Tag: science

Feb 02 2010

Why is that butterfly blue?

Some colours come from the properties of individual molecules, some colours come from the shape of things. This is a post about the colour from the shape of things – structural colour, like that found in the Morpho rhetenor butterfly pictured on the right.

To understand how this works, we first need to know that  light is a special sort of wave known as electromagnetic radiation, and that these waves are scattered by small structures.

For the purposes of this post the most important property of a wave is it’s wavelength, it’s “size”. The wavelengths of visible light fall roughly in the range 1/1000 of a millimetre to 1/2000 of a millimetre. (1/1000 of a millimetre is a micron). Blue light has a shorter wavelength than red light.

The Spectrum of visible light (Image from Wikipedia)

Things have colour either because they generate light or because of the way they interact with light that falls upon them. The light we see is made of many different wavelengths, the visible spectrum. Each wavelength has a colour, and the colour we perceive is a result of adding all of these colours together. Our eyes only have three different colour detectors, so in the eye a multiplicity of wavelengths is converted to just three signals which we interpret as colour. The three colour detectors are why we can get a full colour image from a TV with just three colours (red, green and blue) mixed together. Some other animals have more colour sensors, so they see things differently.

The problem with viewing the small structures that lead to the blue colour of the butterfly wings is that they have interesting features of a size about the same as the wavelength of light, and that means you can’t really tell much by looking at them under a light microscope. They come out blurry because they’re at the resolution limit. So you resort to an electron microscope, electrons act as a wave with a short wavelength so you can use an electron microscope to look at small things in much the same way as you would use a light microscope except the wavelength of the electrons is smaller than that of light so you can look at smaller things.

So how to explain resolution (how small a thing you can see) in microscopy. I would like to introduce you to a fresh analogy in this area. Summon up in your mind, a goat (tethered and compliant), a beachball (in your hands), and a ping-pong ball (perhaps in a pocket). Your task is to explore the shape of the goat, by touch, via the beachball, so proceed to press your beachball against the goat. The beachball is pretty big, so you’re going to get a pretty poor tactile picture of the goat. It’s probably going to have a head and a body but the legs will be tricky. You might be able to tell the goat has legs, but you’re going to struggle to make out the two front legs and the two back legs separately. Now discard the beachball and repeat the process with the ping-pong ball. Your tactile picture of the goat should now become much clearer. The beachball represents the longer wavelength of light, the ping-pong ball the shorter wavelengths of electrons in an electron microscope.

And now for scattering; retrieve your beachball; step back from the goat. You are now going to repeatedly throw beachball and ping-pong ball at the goat and examine where the balls end up having struck the goat. This is a scattering experiment. You can see that how the ball bounces off the goat will depend on the size of the ball, and obviously the shape of the goat. This isn’t a great analogy, but it gives you some idea that the shape of the goat can lead to different wavelengths being scattered in different ways.

So returning to the butterfly at the top of the page, the iridescent blueness doesn’t come from special blue molecules but from subtle structures on the surface of the wings. These are pictured below, because these features are smaller than the wavelength of light we need to take the image using an electron microscope (we are in ping-pong ball mode). The structures on the surface of the butterfly’s wing look like tiny Christmas trees.

Structures on the surface of a morpho butterfly wing (scale bar 1.8 micron)

These structures reflect blue light really well, because of their shape, but not other colours – so the butterfly comes out blue.

Another example of special structures that interact with light is this is a *very* white beetle:

Cyphochilus beetle (Image by Peter Vukusic)

The cunning thing here is that the beetle manages to make itself very white, meaning it reflects light of all wavelengths very efficiently, using a very thin scales (5 micron). This is much better than we can achieve with synthetic materials. The trick is in the detail, once again the scales have a complicated internal structure as you can see in this image from an electron microscope:
Cross-section of a beetle scale (scale bar is 1 micron, Image by Peter Vukusic )

It turns out that the details of the distribution of the scale material (keratin) and air in the scale conspire to make the scale highly reflective. Making things white is something important to a number of industries, for example those that make paint or paper. If we can work out how the beetle does this trick then we can make cheaper, thinner, better white coatings.

