Naked Science Q&A Show

This week on the Naked Scientists we discover novel drugs in carnivorous plants, genes pointing to prostate cancer and a way to capture waste wattage whilst walking. We hear about...
10 February 2008
Presented by Chris Smith, Dave Ansell


This week on the Naked Scientists we discover novel drugs in carnivorous plants, genes pointing to prostate cancer and a way to capture waste wattage whilst walking. We hear about the future of 3D TV, the bio fuel carbon debt and how Pirate Bay could be about to walk the plank! Also, we take on your questions, such as why do electric lights stay on in a flood, how do animals evolve camouflage and why does a fresh cut throb? Plus, we have a shocking question of the week about the workings of electric eels, and in Kitchen Science we find out how to tell which drink is diet!

In this episode

Nepenthes alata photographed on Mount Ayam Bukong, a flank of Mount Halcon, Mindoro (Alastair Robinson, May 2007) - upper pitcher.

Carnivorous plant’s deadly recipe reveals antibacterials

Nepenthes alata - also known as the pitcher plant for its bottle-shaped leaves - is a killer.

It attracts insects with a sweet-smelling chemical broth and then dissolves the poor, unsuspecting creatures as they fall, intoxicated into the depths of its inescapable trap.

This evil and rather exciting green carnivore has now had its secret recipe revealed by scientists in Japan, who have separated the proteins by gel electrophoresis and matched them to proteins in a public database.

And some of its sweet but deadly proteins are natural antibiotics. By inhibiting bacterial growth, the plant can absorb as much nutrition as possible from its tiny victim, without any competition from bugs.

Nepenthes alata - The Pitcher Plant


Heat powered glider explores the oceans

It is often said that we have seen more of the surface of Mars than we have of our own planet. This is because 2/3 of our planet is covered with ocean, which is opaque to most of the forms of light we use to find out so much about the land with. You can send probes down to visit the bottom of the ocean but this requires a hugely expensive ship on the surface to power them and move them around.

Glider Surfacing
A thermal glider surfacing. The Tubes underneath contain the © Webb Research

Various groups have come up with a way of moving autonomous robots around the oceans powered by the water itself. If you throw a paper aeroplane, it falls down, but because of its aerodynamic shape it doesn't fall vertically it glides down following a diagonal course powered by its potential energy. You can do the same thing in the ocean so if you sink 4km you can glide up to 20km forwards, you then have to stop as you have reached the bottom of the ocean, unless you can make yourself buoyant again, as you can then glide another 20km upwards, you can then work out where you are using GPS and communicate with your base station then, loose some buoyancy and sink again.

The problem is that you need energy to gain and loose the buoyancy required to float and sink which uses up power in your batteries. A company called Webb research has harnessed the difference in temperature at the top and bottom of the ocean to provide this energy and so power the glider.

Inside the glider they have tubes of wax which when it heats up near the surface expands compressing gas which is stored in a tank. The glider then allows oil to flow from a bladder outside into the body, reducing the glider's volume, making it sink. When it reaches a pre-set depth the compressed gas is used to push the oil back out again making the glider float back up to the surface.

Thermal GliderGliding Upwards
The the thermal glider surfaced, where it could be communicating by satellite with its controllers. © Webb ResearchA Slocum thermal glider gliding upwards © Webb Research

The glider can also extract some electrical energy from this temperature difference by using peltier coolers in reverse so the test vehicle has so far travelled 1400km across the Virgin Islands Baisin in the West Indies, sinking and floating at least 20 times, moving at between 1 and 2 kph with no interference from outside.

In theory this vehicle should have a range of 40000km and only have to be picked up every 6 months or so giving us an unprecedented view of what is going on in the oceans.

Two mice; the mouse on the left has more fat stores than the mouse on the right.

Food for thought as researchers uncover appetite activator

Scientists looking for ways to combat obesity have found an enzyme that activates an appetite-stimulating hormone.

Obese MouseResearchers have been hungry to track down this target since blocking its action could help to stifle food cravings in people who are trying to lose weight.  Now, by using a genetic screening  technique, University of Texas Southwestern researcher Mike Brown has found it.  Dubbed "GOAT" (short for ghrelin O-acyltransferase), the new enzyme adds a chain of eight carbon atoms to a hormone called ghrelin, which is produced by the stomach and stimulates appetite.

When injected into animals and human subjects ghrelin boosts the urge to eat, whilst obese animals which have been genetically modified to lack the hormone or its receptor instead lose weight.  But the hormone only exerts these appetite-inducing effects after it has been chemically modified by the addition of the carbon tail.  Previous research in fruit flies had shown that enzymes that add carbon chains to proteins like ghrelin all share a similar fingerprint sequence.

