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Breaking Science: Malaria, volcanoes...

Updated Friday 10th October 2008

Volcanoes, malaria, DNA testing, hydrogen storage, gold mines and brain capacity.

This week the Breaking Science team examines the reality of hydrogen powered cars, how to listen to a volcano and reveal the latest way to test unborn babies for disease.

Plus in 'Stuff and Non-Science', the old wives tale that people only ever use ten per cent of their brains. Is this really true?


Copyright Naked Scientists


Chris Smith: Hello, welcome to the Naked Scientists: Up All Night, which is produced in association with the Open University. I’m Chris Smith. In this week’s show, how to tell when a volcano sounds like it might be about to erupt.

Helen Scales: Well, essentially, the first signs that a volcano is about to blow are often low frequency groans and tremors in the surrounding rocks, and it’s a little bit like musical instruments making different noises in different ways. So if we can find out more about where these noises are coming from and how they’re made, hopefully we can then make better predictions about how the eruption's going to take place and where.

Chris Smith: So only the groanly, how researchers are tuning into volcanoes, that's coming up very shortly. Also how a mother’s blood could hold the key to testing her baby for genetic diseases.

Steve Quake: There is DNA that circulates in the blood of people that's not associated with any cells. It’s from cells that have died and the membranes have been disrupted and the DNA just gets thrown out into the blood, and so there's a certain amount of cell-free DNA from the foetus that circulates in the mother’s blood stream and it can actually be quite a large fraction, tens of percent of the cell-free DNA can be from the foetus, and this gives one a window into the genetics of the baby.

Chris Smith: Steve Quake, who’s found a safer alternative to amniocentesis tests for Down’s Syndrome. And is it true that we use only ten percent of our brains at any given time. Well we’ll be exercising a hundred percent of our brains to find out the answer in this week’s Stuff and Non-Science. That's all coming up on this week’s Naked Scientists: Up All Night.

First up, let’s take a look at some of this week’s top science news stories from around the world and with her finger on the pulse here’s Helen Scales. And you’ve got some good news for the planet when it comes to powering the cars of tomorrow, Helen.

Helen Scales: Yes, researchers from Greece have taken the world a step closer this week to the reality of hydrogen powered cars with a study that looks at a new way of dealing with the major stumbling block that stands in the way of using hydrogen as a fuel, and that is basically how to safely store this rather flammable of gases. Well Georgious Froudakis and his colleagues from the University of Crete have published a paper in this week’s edition of the journal Nano Letters, and they describe how they built computer models of a novel hydrogen storage cell based on a special type of carbon nanotube.

Chris Smith: So how’s it work?

Helen Scales: Well carbon nanotubes, as you probably know, are these minute cylinders of carbon that are about fifty thousand times thinner than a human hair, and since they were first created scientists have hoped that carbon nanotubes could be a really good material for storing hydrogen in fuel cells, and that's because essentially these tubes are so thin that they provide a huge internal surface area across which weak atomic forces called van der Waals forces can grab onto molecules of hydrogen and then, also importantly, they can let go of the hydrogen when it’s needed to be used. But until now carbon nanotubes have actually been a little bit disappointing and not proven to have quite the necessary capacity to hold quite enough hydrogen to make them useful as fuel cells.

Chris Smith: So what's the step forward that is in this team’s model that they say will change that?

Helen Scales: They are looking at basically another aspect which is porosity, how porous the material is. They’ve actually played around with the carbon nanotubes and added something else, another kind of arrangement of carbon called graphene sheets - which are one atom thin sheets of carbon. And if you could see the individual atoms, it would look a bit like sheets of chicken wire. And they’ve taken sheets of these carbon sheets and linked them in together with short carbon nanotubules, and the carbon nanotubes, if you could see them, look like hollow cylinders made out of the same chicken wire if you like. So they’ve made the structure in the computer which is layers and layers and layers of these thin sheets of carbon, interconnected, which should they think increase the surface area and the porosity even more than just having carbon nanotubes on their own.

Chris Smith: So two questions. One, how are they going to make this stuff? Is it feasible? And two, why aren’t we doing this already?

