Dr Administrator

Author's posts

Feb 21 2010

The Misanthrope

This is a blog post about other people, and their cow-like impassiveness whilst obstructing the path of the righteous. It’s also a chance to be a bit pretentious since I discover that Jean-Paul Sartre wrote in his play, “No Exit”:  that “L’enfer, c’est les autres” or “Hell is other people”, and the title of this blog post itself is that of a play by Moliere.


Mrs SomeBeans and I have just returned from holiday, so the focus of today’s rant is largely the people we have come across in the process (v. nice holiday, some pictures here). A similar species can be found around most supermarkets, on the streets of Llangollen.

It starts off in the airport, where mysterious large groups of sociable people travel together, weird extended families. Typically you’ll first meet an outrider in the queue to check-in (for us this usually happens at about 5am when we are not at the peak of our reasonableness), but then a gathering horde appear who can’t join the back of the queue: they have to join in front of you with the outrider. And nothing is simple for them, once at the check-in desk there is a great shuffling of passports and luggage as they casually mention that one member of the group will be along shortly.

Then there’s the security control, here my ire is split between authorities and punters. I mean, how the hell am I going to injure anyone with Lipsalve? To credit the cow-people they slowly seem to be coming around to the idea that they have to do a load of weird stuff for the benefit of security theatre. 


Then there are the duty-free shops, I’ll ask the rhetorical question “Why, oh why is so much space committed to the sale of duty-free which could so much more usefully be dedicated to something useful like seating?”. I know the answer, it’s because shops pay rent, punters are just self-loading cargo. It doesn’t make me less angry. I spent an hour in Salzburg’s post-security hell-hole wondering how best to foment revolution. I considered standing on a bin and urging the crowded mass to invade the duty-free shop and cast the merchandise to the floor, and lie down upon the vacated shelves.

Then you get on the plane, and it seems no one has planned for this eventuality and spends 10 minutes taking things out of their carry-on bag, putting the bag in the overhead locker, sitting down, standing up, taking more things out of the bag and putting some away again, repeat. All the while the cabin crew keep saying “Please get on and sit down so we can take off”.

Then you get off the plane and a group of teenagers have made it down the stairs off the plane and just stopped dead at the bottom. This is a recurring theme: there are places to stand, an infinity of them, where you disrupt no one elses business. However, the cow-people seek out those places where they maximally obstruct others, gazing at each other with cow-like eyes, lowing gently.

Next is baggage reclaim. At the risk of sounding like an old fogey here, there’s no way that my parents would have let me frolic about the luggage carousels in the airport, as modern children seem to be encouraged (partly because we never flew to go on holiday). There’d definitely be sharp words and clips round ear, but not these days. If it was down to me I’d be equipping luggage carousels with special finger-slicing blades.

Skiing offers special opportunities for standing in the way like a cow-person; ski lifts are natural constrictions: a world of skiers is funnelled into a narrow gap, through electronic barriers to some lifting device. So naturally you’ll find half-wits that zoom into the constriction and only then decide that they cannot proceed without friends or family. And you try acting nimbly whilst wearing skis. The people featured here:


… look like they acting purposefully, but they’re not – they’re dithering.


Naturally, through all of this we never say a word. Except now.

Feb 21 2010

Westendorf

Mrs SomeBeans and I have been skiing for the last week, and this is a small set of photos from our trip. The family will be subjected to the full 120 photos but you, gentle reader, get the edited version. We went skiing in Westendorf, in the Austrian Tirol, this is where we learnt to ski in January 2001 (a tale of misery, pain and addiction).

On our return we discovered that Westendorf was the village my mum visited most summers. We’ve been back a few times since, each time there are a few more ski lifts, pistes and restaurants to try. Last week was half-term in the UK and several European countries, so airports and so forth were pretty busy. We managed to avoid most of the crowds by making an earlier morning start and keeping to the quieter bits of the mountain.

The first few days of our trip were cold and clear, actually that’s not quite true, it was clear at the top of the mountain and murky at the bottom because of an inversion layer (meterologists: feel free to correct me)

The cold weather was associated with snow, which covered the trees:

We saw sundogs, once again, but I found them impossible to photograph using my compact camera, however I did catch an okayish picture of a related effect – the pillar of light is a real effect you can see with your own eyes – not lens flare.

If I’d have dropped down the slope a little to take the photo the brightest spot would be floating a little way above the ground. Mrs SomeBeans saw this but kept quiet, assuming she was hallucinating! I believe it’s caused by a reflection of sun from aligned plate-shaped ice crystals in the air.

Over the last few years there’s been a big change in ski wear – most people now wear ski helmets, here you can see me sporting my new purchase:

Mum was with us this time, she’s a bit leery of trying downhill skiing but does a bit of cross country skiing:

You’ll notice that few people feature in my photos, this is because I am something of a misanthrope – more of which later. As we left Westendorf it was snowing once again… and we returned to England yesterday to more snow overnight.

Feb 10 2010

Publication, publication, publication

I thought in this post I thought I would write about academic publication, focussing on the journal article or “paper”, I may try to introduce a tortured analogy at some point. This is all rather topical because some people in stem cell research have just complained loudly about the unfairness of it all. In fact there’s a whole slew of comment on this around at the moment by, for example, Cameron Neylon, Russ Swan, Suzan Mazur, and Mark Henderson. My goal here is to explain to the lay reader scientific publishing, what on earth we’re all so ventilated about and drop in a couple of comments for practioners.