So the researchers set about screening the mouse genetic code to look for signs of the same sequences. Using this approach they tracked down 11 genes and with one of them they hit the jackpot.  By adding the gene to cells in a dish they were able to trigger the cells to produce the active form of ghrelin, demonstrating that they had identified the right gene.

Promisingly, ghrelin seems to be the only hormone in the body, at least as far as scientists can tell, that carries this 8-carbon unit activating tail, so scientists think that it should be relatively simple to block it and so combat the urge to binge.

"The discovery of GOAT opens the way to a search for chemical inhibitors that may be useful in controlling appetite" say the researchers.  The proof as to whether it works or not will, of course, be in the pudding, or rather the lack of it!

Femur, from Grays Anatomy

Polymer to mend bones

A biodegradable polymer made with green solvents can mend broken thigh bones in mice, UK researchers have shown.

Femur, from Grays AnatomyThe sponge-like polylactic acid scaffold was coated with vascular endothelial growth factor protein and seeded with human bone marrow cells to mimic the biological factors that stimulate natural bone regrowth. After slowly delivering its contents, the polymer is metabolised by the body leaving no trace.

The breakthrough means the innovative polymer is a step closer to being used in hospitals. According to Richard Oreffo of Southampton University, who works on the team, human trials could be less than 5 years away.

Many researchers are working on similar systems because they promise to avoid the problems of harvesting bone grafts from patients and donors. But a key difficulty is how to make a polymer that's holey and sponge-like, but which also encapsulates a highly expensive and delicate protein or drug inside.

The solution Howdle's team has been developing over the last decade is to use supercritical carbon dioxide - a solvent with properties midway between those of a gas and a liquid. Formed under pressure, the supercritical fluid melts the polymer and allows any delicate protein to be mixed into it just above body temperature. When the pressure is released, carbon dioxide gas foams up this mixture, automatically forming the porous scaffold ready-coated with active drug or protein.

Prostate cancer cell imaged using electron microscopy and coloured artificially

11:24 - Genetics of Prostate Cancer

Prostate cancer is the most common form of cancer for men in the UK, and now researchers at the Institute of Cancer Research have found seven genes potentially very important in the disease.

Genetics of Prostate Cancer
with Dr Ros Eeles & Professor Doug Easton

Chris - Now also in the news this week scientists have been looking into the genetics of prostate cancer.  That's actually the most common cancer that us guys suffer from.  The Naked Scientists' own Kat Arney actually works off air at Cancer Research UK.  She's going to let us know what this paper published in the journal Nature Genetics is all about...

A Prostate Cancer CellKat - Today sees the publication of a big new discovery by CRUK-funded scientists at the Institute of Cancer Research.  Using genome scanning technology the researchers have tracked down seven regions of DNA that harbour potentially important genes involved in prostate cancer.  This is significant because we know relatively little about the genes and molecules involved in this disease which has meant that research into prostate cancer hasn't progressed as fast as it has with other types of cancers such as breast cancer.  The research was led by Dr Ros Eeles.  She explains how the team carried out their ground-breaking work.

Ros - What the study did was that we analysed DNA, genetic material from blood samples from over 10,000 men and we compared genetic variance in men who had prostate cancer with a control group and in collaboration with the Protec study.  Men who were in that study gave blood samples and we used their samples as controls.  What we did was we ran genetic experiments and they looked for genetic variations, changes in the basis of the DNA code looking to see if the men with prostate cancer had a different overall profile from men who had a very low risk in the control group.  We found there was a marked difference, particularly in seven areas of the genome.

Kat - This kind of study was only possible thanks to recent advances in DNA analysis.  Another of the study's authors, Professor Doug Easton, explains more.

Doug - In the period since the human genome became sequenced we've been able to identify many millions of genetic changes, perhaps about 10 million that are known.  But at the same time we've also managed to develop a particular technology based on the arrays of these variants or SNPs which allow very large numbers of them to be tested simultaneously.  Also the costs have come down a lot so it's now possible to test many hundreds of thousands of SNPs on many thousands of people and that's really made the search for these more common genetic variants possible when it wasn't possible before.

Kat - But what does this all mean for the 30,000 men who are diagnosed with prostate cancer every year in the UK?  Well, right now probably not a lot but the hope is that in the future these new genes may lead to better screening tests and even more effective targeted treatments.

The biomechanical energy harvester comprises an aluminium chassis and generator (cylindrical component at the top of the chassis with green plastic attached) mounted on a customized orthopaedic knee brace (black), totalling 1.6 kg mass.

14:28 - Wattage Wasted While Walking

Could we generate electricity from the energy we waste while walking? Professor Max Donelan has developed a way to turn people into the human equivalent of a hybrid car...

Wattage Wasted While Walking
with Professor Max Donelan, Simon Fraser University

Chris - We're now going to be joined by Professor Max Donelan.  He's a researcher at Simon Fraser University in Canada and he's found a way to turn people into the human equivalent of a Hybrid car.  Max, tell us a little bit more.  How does this work?