Helen Scales: That is the next question and that is the challenge that now faces scientists is to make this stuff. All they’re doing is making the model in the computer and basically what they’re doing is testing to see if we do go to the effort of making it, which is someone else’s job, is it going to be worthwhile. And their answer to that is it probably is. And also the other thing they’re adding in is lithium irons throughout this structure which will increase the hydrogen capacity too, and they think they’re almost at the point where they will reach the US Department of Energy targets for 2010, for the amount of hydrogen that they want to see being absorbed and held within the fuel cell. Which is, they want to see 45 grams per litre of material, and they think that this new thing, this new arrangement of carbon nanotubes will be 41 grams per litre. So that's pretty good. They’re getting there in the right direction.

Why aren’t we using it already? Because no one came up with the idea I think of actually arranging the carbon in this way and making better use hopefully of these carbon nanotubes.

Chris Smith: So rather than put a tiger in your tank, it’s going to be put a nanotube in there in future. Thanks Helen. Now this is interesting because we’ve got a problem with volcanoes going off around the world and not really understanding when they’re going to go off and why they sometimes go off and what the underlying principles are. But now scientists have found a way to recreate them in the lab.

Helen Scales: Yes, that's right. We’ve got synthetic volcanoes in the lab, which is rather exciting, although they are very, very much smaller than the real ones. And this is a paper in the journal Science this week published by Philip Benson from the Rock and Ice Physics Laboratory at UCL in London and his colleagues from Canada and Italy. And essentially what they’ve done is taken bits of rock from Mount Etna in Italy and they’ve bashed them up in the lab, and using an array of extremely sensitive detectors they listen in to the noises that the rocks make when they’re deformed and they’ve pinpointed exactly where it is the noises are created.

Why are they interested in this is, well essentially the first signs that a volcano is about to blow are often low frequency groans and tremors in the surrounding rocks. And it’s a little bit like musical instruments making different noises in different ways so that volcanoes also make different noises depending on the physical process that creates that sound in the first place. So if we can find out more about where these noises are coming from and how they’re made, hopefully we can then make better predictions about how the eruptions going to take place and where.

Chris Smith: And is that what they’ve managed to do? So by creating these artificial volcanoes in the lab, I mean presumably there's not lava flowing everywhere.

Helen Scales: What they found is that the noises they pick up in the chunks of rock were created actually by fluids. They didn’t use magma. They used something else in the lab that fills the pore of the rocks - which in the real world really corresponds to those liquid magmas. And as the rock was squeezed and pressure builds up to a similar amount that's measured in real volcanoes, suddenly the fluids will burst out and run through tiny cracks, and it seems that it’s this movement and flow of fluids through convoluted torturous cracks that might be leading to these low frequency sounds being generated.

Chris Smith: Well that's good, and talking of the movement of fluids and big mountains and things, the Himalayas have been under scrutiny and now scientists reckon they understand why, despite the fact that there are rivers raging all over the place, they haven’t eroded this very high plateau, the Tibetan Plateau in the Himalayas.

Helen Scales: Yes, the Tibetan Plateau which is quite a sight indeed. This is a mountain of a puzzle that has been on the minds of scientists for a long time. But now maybe the answer has come up in the journal Nature this week. The question is why exactly is it that the mighty Sang Po River in Tibet hasn’t worn away the great Tibetan Plateau as it plunges down towards the Bay of Bengal. And essentially what it is it’s a great edifice up there in the Himalayas and it plunges down from around ten thousand feet to only around a thousand feet in the course of just a hundred and fifty miles. And rivers with so much energy and power are notorious for their eroding power. If you just look out of the plane window and see meandering rivers, that's the power of the river coursing its way through landscape and changing things. So why has this Tibetan Plateau stayed so solid, as it has for thousands of years, well now a team…

Chris Smith: What despite having these rivers running straight across it and effectively having the power to erode it and scour it to pieces and it hasn’t happened?

