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Sunday, March 28, 2010

Bug-eyed monsters from the planet Tharg

In a shameless piece of idea stealing I thought I'd write about how fiction informed my enthusiasm for science. Lucy Inglis at Georgian London started it, with her post on historical fiction had fed her enthusiasm for history. The Gentleman Administrator added his own thoughts, which are a little different. Then Jon Butterworth, a fellow scientist, mentioned sci-fi over on his blog so I thought I better get on with it before I was scooped!

Over the years I've read a huge amount of science fiction, from a huge number of authors but it's always felt like something you don't admit to in polite company. It's always felt like a genre to be looked down upon by literary society. I think it's the most imaginative writing there is.

Science fiction is a broad church ranging from almost entirely impersonal such as Last and First Men by Olaf Stapledon, to the very intensely human such as The Time Traveller's Wife by Audrey Niffenegger.

Sometimes science-fiction is simply a back drop for a story: a thriller, a horror story, a romance - the fact it takes place on another planet, or in a whole different universe is entirely unimportant to the story. Sometimes science-fiction is about reflecting the fears of the day: the end of the world through nuclear war, a jingoistic enthusiasm for conquering new territories, or a reflection of a socially liberated society. Sometimes science-fiction is about a scientific idea, a what-if question. The best science-fiction mixes all three of these elements.

I can't resistant adding in a few of my favourite ideas based science fiction here: Brian Aldiss' Helliconia Trilogy is about a planet with century-long seasons, and how this impacts the animals, and "people" that live on it. Babel-17 by Samuel R. Delany is a classic science-fiction of ideas: what if there were a language, the knowledge of which let you think and act much faster? The Forever War by Joe Haldeman considers seriously the problems of fighting an interstellar war with combatants "lost in time" through the effects of time-dilation achieved by travelling at speeds approaching that of light, no doubt also influenced by his experience of the Vietnam war. Against a Dark Background by Iain M. Banks is about an isolated planet, subject to civilisation for many thousands of years, whose inhabitants have never left the planet surface in contrast to most science fiction where heading off to the stars is an early achievement. Kim Stanley Robinson's Mars Trilogy is a detailed exploration of the mechanics (and sociology) of how we might really colonise Mars.

That's just a tiny selection of the ones I can remember, there are so many other ideas from science fiction for which I just retain fragments. In writing this I've really struggled to keep the number of references to reasonable levels.

The attraction of science fiction for me are dreams of where we're heading. Science in the lab can take years to work its way out into the real world, and often the impact of any particular experiment is rather small. Science fiction leapfrogs all that tedious waiting for an effect: it gives you the future, now.

Sometimes it can be surprisingly difficult to work out the potential impact of a new technology, who'd have thought that the ability to send 140 character text messages would be such an important use of mobile phone technology? To take an older example, in the late 18th century there was an enthusiasm for hot-air and hydrogen balloons but imagining their applications turned out to be surprisingly difficult task: principle amongst the proposed applications seemed to be the idea of using balloons to lighten terrestrial loads, not lift them entirely into the air. Search around a little and you'll find people stating that they couldn't see any reason why someone would have a computer in their home. Science-fiction gives you permission to loosen some of the bonds of strictly logical thinking, and say "Ignoring a couple of little problems, what really could it be like?".

There are links to the historical novel from science fiction, for example The Difference Engine by William Gibson and Bruce Sterling imagines a past where Charles Babbage's mechanical computers really took off. And the fabulous Baroque Cycle by Neal Stephenson is set in the period around the founding of the Royal Society and features many of the scientists of the day.

Science fiction has given me dreams of living in space, around the solar system, amongst the stars, in virtual worlds, with an augmented mind, with an augmented body. As I grow older, I realise that many of these dreams will forever be unfulfilled but I'm glad I had them.

Bashing the bishops

I'm sorry, I try really hard to be a quiet little atheist and not cause needless offence, but sometimes the perfect storm hits and I go a bit "Richard Dawkins".

The spark that lit my ire today was on Radio 4's Sunday program. It was the juxtaposition of the reports on further problems the Catholic church was having with covering up child abuse by the priesthood with a complaint that Catholic adoption agencies, unlike any other adoption agency, should be allowed to discriminate against gay couples because they didn't think any gay couple was suitable to look after children.

Can you hear the sound of me bursting a blood vessel here?