As an university scientist I, my boss, my students, would do research. Every once in a while we would consider it appropriate to publish a paper on this work. This was important because through our careers those papers are a measure of our academic worth, when you apply for a job the appointment panel will go through the list of your papers to get an idea of how a good a scientist you are. As a personal rule of thumb I reckoned on an average one paper per person per year. This is a bit low (even for me, since I have my name on 29 papers over an 18 year active research career), it varies with academic discipline, and even within academic disciplines.

So what does it look like? Well, you can see one of mine here. There’s a bunch of authors whose functions are opaque to the reader, a set of fairly standard sections which roughly comprise: Abstract, Introduction, Methods, Results, Discussion, Conclusions, References.

Your paper will be decorated with little markers pointing to papers in the reference section. The idea is that you indicate the support for a particular statement or idea via the references. The paper I linked to above is described like this:
Brujic, J., S. F. Edwards, D. V. Grinev, I. Hopkinson, D. Brujic, and H. A. Makse. “3D bulk measurements of the force distribution in a compressed emulsion system.” Faraday  Discussions 123, (2003), 207-220.  
That’s to say: a list of authors, a title, the journal it appears in, the volume number, year of publication and the page range – it pins the paper down pretty thoroughly. I can go and find the paper (and make up my own mind as to whether the reference was appropriate). In a way this is what peer-review system is about, it isn’t really about correctness in anything other than the broadest sense, it’s about reputation and discoverability.

Just so you know, in the list of authors above: Jasna Brujic was the PhD student who did the experimental work, Sir Sam Edwards is a theoretician who works on granular materials, Dmitri Grinev worked with Sir Sam on the theory, I supervised Jasna, Djordje Brujic is Jasna’s dad and wrote the image analysis code and Hernan Makse is a computer simulator of granular materials.

After you’ve written the paper, you send it off to an academic journal of your choice (there’s a big field to choose from, and practioners know the relative prestige of each of these journals and there are published Impact Factors which attempt to quantify this). The journals send it off to roughly three other academics for “peer-review”, on the basis of whose reports they will accept or reject the paper. If rejected you’ll likely send it off to another, less prestigious, journal. At the same time you will curse the anonymous reviewer that lead to this ignominy, a bit like this, in fact.

I’ve peer-reviewed papers, my approach is as follows: read paper, check for obvious lunacy, check for obvious previous publication, check to see if you’re referenced, write a few lines of recommendation to the editor, which in total  takes me a couple of hours or so. I make a more in-depth reading of a paper if I’m trying to replicate results or, as I have done once before, been writing a review in which case I repeat calculations and re-plot data. This level of effort doesn’t seem worthwhile for an anonymous activity with no payment; reading referees reports on my papers then it would appear my approach is par for the course on peer-review.

In truth the real test of a scientific paper is what happens after it’s published, there are three possibilities:

  1. everybody ignores it, 
  2. they refer to it in their papers to point out it was wrong, 
  3. they refer to it in their papers to support their work.

Academic search engines will tell you the aggregate of possibilities 2 and 3, that’s to say the citations: the number of times your paper occurs in the reference sections of other papers. This is the exciting bit, most of my papers have somewhere under 10 citations, there are a few with 30 or so citations and a couple with 60 or so. Actually this is a habit I carry over to blogging, since bit.ly links come with statistics on how many times they have been followed I can get exciting real-time feedback of how many people retweet a link to my blog posts on twitter, and how many people have at least looked at my post. As far as I can tell my blog posts are better read than my papers.

Academic publishing is pretty lucrative for commercial publishing organisations, this report cites profit margins of 30%, and there is a more general discussion of costs in the UK here. It’s all a bit odd really academics, like me, write articles for free, we send them to journals (whose academic editorial boards are often unpaid) who then send them out to more academics to review (for free), we then buy back our material in the form of journal subscriptions, which can be very pricey (£1000 per annum per 12 issue journal is not uncommon). The latest wheeze is to replace journal subscriptions with an “open access” model, whereby the author pays the journal to publish a paper.

Really academic publishing is all about reputation, your reputation as a scientist depends on how many articles you get published in high reputation journals as a proxy for your own reputation and the absolute quality of the paper you have written. But do we really need specialist journals any more? You can see how easy it was for me to make the paper I referenced above visible. I could have made my paper visible on a blog, and interested people could post their comments (like peer-review), I could promote my paper through twitter. We could have a soup of articles re-sliced by keywords, spread across the web, or leave it to individuals to curate their own sets of papers. We could leave it to academic departments to host the papers of their staff, they’re paying through the nose for library access, and these days as often as not they’re hosting electronic reprints already on the personal web pages of their staff. The programming solution site, stackoverflow.com has an interesting reputation model, which seems to work well – couldn’t this be adapted for academic use?

Are you missing a tortured analogy? How about this: the current publication model is like buying all the ingredients for a cake, making a cake, then taking the cake to a shop who then charge you to take the cake away again. We should break free of the hegemony of the cake shop!

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.