Helen Scales: Exactly, yes, this Tibetan Plateau does have this amazing river flowing over it but doesn’t seem to be very much affected by it. And now a team of geologists led by Oliver Korup from the Swiss Institute of Snow and Avalanche Research in Davos Switzerland have surveyed three major tributaries of the Sang Po and found evidence in the rocks that for the last 10,000 years walls of ice and rock debris, known as moraines, have actually acted as dams at the edge of the plateau, which have transformed this raging river into much more like a placid lake, really taking the anger out of it, if you like, and the power, so that in fact the river really doesn’t have the same eroding power that it normally does have. And this ice and rock formed by the glaciers high up in these very high mountain ranges, they do themselves actually erode the landscape as well, but not as deeply as the rivers do - they actually just sort of shave the top layer off if you like. And by being there and having these glacial moraines at the edge, they’re actually stopping the rivers from eroding the plateau back further up stream, even though they carry on to then plunge down towards the Bay of Bengal in some of the deepest ravines that we can find anywhere on the planet.

Chris Smith: Fascinating stuff. Well, from the tops of the World, the roof of the World, to the deepest crevices on Earth and some of the deepest gold mines, there's some very interesting things going on in South Africa when it comes to microbes and mines.

Helen Scales: This could well be the World’s most antisocial living thing, which forms an entire ecosystem all on its own living deep, deep down inside the Earth. A team of researchers led by Dylan Chivian, from the Lawrence Berkley National Laboratory in the US, found a type of bacteria lurking three kilometres down among the rocks of a gold mine in South Africa, and it seems this lonely critter gets along just fine all on its own, without any help from anything else. And in this week’s journal Science they’ve called this bug Candidatus Desulforudis audaxviator, which is a bit of a mouthful, and this lives in conditions that are extreme to say the least. It’s very hot down there, maybe as high as around sixty degrees centigrade. There's no light, no oxygen and yet the DNA in this solitary bacteria comes equipped with all the necessary genes for independent life support, including the ability to fix carbon and nitrogen, it can detect and move towards sources of food, and it has the ability to create hardy spores that will survive if conditions down there get even tougher.

Chris Smith: So how’s it surviving if it’s not near any other sources of energy because what we think about the Earth is that we need input from the Sun to keep us alive? What's it doing?

Helen Scales: Yes, well we do know that life can survive away from the Sun, but this is really quite extraordinary though, it does it all on its own. It has all the necessary things to fix energy not from the Sun but from chemicals - all that's wrapped up in just under two thousand two hundred genes, which is incredible. So this really is the World’s smallest ecosystem, if you like, because we think that this DNA from this one bacteria makes up basically a whole ecosystem.

Chris Smith: This is fascinating because, a couple of years back, scientists also discovered bacteria flourishing in a goldmine that were living on the radiation produced by uranium in the rocks. So it looks like goldmines are a pretty fertile place to find new forms of life.

Helen Scales: Yes, indeed, it definitely tells us a lot about the fundamental requirements for life but in particular, in such extreme conditions, what can you get by? Well you could get by on whatever you can find, whether its rocks, radiation, nitrogen or whatever. So, you know, it’s really telling us more about how life can survive away from the Sun.

Chris Smith: And I suppose it also lends credence to the idea that hostile other planets and worlds in our solar system. If they’ve got the right sorts of conditions, could nonetheless, despite being frozen waste lands a long way from the Sun, deep inside the planet might play home to bugs like this.

Helen Scales: It could do, and I think that's right. It’s a way of looking differently at life. Life doesn’t have to be how we think it should be. There's all sorts of other ways that life can persist and thrive, and why not out there in the rest of the universe - who knows?

Chris Smith: Thanks Helen. That was Helen Scales with some of this week’s top science news stories. And if you’d like to follow up on any of those items, they’re all on the Open University’s website at open2.net/nakedscientist.