Finally, this is something a little different. If you’ve got eyes, then you want to get as much light into them as possible. The problem is that some light gets reflected from the surface of an object, even if it is transparent – think of the reflection of light from the front surface of a clear glass window. These structures:

The surface of a butterfly’s eye (scalebar 1micron, Image by Peter Vukusic)

known an “anti-reflective nipple array”, are found on the surface of butterfly eyes. The nipples stop the light being reflected from the surface of the eye, allowing it instead to enter the eye. Similar structures are found on the surface of transparent butterfly wings.

In these cases animals have evolved structures to achieve a colour effect, but more widely we see structural colours in other places like rainbows, opal, oil films and CDs. The sky is blue for a related reason…

Sources
The work on butterflies and beetles was done by a team led by Peter Vukusic at Exeter University:

Jan 28 2010

Mother, do you think they’ll drop the Bomb?

I thought in this post I would touch on science and morality by means of the Manhattan Project.

The picture at the head of the page is of the very early stages of an atomic bomb going off. The roughly spherical fireball is approximately 20 metres across at this point. It was taken using a “rapatronic” camera, invented by Harold Egerton for just this purpose.  The exposure time for this camera can be as short as 1/500,000th of a second (2 microseconds). Cameras were fired sequentially at periods less than 1/1000th of a second (1 millisecond) after detonation, to produce a sequence of images of which this is just one. The camera is triggered by a photocell, which picks up the x-ray flash as the bomb goes off, and a delay circuit. The shutter contains no moving parts, it is a “Kerr cell” placed between two polarizers arranged such that they let through no light. When a current flows through the Kerr cell the polarisation of light is rotated and so can make it through both polarizers – no current and no light gets through. This is all done electronically so can happen really fast.

The bomb was detonated on a gantry tower supported by guy wires, the bright spikes beneath the round explosion are known as “rope tricks“, they are where the metal guy wires have been vapourized by the light from the initial detonation. If you cover the guy wires in aluminium foil the rope tricks disappear because the light is reflected, paint them black and the spikes appear larger because more light is absorbed. The distorted shape of the fireball is a relic of irregularities in the bomb casing, and the small shed at the top of the gantry tower in which the bomb is placed.

To me the story of the making of the atomic bomb is fascinating and exciting. In the period of a few years from 1939-1945 methods were found to extract scarce isotopes of uranium in kilogram quantities; manufacture plutonium; the fundamental radioactive properties of the substance were discovered; calculations were done to work exactly how much uranium you needed for a bang, how quickly you had to get it together and the whole thing converted into a working device that could be carried in an aeroplane. And they did a lot of this work twice, since the bombs dropped on Hiroshima and Nagasaki are quite different in design.The story about the rapatronic camera shutter is just a relatively little-known footnote to the whole endeavour.

The Manhattan Project was served by a considerable number of scientists, including twenty Nobel Prize winners, amongst a staff of around 130,000. These scientists represent a large fraction of the most renowned scientists of the period. I think I can imagine how I would have felt to working on the bomb, I would have been keen to be part of the war effort, I’d have been thrilled by the intellectual firepower of my colleagues, I’d have been excited by the technical challenge of actually making a real thing.

And then there was the Trinity test firing, I think at this point I would have become really aware of the enormity of what I had been involved in. J. Robert Oppenheimer, who directed the Los Alamos site where the bomb was constructed, later said he thought of this line from the Bhagavad Gita:

Now I am become Death, the destroyer of worlds

Which always struck me as being a bit pretentious, but maybe that’s a result of my ignorance. Whilst Kenneth Bainbridge, the director for the Trinity test, is reported to have said:

Now we are all sons of bitches

Which strikes me as a rather more plausible response. I have to say, with a little embarrassment, that I would have been thrilled by the size of the bang I had made.

Less than a month after the Trinity test an untried version of the atomic bomb was dropped on Hiroshima, instantly killing 80,000 people; then a few days later a second bomb, identical to the Trinity test bomb, was dropped on Nagasaki killing another 40,000. Subsequently many more people died of their injuries.

I’m not sure how I would have felt at this point I think I would have been a bit shocked, I struggle to conceive of that many people dying. The world was at war so I would have been familiar with the idea of people dying in, for example, the air raids in the UK. So maybe I would have thought this was justifiable, that the war against Japan couldn’t have been won in any other way or at least any other way would have led to just as many deaths. Maybe it would have been clear to me at the time that the atomic bomb was as much about the Soviet Union as it was about the war with Japan.