The Biomechanical Energy HarvesterMax - What we've done is take advantage of the inherent uneconomical nature of walking.  So, as you mentioned, we can take advantage of walking like a hybrid car takes advantage of stop and go driving.  That is, within the walking stride the muscles are first accelerating and then decelerating the body.  A hybrid car takes advantage of the decelerating, braking by using a generator to brake rather than a traditional brake which just dissipates as heat.  The generator produces electricity which we can then use in a productive way.  We've done a similar thing for walking where we've tried to use generators help the muscles slow the legs down.  In doing so the generator can assist the muscles and it also creates electricity at the same time.

Chris - It sounds a bit counter-intuitive to think that your legs would be so inefficient, that they need help in slowing down and that you can actually get useful energy out of this.

Max - Yes, I think it is a little counter intuitive but the main point: if you think about walking at a constant speed on the level then there's no net change in your mechanical energy so on average you're not moving any faster or any slower.  You're not going uphill and downhill so that means for every little bit of energy that your muscles put in, something also has to take it away.  It's mostly your muscles that take it away.  You don't need them to do it, you could use something like a generator instead.  The generator can take the mechanical energy away from the body and put it through the generator and produce electricity at the same time.

Chris - So in other words, as your leg's swinging to return to the starting position so you can take the next step you would normally need a muscle to kick in and stop the leg from moving at that point.  Your generator exploits that effect and instead of the muscle doing that work you're diverting that effort through your generator and it recovers the energy the body would otherwise have to expend.

Max - That's exactly right. So where we do it is at the knee and towards the end of the swing phase - so when you're moving your foot forwards to begin another step.  Your hamstring muscles, which are the muscles down the back of your leg, they turn on to slow down your knee extension.  Our device mounts at the knee that generator engages at that period and helps those hamstring muscles in slowing down the extension of the knee.  We can measure this through the fact that when we use the generator it actually allows those muscles to turn down by about 15%.  The muscle activity decreases.

Chris - The difference in the energy expenditure is what you're generating with your device.

Max - The idea is that people don't have a difference in energy expenditure, so generating electricity or not generating it is about the same effort you put in, but you still get the electricity out. So you're getting 5W of electricity without increasing their effort by a meaningful amount.

Chris - So what does this device look like when it's in situ on a person? Is it very ungainly, is it going to get in the way?

Max - In the current version I would say it is a bit ungainly so it looks like a normal orthopaedic knee brace with a chassis mounted to the side of it.  It's a bit bulky and a bit big but that's because it's really designed for convenient experimentation so you can pull gears out and generators out.  The final version will be less than a kilogram and it will easily sit underneath a pair of pants.  Currently too big but no problem getting it smaller.

Chris - When someone's wearing this thing how much energy physically are they able to produce with it?

Max - There's two modes. One mode gives 5W of electric and for context 5W is enough to charge ten mobile phones at the same time or to produce ten minutes of call time for one minute of walking.  That's not to say I think we're going to charge mobile phones in the near future but it gives you some context of how much power.

Chris - I'm not being flippant, Max, if I want to charge my mobile phone I plug it in.  So why would I want this?

Max - I think you're absolutely right.  For us plugging in a mobile phone is just a matter of convenience, but for many people their lives depend upon resources for power.  Consider for example if you had a powered prosthetic leg or a power device that helped you walk every stroke for you it's not always as simple as plugging it in.  For example, some of these prosthetic legs might run out of power within four hours or so.  If you can use your healthy leg to generate some electricity to power your artificial leg then you can walk farther.

Dave - I was wondering whether you could put it into a mode so that when you're walking downhill or down a big mountain you can make it absorb lots and lots of energy. I find that very, very uncomfortable when walking out in mountains.

Max - That's a great question so, you've hit on it exactly.  Walking downhill, there's a lot more energy available because essentially what your muscles are doing is making sure that you don't arrive at the bottom at the speed that gravity wants you to.  They're taking the potential energy you had at the top of the hill and your muscles are dissipating it all as heat so you walk down it in a controlled way.  If you can use a generator to do that instead you can produce lots and lots of electricity.  We find that if you walk down a hill you produce more electricity or if you walk faster.

Chris - Thank you very much, Max.Max Donnelan watching the Biomechanical Energy Harvester at work

Why did my light work when soaked?

