the public anymore. What's going on?

Geoff Brumfiel: Well, that's really what's interesting and what we are looking at with this piece is that the internet has facilitated the rise of, sort, of a new wave of science communication which has actually been done by scientists themselves, so we found that science blogs are becoming increasingly popular and they are becoming instead of, sort of, mainstream, you know, Discover Magazine and Seed Magazine which are two science publications in the US have both started aggregating blogs and using them as a sort of mainstream way of reaching their readership. And at the same time we have found that press officers have become more involved in communicating science directly to the public, so you may remember NASA had this Phoenix Lander on Mars and it became very popular because it was twittering from Mars, so they had a little twitter feed that everyone can follow, things like that have certainly caught the public's eye.

Kerri Smith: So that's okay then arguably there's still scientific information reaching the same people as it was before.

Geoff Brumfiel: Yeah, I mean I think there is an argument we made and that's the case because certainly you know there's this feeling within the media that there's a crisis and everything, you know, science journalism is going down the tubes but you know there really is something else that's filling in where the media once was. At the same time, what we've found is that I think there's some very good arguments being made by sort of the more old school reporters, so Peter Dykstra who was head of CNN Science, you know, which closed in December of last year sent to me well you know it's all finding good that all these bloggers are out there, but who is going to find the blogs, you know who is going to look at these blogs. It's going to be people who already know about science and environmental issues and so it's really a self selecting audience and what's being lost is this communication to the masses.

Kerri Smith: And it's what people thought was narrowcasting rather than broadcasting.

Geoff Brumfiel: Yeah, that's exactly right. So the information is out there but you have to want to find it. There's also of course the issue of independence, the one thing about journalism is that, theoretically at least, it is supposed to keep a watch over whatever area it's covering; and real scientists aren't like anyone else, they self promote sometimes, they can be corrupt, they can falsify data; I have done stories like that in my career and so you know you need journalists there watching over the scientists as well, although I am sure a lot of our listeners might disagree.

Kerri Smith: So you also conducted an online survey which was applied to by around 400 science journalists. What was the kind of main results that came out of that?

Geoff Brumfiel: Yeah, well full results will be available along with this story this week, but the main results confirmed a lot of what people have thought previously which is in the US and Canada there do seem to be a lot of people who have seen layoffs recently within their news organization. People are being asked to do more, sort of blogs and podcasts and all sorts of things, than they were five years ago. And then also it showed that there is a very heavy reliance on press offices for getting news ideas. And I guess the last thing I will just say is that interestingly enough the blogs of working scientists were actually a pretty major source of stories for the reporters, so that was also an interesting point.

Kerri Smith: So just head to for the full report and those survey results too.

Geoff Brumfiel: Well we've come to the end of another podcast, but we couldn't go without mentioning the musical highlight of the week, the Geek Pop festival. An online jamboree dedicated to bringing you the nerdious songs from the geekiest bands around.

Kerri Smith: The festival ran until the 15th of March, but all the songs are available online for the next year. Check out for the full line up across all four virtual stages including the Tesla tent and the experimental stage, but for now enjoy the dulcet tones of Spirit of Play with my favourite song from the festival Wave or Particle. I'm a wave.

Geoff Brumfiel: And I'm a particle. Thanks for listening.

(Song: Wave or Particle)