In a moment we’ll be hearing how scientists have discovered that malaria has stolen some of our genes to help to hide itself from the immune system but first to Down’s Syndrome. This occurs when a baby carries an extra copy of chromosome number 21, and it affects about one in a thousand births. The older a mother is when she conceives a baby, the higher the risk. But, currently, the only way to diagnose the condition is to use invasive techniques like amniocentesis, where a very long needle is used to collect cells from the amniotic fluid that surrounds the baby, or there's a related method called chorionic villus sampling, where doctors remove a small piece of the placenta. These procedures enable geneticists to count the baby's chromosomes to ensure that the right numbers are present. The process also carries a small but significant risk of triggering a miscarriage. Instead, Steve Quake and his colleagues have gone down an entirely different path.

Steve Quake: So we have been trying to find a completely safe way to do foetal diagnostics on pregnant women to understand the genetics of their baby without having to stick needles close to the foetus. We look for Down’s Syndrome and other chromosomal, the technical word is aneuplodies but basically situations where the baby has an extra copy of one chromosome.

Chris Smith: And at the moment the way we’re obviously doing that is by sticking needles into women when they’re a certain stage of pregnancy in order to get fluid from round the baby that's got cells and therefore foetal DNA that we can analyse. So what's the alternative?

Steve Quake: There is DNA that circulates in the blood of people that's not associated with any cells. It’s from cells that have died and the membranes have been disrupted and the DNA just gets thrown out into the blood, and so there's a certain amount of cell-free DNA from the foetus that circulates in the mother’s bloodstream, and it can actually be quite a large fraction, tens of percent of the cell-free DNA can be from the foetus, and this gives one a window into the genetics of the baby.

Chris Smith: So how do you go about analysing that DNA from the mother and working out whether or not the baby has got extra copies of chromosomes like as it would do if it had Down’s?

Steve Quake: So we do it by counting molecules. We take the cell-free DNA and we sequence those molecules, millions of them, and then we map them back to their chromosome of origin. So we look at the sequence that we got and we say what chromosome did that sequence come from, and we sort of let them vote for the different chromosomes. You know, it’s election season in the US right now and each molecule gets a vote and we look for chromosomes that are over represented - sort of like trying to find voter fraud.

Chris Smith: So you should have the same number of bits of sequence for each chromosome if there's the same number of all chromosomes. But if there's an extra chromosome of something, that one has more copies than it should and it’ll stand out on the graph.

Steve Quake: Exactly. It’s a little more complicated than that because the chromosome would turn out to be different sizes, but when you take the sizes into account, which you’ve said, it’s exactly correct.

Chris Smith: And how have you actually tested and validated this, presumably on real clinical samples?

Steve Quake: That's right. We did a clinical study here at Stamford University in the hospital, and we analysed cell-free DNA from eighteen pregnant women, nine of whom were carrying Down’s positive foetuses and nine of whom were not. We correctly called all eighteen samples, hundred percent correct, and they were verified independently by other means such as amniocentesis.

Chris Smith: Now one of the things that people would like to be able to do is to diagnose these kind of conditions much earlier. Because if you want to do something about it, and that's up to the individual, of course, it’s better if you do that sooner rather than later. So how early in pregnancy can you do this sort of diagnosis?

Steve Quake: So the sort of fraction of cell-free DNA in the mother’s blood that's of foetal origin increases over time. In our study that we published this week, the earliest Down positive sample we had was in the fourteenth week, the earliest normal that we tested was in the tenth week, and we called both of those correctly. My guess is that we can do it as early as the fifth week, and that's something that we’re going to try to prove going forward.

Chris Smith: Now one thing that has come to light in recent years is that you sometimes get trespassing cells. They come out of the foetus and they take up residence in the woman for the rest of her life. So if you had a woman who was pregnant with a Down’s baby and then she gets pregnant again, is it possible that those trespassing foetal cells from the first pregnancy could still be spitting out extra DNA molecules that you might pick up and therefore you’d false call the new pregnancy?

Steve Quake: Technically, yes, but what studies have shown is that cell-free DNA of foetal origin goes very rapidly to zero after the baby’s delivered. You know, within a day. And so when you sort of, again do the numbers and ask how many of those foetal cells are maybe sticking around, even if they all laced immediately and dumped their DNA into the mother’s blood stream, it would be, I think, unmeasurably small.

Chris Smith: And how much do you think this costs, and what will happen to the cost over time? Presumably, as you do more of these tests it will come down.