Chris: So Martin's ceiling rose almost became a shower rose, Dave. Why didn't it go bang?Dave: Do you have a trip switch in your house? Martin: I do have fuses, yeah.Dave: Oh. Fuses are just things which will break if you draw too much current. Have you got one of the trip switches, sort of residual current devices which will trip if any current's going to earth?Martin: No.Dave: Ok. If you haven't got a trip switch the only thing which is going to cause the electricity to turn off is if you're drawing more current than one of the fuses can take so that would involve more than 40 or 50 amps of current. As long as there's less current going through the water than forty of fifty amps then your house just thinks someone's plugged in a whole load of lights so maybe a heater in your ceiling rose. If you did have a trip switch and the water was connected to something earth like a water pipe or central heating system to the earth then the trip switch would detect that there was some current running from the mains to the earth down the earth wire. A trip switch would think oh no, something's wrong maybe the central heating system's exploded, we'll turn the power off now. Without a trip switch there's no reason why your power shouldn't carry on. Chris: These lights are definitely not 12V, are they?Martin: I've not got a clue.Chris: Because one of the other fancy things that people tend to do in kitchens and other places round the house is that they tend to have a 12 volt system running those little mini halogen lights. They're very, very bright because all they do is draw a much bigger current but at a lower voltage. Because water isn't a terrifically good conductor like Dave said then at 12 volts it often won't actually make that much difference because there's not a big enough potential difference to flow the current through the water. So if it's 12 volts, that may be why it didn't go bang.

How do living things know how to evolve?

It's not really a question of the animal knowing what to evolve into but this is a really beautiful example of evolution in action: mimicking the surroundings so animals are well-hidden and protected from predators. A particular species of seahorse will find a good bit of seaweed to actually hide amongst and gather food in a really nice place for it to live. As the seahorses breed and as new generations of seahorses are born small genetic mutations will change their appearance and change certain things about them. As their appearance changes you might get a mutation that makes them a slightly different colour that's similar to the seaweed, for example. A seahorse that's a very similar colour to the surrounding seaweed would be better protected because it would be camouflaged much better so hidden from predators. More of those colours, of course, would survive so eventually all of the seahorses would eventually resemble the habitat in which they live.

Other animals have evolved other ways to disguise themselves - with some disguises making them look poisonous, to put predators off.

Could ghrelin be used to stimulate apetite?

Connie was referring to the news story about "GOAT" (ghrelin O-acyltransferase), which adds a carbon chain to the hormone ghrelin. Ghrelin is produced by the stomach and stimulates appetite, so targeting it could help develop anti-obesity drugs.

That's a very good suggestion and I suspect the answer is yes. Researchers are eager to find ways to help people who have eating disorders and increase their ability to take onboard food. I don't know if it's actually been trialled though, in the context of people who have an eating disorder. I think it's just healthy volunteers they've tried it on so far but it's a very good point and yes you could make a case for doing that because people are often surprised to learn that the class of psychiatric condition which is associated with the highest rate of suicide and death is not all the things like schizophrenia and bipolar disorder (manic depression) although they have a very high suicide rate, the rate of death is actually highest amongst people with eating disorders. Anorexia Nervosa, is I believe, associated with more people dying than virtually any other condition. Certainly in young people it's a leading cause of death. Anything that can be done to help them is a really big step forward.

We also had this comment from Rachel in Cambridge:

In eating disorders appetite isn't the driving force behind them. A drug that stimulates appetite might therefore not help because the problem is not a lack of desire to eat but actually not allowing yourself to eat.

How fast should I set the fan to defrost the windscreen?

The thing that's going on when you blow on your hand is you tend to blow on it from far away. Especially if you're blowing with pursed lips. If you breathe slowly, especially if you're close, then all the air to your hand is the nice warm air from your lungs. When you're blowing on them with pursed lips, partly it's going to be further away so the air will be cooled down a bit more. Also, as you're farther away it will tend to catch cold air from the surroundings and drag that along with it. You're not just blowing along through your lips there's also a load of cold air mixed in. Also, the faster the air's moving the more you'll tend to evaporate moisture from your skin which will cool you down as well. I think if you're blowing with a big fan very close to your windscreen which is the way it works the higher the fan is the more it will defrost your window.


Why did my thumb throb when injured?

[This answer has now been updated to reflect more recent research findings.]

Historically, it was claimed that the throbbing nature of the pain occurred owing to arterial pulsations which produce repetitive wave sensations.

The argument went that inflammatory chemicals are produced in response to the injury as part of your body's defence to prevent infection to that wound. These chemicals stimulate sensory nerve endings including sensory receptors that are mechanically stimulated. So, as your artery throbs with the beat of your heart, that stimulates the sensitised nerve endings and you get this throbbing, drumming pain.

However, the claim did not stand up to scientific scrutiny by a team at the University of Florida, who measured simultaneously the rate of arterial pulsation and the perceived rate of pain throbbing in human volunteers with toothache.

According to their findings, published in the Journal of Neuroscience in 2012, "Contrary to the generally accepted view, which would predict a direct correspondence between the two, we found that the throbbing rate (44 bpm) was much slower than the arterial pulsation rate (73 bpm, p< 0.001), and that the two rhythms exhibited no underlying synchrony."