After the war many scientists returned to normal life. Some didn’t, Edward Teller enthusiastically promoted the thermonuclear bombs for just about any application imaginable. Joseph Rotblat left the Manhattan Project before the bomb was dropped, and whilst continuing scientific work, he helped found, and run, the Pugwash Organisation and spent the rest of his life campaigning for peaceful conflict resolution.

Do scientists have a special moral responsibility? They certainly took the initiative in terms of highlighting the potential of an atomic bomb before the war, but actually making the bomb and deploying it took far more than just a few scientists. As to the morality of killing people in war, then I don’t think scientists can claim any special moral insight here.

Finishing in this way seems a bit trite, and it feels in some ways an abdication of responsibility. I think the point I’m trying to make is that scientists are just people, and we bear the same moral responsibilities as anyone else. The only difference is that scientists have the potential to open up new moral questions: “Is it more wrong to kill 100,000 people with one bomb, as opposed to many bombs?”. Maybe we have the ability to close old moral questions through evidence.

Jan 23 2010

Caverns measureless to man

I thought this week I would talk about conferences, since they are something that is very much part of life as a scientist and which are perhaps are a little alien to people.

My first scientific conference was in Durham, where I did my PhD, I took the opportunity to find accommodation in the town before I moved up from Bristol. There was a problem with this: the conference supplied us all with name badges on which we were to write our names in our own fair hand. I was sitting opposite to an elderly academic at lunch who felt my name was somewhat small and indistinct. So I re-wrote it in large capitals with my biro, going over the letters repeatedly to get a “bold” effect. Now my handwriting isn’t great at the best of times, doing large-size capitals freehand has the look of the scrawling on the lunatic asylum walls. Later I went off looking at rooms in houses, but felt I was getting funny looks when I asked for directions. Later I realised why: not only did I still have my lunatic-asylum name badge on, I had it on upside down!

In many ways that first conference set the pattern for future ones, accommodation was primitive: in Durham Castle, which is used as student accommodation during term time. I met an old chap who, on hearing what I was doing swore blind he had done it all 10 years ago (I checked, he hadn’t, they never have). I learnt interesting things from esteemed academics in the bar.

For most the price of attending a conference is to present a poster, or a talk. This means I am accustomed to public speaking, just an odd sort of public speaking. In fact when I’ve had to speak at weddings, I’ve felt the lack of an overhead projector and had to resist the temptation to “thank the organisers for inviting me”, this is nearly appropriate but needs rephrasing. Conferences have also given me ninja buffet skills, and an appreciation that if you march off confidently in any direction (in my case in search of lunch), then quite a few people will follow you for no better reason than it looks like you know what you’re doing.

I’m not sure how widespread the idea of a poster presentation is outside of science, the idea is you convert your most recent work into…. a poster, a jumble of text boxes, figures and graphs (see below). If you’re flash, and organised, you print it out as a single sheet on laminated paper at some central service and then carry it around in a special tube. Otherwise you print it out on a load of A3 sheets. Posters are typically viewed in an over-crowded hall whilst drinking warmish white wine and eating finger food, text on the posters is normally too small and you’re too far away – the combination of these things always gave me a splitting headache. Supervisors attempt to get their students to defend their posters, that’s to say chat to anyone who wanders up.

Conferences are where you learn all the interesting stuff that people don’t write down, like how it took some poor PhD. student months to get an experiment to work once and they’ve never quite managed it again, or how a little fix is required to get a numerical simulation to work. You also learn lore from the more senior members of the community: how X has been doing Y or small variants thereof for the last 20 years. How Z has been wrong for all of living memory. How W, although publishes great work is not a very nice man. You may get some idea of what someone’s master plan is (you’re certainly not going to get it from journal articles), you’ll get to appreciate that other academic groups work in radically different ways. I also learnt that science transcends barriers of language and culture, the scientists I meet on tour are my tribe, my closest relatives beyond my real family.

All these conferences mean I’ve done a fair amount of travelling, personally I don’t consider this a great benefit. Business travel rarely gives you much time for sightseeing and the places you end up there may not be sights to see, and if there were I’d much prefer to go with my wife rather than a random collection of other scientists. I’ve visited Rhode Island, Boston, Sante Fe, Heidelberg, Sitges, Akron (Ohio), Philadelphia, Cancun and numerous towns around the UK. The only upsides of Cancun were the tropical fish just off the shore, the ever present iguanas and the Mayan ruins, otherwise it’s an overpriced tourist hell-hole.