Steve Quake: The costs of sequencing are dropping almost by the week. When we did our study it cost us about seven hundred dollars per sample to do the sequencing. In the US, an amniocentesis costs between a thousand two thousand dollars. So it’s already very close. And for our next round of studies, we’re expecting the sequencing cost to be three hundred dollars, and it’ll get even cheaper.

Chris Smith: So much cheaper potentially than an amniocentesis. Is there any way in which your assay could go wrong? Could it miss something, and if so how?

Steve Quake: If you get an ambiguous result, you can just sequence more molecules and keep sequencing to improve the sensitivity to achieve whatever confidence level you like. Now, that all said, you know, I don’t think on the basis of a study of eighteen women that we’re going to go around, start using this as a medical diagnostic yet, and the next step is to do a study with hundreds of women to complete the validation.

Chris Smith: Steve Quake with a new and much safer way to diagnose Down’s Syndrome and conditions like it, and that's using just a small sample of a mother’s blood. He’s based at Stamford and that work’s published in this week’s edition of the journal PMAS.

And now from sequencing foetal DNA to sequencing parasite DNA and specifically malaria - malaria is also known as Plasmodium and it’s a major health problem worldwide. In fact it kills about three million people every year. But now by studying its genetic material scientists have uncovered some of the secrets that make malaria so successful, including the fact that it seems to have stolen some of the genes from our own immune system, which it then uses to disguise itself once it’s inside the body. Here’s Arnab Pain.

Arnab Pain: We have been cracking the genome of a predominately monkey malaria parasite, which can also cause human infections, and it’s called Plasmodium knowlesi. So the idea behind sequencing this particular malaria parasite is to crack the genetic material of this parasite and then compare them with other malaria parasites in order to understand where exactly they differ and what is being shared between different parasite sequences to date.

Chris Smith: So by comparing different species of malaria that not only attack humans but also attack animals and seeing what's common and what's different, this can give you presumably clues as to how the different diseases are adapted to the different animals, and this tells you effectively a bit more about how they make the animal sick.

Arnab Pain: Absolutely. In fact when we analysed the genome of this particular parasite, we saw that about eighty percent of the genes are shared between Plasmodium knowlesi and also Plasmodium vivax and Plasmodium falciparum, so the other two are also primate infecting malarias, human malarias as you know, and then twenty percent of the genes are presumably species specific and they probably allow the parasite to interact with the host.

Chris Smith: Presumably, a lot of that host interaction is going to be getting around the immune system because this is a parasite which has got to get into the human body, grow in the human body, inside their own cells, and then get out of the human body again without the immune system jumping on it.

Arnab Pain: Yes, absolutely. We find a very dramatic example of molecular mimicry in Plasmodium knowlesi genome. What we particularly find is that several members of a gene family, we call them kier, that contained sequence signatures that loosely resemble a key human gene involved in the relation of human function. So we believe that this form of molecular mimicry is likely to be crucial for survival and propagation of the parasite in the body.

Chris Smith: Do you think, or does the evidence suggest that the malaria has stolen those genes from its host, ie us and the monkeys, and it’s now using them to disguise itself, or has it just evolved to have genes that are very, very similar to ours to achieve the same result?

Arnab Pain: What we think is that this is a very unusual form of mimicry whereby the parasites probably acquired these fragments from the host and then now incorporated it on its own genes and then present these genes to the host to confuse the host in some way. But how precisely it actually accured it in terms of mechanism is yet to be determined. We don’t have enough evolutionary signatures that's available to us at the moment that allows us to determine the set mechanism.

Chris Smith: And what do you think the other major implications are of having now got the genome? Where will you take this next or where do you think other scientists will take your work next?