This isn't an isolated incident either, also in the news today: a  letter by six bishops to the Daily Telegraph complaining of the treatment of a nurse who was asked to remove her crucifix necklace, or wear it  inside her clothing. The hospital involved has a policy on uniform which excludes the wearing of necklaces, this seems quite reasonable in my view. I don't want anyone's necklace dangling in my wounds, regardless of the form it takes. Now it may be that necklace wound dangling isn't a problem, and the whole policy is pointless. But that isn't the argument that the bishops are making, they're happy with the idea that any random atheist should be prevented from wearing, for example, their bourbon chocolate biscuit necklace but the same rule applied to a Christian is a great offence. It's a dogmatic position too, wearing the necklace inside her clothing (an entirely acceptable solution I would have thought) is not acceptable to the bishops either.

These aren't isolated incidents, there are exceptions in law covering the slaughter of animals for both halal and kosher slaughter. So whilst it's a illegal to slaughter an animal without first rendering it unconscious if you're a Christian or an atheist, as a Jew or a Muslim it becomes legal. What part does the slaughterer's religion play in the cruelty or otherwise to the animal? Also in the news recently were the ceremonial daggers worn by Hindu's. In this instance a child was withdrawn from school for continuing to wear his ceremonial dagger, personally I think banning children from taking knives of any sort into schools is a fairly good idea and once again notice the dogmatism - a compromise solution of a knife welded into it's scabbard was not acceptable.

We have a wide range of laws which restrict our behaviour for one reason or another, some of those laws are good and, no doubt, some of them are bad. My argument is that no behaviour is unacceptable for one person but acceptable for another simply on the grounds of their religion.

Thank you for hearing my rant!

Thursday, March 25, 2010

Seeing Further: A Blaggers Guide (Part 1)

I originally intended to describe this post as a book review, but really it isn't. It's a blagger's guide for those that haven't read the book in question, (Seeing Further: The Story of science and the Royal Society edited by Bill Bryson) or who have read it, but need reminding of the contents. If you want to read a proper review then I suggest Clare Dudman's review at Bookmunch.

Seeing Further is a collection of essays from a wide range of authors, all relating in some way to the Royal Society which celebrates it's 350th anniversary this year. I've read other work by most of the authors - they are all excellent.

Since I've written notes on each chapter this has become quite a long post, so I've broken it into two parts. Part two can be found here.

Bill Bryson starts things off with an introduction, providing a brief sketch of the history of the Royal Society and introducing a few of the distinguished fellows. His favourite is Reverend Thomas Bayes. Bayes' most important work was on probabilities, published two years after his death in 1761. Few will have heard of Bayes, but his work is central to modern statistics. I must admit this chapter made me curious as to the origins of other learned societies across Europe.

Then the fun begins with James Gleick, who has written excellent books on chaos and Richard Feynmann amongst many other things. He writes of the Society as an earlier version of the internet and the first place where people started recording and communicating observations systematically. They also conducted their own experiments. The international reach of the Royal Society was an essential component, managed effectively by it's first Secretary, Henry Oldenburg.  Perhaps wisely the fellows instituted a ban on discussing religion or politics.

Margaret Atwood writes about the development of the idea of the mad scientist as portrayed in the 50's B-movies. She sees the Royal Society, satirised by Jonathan Swift as the Grand Academy of Lagado in Gulliver's Travels, as the link between Dr Faustus and the modern mad scientist. Travelling by way of Mary Shelley's Frankenstein and Robert Louis Stevenson's Dr Jekyll and Mr Hyde.

These days it is broadly a given amongst scientists that the physical laws they determine here on earth extend throughout the cosmos. Margaret Wertheim writes on the genesis of this idea, the point when the boundary between heaven and earth was removed in mens minds and the heavens and earth started to be considered as a continuous whole, obeying the same physical laws. This transition had largely taken place prior to the formation of the Royal Society.

Neal Stephenson writes on Gottfried Leibniz and his monads. Stephenson is author of The Baroque Cycle, a historical science-fiction trilogy set around the time of the founding of the Royal Society with many of the early fellows featuring as characters. Monadology was Leibniz's philosophical program for understanding the universe, looked at with a modern eye one can see intriguing insights but ultimately our current understanding of the universe is quite distant from Leibniz's conception of monads. Nowadays it's recognised that Leibniz and Newton invented calculus independently and simultaneously, although Leibniz published first. The priority in this area was greatly disputed, with the Royal Society standing firmly behind Newton, latterly their President.

Next up is Rebecca Newberger Goldstein on how the establishment of the Royal Society marked the coming together of the rationalists, whom we would probably call theoreticians now, and the empiricists, or experimentalist in modern parlance. Contrasting these two more modern movements with the teleologists of ancient Greece who believed that the world was designed with a purpose and so their philosophical program was to identify the purpose of all things and the progress of those things towards their final ends. Although the teleologists observed, they tended to do so passively whilst the empiricists actively experimented: setting up nature to reveal underlying processes. The immediate precursors to the Royal Society were represented by empiricists such as  Francis Bacon, William Gilbert, and William Harvey and the rationalists represented by Nicolaus Copernicus, Johannes Kepler, Galileo Galilei and Rene Descartes. John Locke, Isaac Newton and Robert Boyle are cited as those at the forefront of the debate on what constitutes an explanation during the forming of the Royal Society.