Instead, based on their findings, the team speculate that "...the throbbing quality is not a primary sensation but rather an emergent property, or perception, whose "pacemaker" lies within the CNS [central nervous system]."

In other words, the throbbin character of the pain sensation appears to arise within the brain's circuits itself, although at the moment no one knows how.

Reference: "Is There a Relationship between Throbbing Pain and Arterial Pulsations?" - DOI:10.1523/JNEUROSCI.0193-12.2012

[Our thanks to Rose Edwards for bringing this paper to our attention.]

Could subersibles be used without pilots for a long time?

Roy was referring to this news story about an underwater thermal glider. Designed to take advantage of changes in temperature to glide long distances collecting information about the sea bed.

You couldn't have a person in this type of glider because of the amount of energy you need to keep the person going; you need to keep them warm and give them oxygen. It would be far more than the energy you could generate. So you'd have little, tiny computer-controlled things which can just travel through the ocean all over the place. In fact the biggest limitation on it is the amount of power it can use because it can't generate very much. You need to have not very power-hungry sensors.

Pannonhalma Archabbey - Cathedral walls have great thermal properties.

29:26 - Rising Stars - In-Wall Wax for Comfy Climate

Heating and cooling the average house takes a lot of energy - but filling your walls with tiny wax capsules could keep you cool in the heat of summer...

Rising Stars - In-Wall Wax for Comfy Climate
with Matthew Richardson

Thermal imaging of a Passive House, with a conventional building in the backgroundMatthew Richardson - Energy saving is big news.  We're asked to turn off computers and ditch the car for buses and bikes.  Did you know that a third of the world's energy is used in buildings, much of it on heating and air conditioning?  It takes a lot of energy to keep you at a steady 20 degrees come rain or shine.  But there's plenty of heat and cold out there already it just tends to be at the wrong place at the wrong time.  In Cambridge we're looking at the ways that natural ventilation can help.   Air in buildings expands when it's heated and hot air rises, just like smoke from the tip of a cigarette.  In the theatre, for example, the heat from the audience drives an air flow.  In the lab we can use simple water models to understand where the heat goes and ways to control it to keep everyone comfy.  Sometimes it can be as simple as opening a window to draw in cold air from the outside.  Then automatic controls could slash energy use, without you even noticing.

Pannonhalma ArchabbeyMuch of natural ventilation is borrowed from history, the Romans used to build under-floor furnaces in their baths and air would rise through chimneys in the walls and out to the roof.  Using this method they could heat the baths up to 50 degrees.  Natural heat flows keep cathedrals cool at the height of summer.  Heavy stone walls take far longer to heat up and cool down so chunky buildings can protect you from extreme temperatures just as the sea protects coastal areas from extremes of winter and summer.  Nowadays though, builders often want to build frame buildings with paper-thin walls.  Here we're experimenting with putting tiny wax capsules into walls to create a similar effect.  Wax may not be as heavy as stone but it can absorb a huge amount of energy when it melts.  If fact, a couple of kilos of melting wax absorbs the same amount of energy as it takes to boil a kettle.  By adding wax we hope to turn your house into a cathedral.

While these methods show promise understanding air flows can be complex and sometimes we're just tempted to turn on the aircon and forget the cost.  Increasingly though, natural ventilation will have a vital role to play in maintaining the climate outside our buildings as well as comfort within.

Hologram installation at MIT Museum

32:17 - Chemistry World - 3D TV, Biofuel Debt and Reading RNA

This week, Mark Peplow comes in to tell us about the moves towards holographic 3D TV, how it could take years to pay back the carbon debt of biofuels, and a new scanner that can 'read...

Chemistry World - 3D TV, Biofuel Debt and Reading RNA
with Mark Peplow, Chemistry World

Chris - Time to catch up with the editor of Chemistry world. That's Mark Peplow. Hello Mark.

Mark - Hello Chris.

Chris - 3D television, sounds fantastic, even on the radio!

Hologram installation at MIT MuseumMark - It does sound fantastic.  It's not quite around the corner but the first major step has been taken towards it.  We're all used to this idea of being able to have a hologram where you can effectively get this image which gives you the illusion of three dimensions.  You can look around this object.  A group of scientists from the University of Arizona have now managed to make that hologram and then found away to erase and rewrite it with a new image.  In theory if you can do that frequently enough you can actually get a moving three dimensional film.  The way that they do this relies on a special type of polymer.  What happens when you're taking a holographic image, laser beams bounce off this object from different angles. Where they bounce back and recombine they hit this light sensitive polymer and it stores the 3D signal in a complex pattern of interference.  They've tweaked the polymer that they use with a special dye molecule and found that as long as they put an electric field across it, it means that the dye molecules are shifted, rotated if you like when the laser light hits them.  That means that it takes them about three minutes to draw a full image and then another blast of full laser light resets the molecules ready for the next image to be written.