Arnab Pain: Well there are several points I would like to mention about this. First of all, this is the first time we are able to compare the genomes of three primate infecting malarias. Secondly, in Plasmodium knowlesi we can also grow them in a flask and we should be able to probe gene function by knocking out the given gene and then look for the effect it has on the parasite. That is possible now because we have provided the whole genetic makeup of this, Plasmodium knowlesi. It will also help to develop more sensitive diagnostic tests for Plasmodium knowlesi, and as you know there has been major problem in that area, misdiagnosis by microscope. So when you look at those Plasmodium under microscope, the Plasmodium malariae and Plasmodium knowlesi, they look pretty similar, but with new and more accurate diagnostic tests we’d be able to now determine the true nature of their human infections and also how parasites invade red cells. That was extensively studied in Plasmodium knowlesi, so we should be able to continue work on those aspects as well.

Chris Smith: Arnab Pain, from the Wellcome Trust’s Sangha Institute, explaining how malaria has evolved to impersonate us genetically to escape from the effects of the immune systems. That works published in this week’s Nature.

This is the Naked Scientists: Up All Night, with me Chris Smith, and time now for this week’s Stuff and Non-Science, where we blitz myths and bash bad science, and using at least ten percent of her brain, we hope, here’s Diana O’Carroll.

Diana O’Carroll: Hello, this week’s 'Stuff and Non-Science' is all about grey matter. The old wives tell me that people only ever use ten percent of their brains. Is this really true? This is Hannah Critchlow with the truth.

Hannah Critchlow: This myth seems to have started in the early 1800s. There was some misinterpreted pigeon experiments, conducted by scalpel yielding Frenchmen, and then there was the case of the unfortunate Mr Phineas Gage - who, whilst constructing a railway, accidentally blew off a large portion of the front of his head. He initially appeared to be unaffected by this missing brain tissue. He could still speak, walk and function normally. But gradually it emerged that his personality had changed. He would no longer show empathy, where before he was caring. He was now impulsive, where before he was a shrewd and restrained businessman.

But it was too late. The myth that we do not need large parts of our brains had already started spreading. Damage to even small areas of the human brain can have devastating effects. Strokes, Parkinson’s and Alzheimer’s all result in damaged brain tissue and affect behaviour or functions. I asked Dr Rick Henson, a neuroscientist at the University of Cambridge, his thoughts on this myth. He tells us that if you image a person’s brain using a technique called PET scanning - which looks at metabolic activity - all areas of the brain are using energy, even when a person is simply lying down in a scanner.

So the myth that we only ever use ten percent of our brains is a false notion. It’s a myth resulting from the misinterpretation and exaggeration of observations that are over a century old.

Diana O’Carroll: So no excuses for not knowing all South American capital cities in reverse alphabetical order whilst trampolining through the streets of London. Your brain is ready to be used to the full. If you have any more science stuff and non-science then send it to me for fixing at diana@thenakedscientist.com

Chris Smith: Thanks Diana. That's Dianna O’Carroll with this week’s Stuff and Non-Science. Well that's it for this time. We’re back next week with another round up of the latest discoveries from the world of science. The Naked Scientists: Up All Night is produced in association with the Open University and you can follow up on any of the items included in the programme by the OU’s website - that's at open2.net/nakedscientists. Alternatively, you can also follow the links from the BBC Radio Five Live Up All Night web pages. The production this week was by Diana O’Carroll from the nakedscientist.com and I’m Chris Smith. Until next time, goodbye!

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Melanie Hinrichs takes a closer look at volcanoes in the lab.


Here's the research used by the team to make the programme.

In the news

‘Laboratory Simulation of Volcano Seismicity’
by PM Benson, PG Meredith RP Young, S Vinciguerra
in Science

‘Environmental Genomics Reveals a Single Species Ecosystem Deep Within the Earth’
by D Chivian et al
in Science

‘Tibetan plateau river incision inhibited by glacial stabilization of the Tsangpo gorge’
by O Korup and DR Montgomery
in Nature

‘Pillared Graphene: A New 3-D Network Nanostructure for Enhanced Hydrogen Storage’
by GK Dimitrakakis, E Tylianakis, and GE Froudakis
in ACS


‘The genome of the simian and human malaria parasite Plasmodium Knowlesi’, by A Pain, et al in Nature

‘Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood’, by H Christina Fan, YJ Blumenfeld, U Chitkara, L Hudgins, and SR Quake in PNAS


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