The best conferences I’ve been to have been the smaller ones, the invitation only ones, the ones where discussion is programmed into the schedule, the specialist meetings for young academics. The larger conferences tend to be soulless and confusing: which of the 10 parallel sessions should I attend? And is it physically possible to switch sessions? There is a fine conference in the UK for the polymer community, which used to be based near Moretonhampstead, but now lives in Pott Shrigley. The presence of the golf courses is significant here, the organisers liked their golf so we had a morning session, an evening session and an afternoon off for golf. The non-golf players went off for walks in the country, which was a fine bonding experience. I remember distinctly my future postdoc supervisor standing on a tussock in the middle of boggy ground suggesting to the rest of the group that we proceed no further. It turns out being a Fellow of the Royal Society does not guarantee good navigation skills!

Is there still a need for conferences, in these days of electronic communication? Although the prospects for online networking via various social media are great, currently uptake by scientists is pretty low in percentage terms and the bandwidth of the communication is low. The amount you learn about a person from just one face-to-face meeting is enormous compared to what you get through electronic media; electronic media are great as an introduction and for maintaining contact but there’s nothing like meeting people.

The “caverns measureless to man” title is in homage to the SIGGRAPH conference I attended in Boston, there were somewhere in the region of 20,000 delegates. It was held in the vast Boston Convention and Exhibition Center.

Jan 14 2010

Making Science and Engineering a Policy Issue

This is a post on the debate organised by the Campaign for Science and Engineering in the UK featuring the science spokesmen of the Conservatives (Adam Afriyie), Labour (Lord Drayson) and Liberal Democrat (Evan Harris) parties. The debate was structured around pre-selected questions presented to the panel. It was chaired by Roger Highfield, editor of New Scientist and hosted at the Institute of Engineering and Technology.

Lord Drayson benefited from not being on the end of another sustained assault regarding the Science and Technology Facilities Council funding difficulties which have been a centrepiece of most of his recent public outings in this type of forum. The consensus seemed to be that outside problems with the STFC, science and technology had done quite well under Labour. The concerns over impact, which I discussed in a previous post made a showing, my view is that Impact is important but so is the way you measure and use it and the current ideas don’t seem to be going in the right direction. Lord Drayson was able to make a fair defence of recent government policy over stimulus which focuses on the shorter term when compared to stimulus packages in other countries, but he seemed shaky over how cuts in the higher education budget would be achieved.

Adam Afriyie suffered from the disadvantage of being in a party who seem to have consciously steered themselves away from concrete policy statements, spending a lot of time criticising the government but unable to enunciate much clear policy of their own. Concrete policies included a deferment of the REF Impact statements for 2 years (announced this morning), and the waiving of student debts for those going on to teach science. The statement that the “zeitgeist” of David Cameron would lead to increased charitable giving to the medical was met with the online equivalent of wry laughter, as a policy this seems particularly empty. The enthusiastic support of Chris Grayling (Tory shadow home secretary) for the sacking of Professor Nutt and his own rather confused position on the hiring and firing of scientific advisors, did not go down well.

Evan Harris, described in the Daily Mail as “Dr Death“, seemed to do particularly well, he may well have known that the audience was broadly on his side, as a party not in power the Liberal Democrats have not had the opportunity to wind up the science and technology community through the routine decisions of government. Furthermore academic scientists at least could well be described as “broadly lefty”. However when engaged in the politic-ing which was inevitable when bringing together politicians in the run up to a general election, he did appear to apply his own twist rather than an obvious parroting of the party line. On the policy front: the Liberal Democrat conference recently approved an amendment, which puts meat on more general mutterings that “something must be done” about libel reform. He also highlighted, as a policy, that money used in the recently rescinded cut in VAT could have gone more usefully into a scientific stimulus package.
All of the spokesman were clear on the importance of science in both policy decisions and in economic terms, and they all seemed keen to make both politicians and civil service scientifically literate.
I believe the existence of this debate is welcome, I don’t recall it happening in the run up to previous elections. To my mind the relatively new technology of a webcast supplemented by background twitter feed (on the #scidebate hashtag), really helps facilitate this debate, particularly in a. The larger question is how do we make science an issue for the wider voting public, given it’s significant policy and economic impact.
It seems inevitable that the next few years will involve some pain in the science and technology sector, as it has across most areas of government. None of the speakers gave any indication that science and technology will receive special treatment over the next few years.