Chris - Three minutes, that's not a very fast frame rate if I'm honest.

Mark - I know. I guess the crucial thing about this is that it's a proof of principal that it can be done at all.  We talked to a hologram chemistry expert called Kevin Davidson who's at the University of Cambridge here.  He pointed out that there's a lot of work gone on in this area but no one's really demonstrated this ability to do this so reliably and at least repeat time after time.

Chris - So it's gonna be a little while before we can play a game of chess like they do on Star Wars with those kind of figures that act it out on the board for us.

Mark - Yes, absolutely, although that would be cool, wouldn't it.

Chris - I can't wait for those days actually.  What's this about biofuels and carbon debts?

Mark - Yeah, biofuels have been getting a rough ride lately.  The Royal Society which is Britain's major academy of sciences has put out some major warnings recently.  About policy makers rushing too quickly to adopt new biofuel policies.  The idea is that rather than burning petrol which we get from oil out of the ground it would be better to get fuel for the car from plants.  Plants grow by sucking carbon dioxide out of the atmosphere and we're trying to reduce the amount of carbon dioxide we're putting out to reduce the rate of global warming.

Chris - That's good isn't it?  You want the plants to take the CO2 out of the atmosphere and turn them into fuel so there's no net carbon gain.  Why should there be a problem with that?

Mark - Absolutely.  The devil is in the detail as with all of these things.  As people have started to grow more and more biofuels, a good example is sugar cane in Brazil where they turn that into fuel for cars (ethanol), people are doing what's called lifecycle analysis.  They're basically looking at all of the energy that you need to put in to make these fuels and also look at all of the carbon that comes out when you're making these fuels.  The latest pair of studies which was just published in Science magazine on Friday really paints a very damning picture.  Effectively when you cultivate land to grow any biofuel you rack up this carbon debt.  You're releasing so much carbon that was trapped in the soil that it can take sometimes centuries to regain and repay that carbon debt through the advantages of using biofuels.

Chris - So the moral of this story is there's no quick fix, is there?

Mark - Absolutely.  It's interesting because people usually talk about the Brazilian example of using sugar cane as probably the best biofuel to use.  They've found it still took 17 years to repay the carbon taken from when, for example, a random tract of savannah was ploughed up to plant that stuff.

Chris - So there's lots and lots of things to consider rather than just the here and now.  What's this about reading the genetic code directly because this sounds amazing!

Mark - Yeah.  This sounds like really Star Trek stuff and it's really exciting actually.  We're all used to this idea of DNA fingerprinting.  This relies on a chemical reaction called the polymerase chain reaction.  What that means is you have this smear of blood that you find in CSI, there will be millions and millions of molecules of DNA in there but still not enough to get an exact chemical read on the data that's recorded in that DNA.  You have to do this reaction that amplifies the DNA sample by multiplying the molecules over and over again in the sample until you've got enough to do a proper analysis.

Now, that takes a laboratory, it takes time and it can introduce errors.  A group in Dortmund in Germany have found a way.  They've proved a principal that they can read a single molecule of not DNA but its chemical cousin RNA using a device which is a special combination, basically, of two different techniques.  What it looks like, really is a tiny, tiny record player needle where the tip of it is just 20nm across.  It's hooked up to a laser.  What happens is that the tip reads along the length of a single molecule of RNA and guides the laser as it goes.  The laser will illuminate the section of the molecule and the light that comes back carries the characteristic signature of the chemical bases as they're called which holds the data in RNA.  They've proved that although the laser blast will illuminate maybe half a dozen bases at once because the tip moves along it one base at a time.  They can literally read along and show that as they move this tip along they can read each base as it comes along.  At the moment this requires some big bits of kit and it's pretty time consuming but it shows that you can read this single molecule of genetic code.  Because of the advances that have come along in these techniques it means that over the coming years it should get faster, cheaper and easier.

Chris - It's amazing to think how far we've come because you say it's big and bulky but then so was the polymerase chain reaction when we first started.  Thank you for coming in, Mark.

Pirate flag of Rack Rackham (Calico Jack)

38:43 - Pirate Bay on the Plank

In the world of technology this week, copyright infringement on the "virtual" high seas as Pirate Bay goes to court, and Microsoft moves to buy Yahoo...

Pirate Bay on the Plank
with Chris Vallance

Meera - I've met up with our resident tech expert, Chris Vallance to find out what's going on in the world of technology this month. Hi Chris.

Chris Vallance - Hi there.

Meera - So there's been news with Pirate Bay. What's that?

