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Wednesday, February 24, 2010

The Age of Wonder: A book review

I thought I would give book reviewing a go, this last week we have been holidaying which means I managed a solid chunk of reading, seated on the balcony of our hotel (see picture*). An ulterior motive is that, casting an eye across my bookshelves, there are interesting books which I have read of whose contents I have no memory. So in this post I hope to remind a future me of what I have read.

The subject of my review is "The Age of Wonder" by Richard Holmes. This is a book on a subset of scientists active in England around 1800. As I have mentioned before I am not up to the reading of original sources required of historians, but it doesn't mean I'm not interested.

A central figure in this book is Sir Joseph Banks, who warrants a chapter of his own covering his round the world trip with Captain Cook, focussing mainly on his time in Tahiti. He travelled at his own, considerable, expense as the voyage's lead naturalist. The attrition for the whole journey was terrible, with half the crew and four of the eight man nature team dying. The voyage was led by the Admiralty with a contribution of £4000 from the Royal Society to observe the transit of Venus from Tahiti. After this journey Banks appears to have acted far more as an administrator and courtier than a personal adventurer, perhaps understandably. He also went on to become the President of the Royal Society and was heavily involved in developing the Royal Botanical Gardens at Kew.

William Herschel, and his sister Caroline, lead in two chapters. In the first instance we find Herschel discovering Uranus, using the rather fine telescopes he had made for himself. He is "discovered" by a fellow of the Royal Society viewing the stars in the street outside his house in Bath. The book reveals a nicer side to Nevil Maskelyne, the Astronomer Royal who has received a poor press through his treatment of John Harrison. Caroline Herschel, who discovered a number of comets in her own right was recognised for it, in part, through his support.

In a second chapter William Herschel's, with Caroline, commission a 40 foot telescope, using a "grant" from King George III totalling £4,000. Converting this into a modern equivalent is a complex process since there really isn't a single answer. According to the National Archive currency converter this is equivalent to about £130,000 in modern money. The Astronomer Royal was then earning £300 per annum, if we scale a modern professors salary (£60k) in a similar fashion then we get a figure of £780k. Other calculations give us figures in the low millions, which is actually not that large: many university labs around the country will contain single items valued in excess of £1million and most will probably host £1million worth of equipment in total. Ultimately the 40ft telescope did not make a huge scientific impact, being rather difficult to use, however Herschel was instrumental in discovering "Deep space", that's to say the appreciation of the vastness of the universe.

There is an interlude on balloonists which stands a little free from the rest of the book, both hot-air balloons and hydrogen balloons were invented at roughly the same time. One enterprising soul, Jean-François Pilâtre de Rozier, bolted the two devices together but came to a sticky end as the fire required to heat the hot air balloon was somewhat incompatible with the flammable hydrogen balloon. The balloonists were broadly showmen and adventurers but their activities had an air of futility to them. Although the leap into the air was significant, ultimately the lack of control in passive balloons limited their applications.

Humphrey Davy makes three appearances, in the first we see some of his early scientific life in Bristol working on various gases at Thomas Beddoes Pneumatic Institute in Bristol. Here, amongst other things, he seems to have entrenched his scientific methodology and experimented on self and others with nitrous oxide (laughing gas). In a later chapter he appears to design his miner's safety lamp - a lamp which would burn safely in mines where methane is present. He comes over in this chapter as a rather arrogant character, a little unscrupulous in claiming the credit for the discovery of iodine and rather tardy in his acknowledgement of the support he received from Michael Faraday in his work.

There is a chapter on Mungo Park who, apart from his name, just didn't capture my imagination. He made a start on the exploration of inner West Africa sponsored by Banks via the Africa Association. To my mind he was ill on arrival then died in transit, which didn't seem to make much of a story.

A chapter entitled "Dr Frankenstein and the Soul" starts with a discussion of Fanny Burney's mastectomy conducted without anaesthetic, which she described in quite terrible detail in a letter to her sister. This leads into Vitalism and the medical experiments of the day, some of them quite horrific, which fed into Mary Shelley's "Frankenstein". There is some discussion of the interaction between various poets of the time, Byron, Shelley, Coleridge, Wordsworth, Keats and the scientists. In a way it seems that it was a time before the two cultures that C.P Snow described.

The final chapter covers young turks rising up against the fuddy-duddys at the Royal Society and forming their own organisation - The British Association for the Advancement of Science.

All in all a very fine read, it seems to fit with Lisa Jardine's book "Ingenious Pursuits" which covers an earlier period in the history of English science, from around the middle of the 17th century to the early years of the 18th, and Jenny Uglow's "The Lunar Men" which covers the period 1730-1810 which is a little before the period covered in "The Age of Wonder" and is interested in particular in the members of the Lunar Society.

I'm now looking for a biography of Sir Joseph Banks, a more complete history of the Royal Society and I feel like I should be exploring some of the other European scientific societies of the period such as the French Académie des sciences.

*The picture is cheating a little, the featured volume is "The Illustrated Natural History of Selborne" by Gilbert White, who crosses paths with Sir Joseph Banks. This was part of The Inelegant Gardener's reading, which I borrowed.

Sunday, February 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.


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.

Wednesday, February 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 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, 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!

Tuesday, February 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...

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