Jan 09 2010

The science of Shrek

A lot of science goes into making a computer animations like Shrek or effects-heavy feature films, such as the remake of The Poseidon Adventure or Pirates of the Caribbean.

This science is something I’m interested in these days: Why does skin look like skin, hair look like hair and fabric look like fabric? There is a traditional physics approach to this which involves measuring stuff with complicated looking equipment and drawing graphs. This is part of the job, but another important component is the work of people interested in photorealistic computer graphics.

If you think computer graphics is all computer games and obvious stuff like Shrek, then check out Autodesk’s Fake or Foto test. Good photorealistic computer graphics are really good these days. Update: Actually, just watch this, full-screen.

There are three steps to making an image, or an animation, using photorealistic computer graphics:

Firstly, make a model of the scene in the computer, this should include the location and type of camera and lights as wells as the shape of objects in the scene. The shape is defined in terms of a “polygon mesh”, this is basically a fishing net in the shape of the thing you’re interested in. Usually “polygon” means triangle in this context. If you’re doing an animation then you can automate some of the scene generation by running physical simulations of objects in the scene. That’s to say, if you want a bouncing ball, you don’t have to make a set of scenes by hand with each scene showing the ball in a slightly different location – you can do this automatically. There is academic research here because efficiently simulating the motion of more complicated things like liquids, or 3601 plastic chairs, is really hard.

Secondly, give the objects in the scene optical properties like colour, transparency, shininess etc. A key feature of the optical properties is the way a material reflects light. This is the difference between a piece of chalk and a mirror, both reflect pretty much all the light that falls on them but if you shine a spotlight on a piece of chalk then that light ends up all over the place, whilst with a mirror the light all leaves in one direction. There is an interesting compromise to be made here, chalk scatters light as it does because of its rough surface. Now this can either be handled by making a very detailed model of that surface roughness (lots of triangles) and then treat each triangle as a little mirror, or I can make a very simple model of the surface and just say “If light hits here it can be scattered anywhere”. This is another area of academic research: how do I efficiently model a complicated material like fabric, because I really don’t want to put in every single fibre in a piece of fabric?

Thirdly, simulate light in the scene: make light come out of the lights and follow it as it bounces through the scene (if it doesn’t hit a camera at the end of it’s journey, it doesn’t count!). This final stage is known as ‘rendering’ or ray tracing. Ray tracing because in this model the photons travel in straight lines, “rays”, between collisions with objects in the scene. This is a laborious process, at best a photon (a little bit of light) can contribute a fraction of one pixel in the final image and worse, when you fire the photon out of your virtual light you don’t know whether it will even hit the virtual camera (which is the only way you’re going to see it). Repeat the firing of photons out of the lights in all different directions, many times in order to build up an image, the more photons you fire the sharper, less noisy your final image will look. In order to build up a reasonable size, reasonable quality image you will need millions of virtual photons. For photorealistic rendering it can take hours to render a single image. There is academic research in trying to do this more efficiently.

Skin is another tricky material to model, the problem is that it’s a little bit transparent: if you simply bounce light off the surface it ends up looking a bit odd. However, if you let light leak into the skin a bit, then things look much better:
The trick is to do this in a computationally efficient way, in fact this work won the Oscar for Technical Merit 2003 and ended up being used on Gollum in Lord of the Rings.

I went to a presentation, at SIGGRAPH (an enormous computer graphics conference) on the special effects for The Poseidon Adventure. The fluid dynamics simulation in this film are fantastic, when the ship sinks waves sloosh around impressively, but it looks a bit odd towards the end. It turns out this is because in the simulation they turned down gravity to make the waves bigger, and then hand paint on a splash right at end, as the Poseidon sinks below the waters. In the end this science serves what is ultimately an artistic, and a commercial, endeavour.

You can play with this sort of stuff for free, Blender is a very fine open source 3D design program used to build scenes (interface takes some getting used to) and luxrender is a physically based render, it’s based on the code described in the book: Physically-based rendering.

p.s. If you what to know how donkeys can talk, I don’t know.