Pirate flag of Rack Rackham (Calico Jack)Chris Vallance - Pirate Bay kind of does what it says on the tin.  Pirate Bay is a Swedish-based website and it claims to be the world's largest Bit Torrent tracker.  Bit Torrent is a place where people share files.  It's a file sharing system and the kind of things that people share on Bit Torrent are lots of legitimate things but also copyright content like films, books, music also gets shared.  Obviously this is very controversial. People who own the copyright don't like this kind of thing: the music industry, the film industry.  Way back in May, 2006 a Bit Torrent [Pirate Bay's offices] was raided.  About 200 police officers raided its offices and we didn't have any charges but last week four people associated with Pirate Bay were charged.  It's a very, very political issue.  Not just on the web but in Sweden as well.  Pirate Bay didn't actually host any of this content.  On their servers you wouldn't have found films, music whatever.  They were just linking to this peer-to-peer sharing system.

Meera - They claim they're not doing anything wrong.

Chris Vallance - Yeah, exactly. If you talk to people who support Pirate Bay, they say look, we're just linking.  In a way what we're doing isn't any different from what a search engine would do.  I spoke to Magnus Eriksson.  Now Magnus Eriksson is a spokesperson for Piratbyrån which I think translates as Pirate Bureau.  He explains that in his view what Pirate Bay is doing wasn't that different from what search engines, forums and other websites do.

Magnus - The prosecution doesn't have much to offer here. What he's trying to imply is that the Pirate Bay, just by starting this service is responsible for what its users stuff on it, that they are somehow aiding them in their corporate infringement.  But if this would be a principle that would mean that anyone developing a community site or a forum site or a mail client or something would have to be responsible for what its users do.  I mean, it's an open service.  The consequences when people share the things that matter to them.  It seems like that at the moment for copyrighted material.

Chris Vallance - Sara Lindbach is a legal specialist with the anti-Piratbyrån.  She takes a very different view.

Sara - The material from the prosecutors shows reason that they had a daily turnover of $3million and Pirate Bay has been making [it] possible for millions of people to illegally file share material.  They are making a lot of money on the rights holder's material.

Chris Vallance - For the film and recording industry what really marks Pirate Bay out is the fact that they were making a lot of money.  This is Jo Oliver, a legal analyst with the IFPI, a body that represents the recording industry.

Jo - Pirate Bay has become something of a destination for those who are looking for illegal content and the scale that's quite staggering.  Pirate Bay claims to have 10 million users world-wide so the steps being taken today to file charges are very important to us.

Chris Vallance - They would say they're merely linking to torrents that are already there and that they don't create those torrents.

Sara - As a user you go along to the Pirate Bay and it provides everything you need to get the infringing material.  Around the world similar types of services have made the same argument but in the end the courts found that they were liable for what they were doing.  I think the difference is Pirate Bay is set up to exploit illegal content.  It's a lot easier to find pirate material in Pirate Bay than it is doing a Google search online.

Chris Vallance - In a way I think what you see emerging is a question about degree.  For the prosecutors what Pirate Bay was doing was so obviously about getting copies of films in their view for people who support Piratbyrån, what they're doing isn't so different from what the search engines enable you to do.  There's definitely a bit of a legal crack down on people who are sharing and engaging in the kind of activity that Pirate Bay does.

Meera - Well, it will be really interesting to see how that turns out.  Is there anything else going on in the world of tech at the moment?

Chris Vallance - Well, I don't think we could get away without mentioning Microsoft and Yahoo.  There's a $23billion offer Microsoft has made for Yahoo.  It's interesting because obviously Microsoft's main competitor is Google.  But Google and Microsoft are very different business models.  Google sees our tech-future, if you like, as being very much based on the web.  But for Microsoft as a software maker, still very much focussed around the PC.  You have Microsoft producing Office software that will let you do spreadsheets and word processing on your PC.  Google producing Google Docs and Google spreadsheets let you do it on the web.  Two very different philosophies.  If you look at Microsoft's move for Yahoo, well is this Microsoft trying to get into Google's territory?  Not just competing on search because obviously Google dominates the search market but it's more about the direction of our future computer use.  I think what's interesting about Yahoo, they own some very interesting properties.  They own Flickr,, they own Upcoming, they're heavily involved with OpenID.  Also what's interesting is the reaction from the community of users because you have Flickr groups now saying we don't want Microsoft owning Flickr, wondering how that's going to go if Yahoo suddenly becomes owned by a software producer.  Of course, in all of this you've got Google who are now trying to snuggle up to Yahoo in an effort to put off that Microsoft bid.  Above that you've got the competition regulators and how are they going to view a very big merger between two big companies involved in the internet computing space.  There's a lot still to play out with this.

Photo of Electrophorus electricus (electric eel) at the Steinhart Aquarium in San Francisco, taken June 2005

44:32 - Self-Shocking Electric Eels?

How do Electric Eels avoid shocking themselves?

Self-Shocking Electric Eels?

We put this question to Dr Mark Briffa, Lecturer in Marine Biology at the University of Plymouth:

First of all, an electric eel isn't really an eel. It's a member of a family of fish called gymnotids or knife fish and the scientific name is rather aptly, Electrophorus electricus. In most animals electric currents are used in nerves to carry information and to control muscle movements. What makes fish like electric eels special is that they can exploit this property of muscle tissue and discharge bursts of electric current into the surrounding water. They do this using an electric organ made out of modified muscle tissue in the tail.If electric eels can generate these strong discharges, what stops them electrocuting themselves? First of all the electric organs are in the flank of their tail and this means that the discharge occurs straight into the water rather than the eels internal organs. Since water is more conductive than body tissue the charge travels away from the eels. The second possibility, and that's that because the discharge is very quick the current doesn't flow for long enough to shock an animal as large as an electric eel. But for its prey which are usually smaller fish the short burst is enough to shock and stun or sometimes even kill them. So electric eels are unlikely to cause a damaging electric shock to humans but it's still not going to be a very pleasant experience to be on the receiving end of one and an impressive 2m long pet electric eel probably isn't a very good idea. It's quite difficult to work out how far the discharge will travel but prey being stunned or killed up to a distance of 2m away from the eel has been reported.We also received this from Dr Carl Hopkins, Cornell University:Electric eels generate electricity in much the same way that every nerve and muscle cell in an animal's body does, by establishing a weak voltage across the cell membrane. In fact, the electric organ is believed to be derived from muscle cells, which over the course of evolution, have lost their ability to contract as muscle, but retain their ability to produce electric currents. The big change during the evolution of the electric organs of fishes is the fact that the weak signals present in individual cells add up in series, like batteries put end to end in series in your flashlight. In addition the time of the discharge is precisely synchronized so that the short pulses occur at exactly the same time - a necessity if the voltages are to add.In order for an animal cell (or any cell, for that matter) to generate an electrical current, it must first use energy from food and metabolism to pump charged potassium and sodium ions across cell membranes so that potassium is high in concentration in the interior of the cell and sodium is concentrated outside the cell. Once the concentration gradient is established, for both of these ion species, the next requirement is that there be a "pore" in the membrane that allows possitively charged ions to go through without letting negative ions through. In animal cells, the membrane is permeable to potassium but not sodium and not negatively charged ions like chloride. Potassium ions start to diffuse out through the membrane and this establishes a voltage across the cell membrane (about 80 millivolts negative on the inside). This is the so-called resting potential. Then, when the electric organ is activated by nerve impulses, sodium ion channels open in the membrane to allow sodium to flow into the cell, changing the membrane voltage from -70 millivolts (mV) to about + 50 mV, a change of 120 mV. This is a transient event lasting only 1 millisecond or so. Since all of the cells in the electric organ discharge synchronously, their voltages add up to produce a substantial signal in the water. This is the electric discharge.To get the weak 130 millivolts discharge large enough to do anything outside the animal, the electric fish arranges the cells like a series of poker chips in a pile -- then the 130 mV signal across each cell adds to the next one. With the electric eel where there may be 5,000 cells arranged in series, the voltage will be 5000 x .130 Volts = 650 Volts. The cells are also arranged in parallel, which increases the ability to generate current in the water.Nobody knows exactly how the electric eel keeps from shocking itself, but the best working hypothesis is that the vital organs like the brain and the heart are located as far as possible from the electric organ (up near the head), surrounded by fatty tissue that acts as an insulator. In cross section through the tail, the electric eel is nearly entirely electric organ.

Sun shining on waves

Why do some places have 2 tides a day and others 4?

First of all 99% of the world just has 2 tides a day and the reason for that is basically the moon and the sun pull on the Earth and on the water around it. If you're close to something massive it's got a stronger attraction due to gravity than something farther away. Water on the side of the Earth closest to the moon is going to get pulled the hardest and the Earth which is in the middle is doing to get pulled slightly less hard and the water on the far side is going to get pulled even less hard. So you tend to get two bulges of water: one is the bulge of water close to the moon and the other bulge of water on the other side which is getting left behind. That's the reason why most places get 2 tides a day.

Some places get 4 - the only place I know about it is Southampton, Portsmouth in the UK by the Isle of Wight. If you look very closely at the map of the Isle of Wight it has funnels on each side of the channel just north of it. As the water rushes up the channel it sort of piles into these funnels and then as it gets narrower the wave gets higher. You actually get a high tide as the water rushes up. You get another one on the other funnel as the water rushes back down the channel so you get twice as many tides as you should have.

Why do I see lights when I do exercise?

That's because when you stand up all of the blood which is circulating round the body suddenly has this big force of gravity pushing it straight down into your legs. The amount of blood coming back up from your legs into you heart to be pumped out into your brain drops. Your retina, the part of the eye that converts light into signals that the brain can understand has the highest metabolic rate of any tissue in the body so if the blood flow to the retina drops very, very slightly for a fraction of a second it starts to fire off abnormal signals. Those are the white lights that you see.


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