Now for Simon Schaffer who tells a tell about the use of scientific advice for public policy development, and public dispute over that advice. The story is set around the tale of a lightning strike in Norfolk which struck the Heckingham House of Industry (a workhouse) on 12 June 1781, causing substantial damage. The building was protected by pointy lightning rods, as recommended by the Royal Society and the tale is of much internal bickering as to whether the lightning rods had been installed properly or whether the advice given by the Society was wrong. This was highly relevant at the time since, for example, you'd want to be really sure of your lightning protection if you ran an arsenal, full of gunpowder. Also interesting is who the fellows of the Royal Society trusted to give eye-witness statements: gentleman! Schaffer never really resolves the issue of the accuracy of the advice but highlights the parallels of this argument with modern arguments about evidence-based policy and how best to make recommendations based on science.

We move on to Richard Holmes, who writes about ballomania. This is the name coined by Sir Joseph Banks, recent president of the Royal Society, for the enthusiasm in France for balloons of both hydrogen and hot air during the 1780's. Outwardly Banks was dismissive of balloons, but in private he appears to have been keeping a close eye on developments. Ultimately the lack of navigability meant that interest in balloons waned. This chapter reminded me that Benjamin Franklin is someone of whom I need to know more, Franklin was Banks' correspondent in Paris where much of the balloon-y action was based. Another snippet, Aeropaedia, published 1786 records a balloon flight from my now home-town of Chester. Richard Holmes is the author of The Age of Wonder, on which I wrote earlier.

Richard Fortey is up next, author of Dry Store Room No. 1, which is about the Natural History Museum, given this background it's unsurprising that he writes about scientific collections. Well-curated collections of real objects are of critical importance to science. Fortey's chapter explains the role that the Royal Society played in setting up such collections, principally through the work of Sir Hans Sloane, a president of the society, whose collection was to form the basis of the Natural History museum via the British Museum. Sir Joseph Banks makes an appearance, for his work in setting up the Royal Botanical Gardens at Kew, as does Carl Linaeus father of taxonomy.

Richard Dawkins, who needs no introduction, writes on the claims for precedence in the discovery of evolution. It's relatively well-known that Alfred Russell Wallace spurred Charles Darwin into action by sending a manuscript to him which captured the core idea of evolution. Darwin's great achievement was the full length exposition of the theory, backed with experiments, in On the Origin of Species. Perhaps less well known are Edward Blyth, who believed that natural selection stabilised those species created by God (which is not really evolution) and Patrick Matthew, who mentions an idea of evolution quite similar to Darwin in the appendix of his book Naval Timber and Arboriculture but seems to have little idea of its significance.

Here endeth the first part of this review, feel free to get up and move around, perhaps have a cake and a coffee. Then move on to Part 2.

Seeing Further: A Blagger's Guide (Part 2)

My writings on Seeing Further: The Story of Science and the Royal Society became unmanageably long, so I have split it into two parts, this is the second part, the first part can be found here.

In the earlier chapters there was much philosophy and history. Henry Petroski writes on bridges, which I must admit surprised me a little as an area of interest for the Royal Society but the link is there. When Robert Stephenson proposed the design for the original Britannia Bridge it was William Fairbairn, soon to become a fellow of the Royal Society, who carried out experiment studies to establish the shape of the iron box-sections. This was done by testing the strength of scale models, and progressively increasing the size of the models - extrapolating the results to the full-size bridge. Later he went on to investigate metal fatigue, which had led to several serious rail disasters in the 19th century.

We're heading into living memory now, with Georgina Ferry's chapter on structural biology through the medium of x-ray crystallography. A field in which Britain led the world in the middle of the 20th century. This period sees the election of the first female fellow of the Royal Society, Kathleen Lonsdale, in 1945, who made some of the first determinations, by crystallography, of the structure of small molecules. Following this Dorothy Hodgkin determined the structure of penicillin in secret work during World War II. This type of investigation reached a climax with the determination of the structures of first proteins, massive efforts taking Hodgkin 35 years for insulin and Max Perutz taking 22 years for haemoglobin. Georgina Ferry's biography of Dorothy Hodgkin is well worth a read and covers in more depth much of the material in this chapter.

Steve Jones, geneticist, provides a chapter on biodiversity. We believe that evolution provides a good explanation of how species arise and change over time. The subject of biodiversity addresses the question: how many species can we expect to find in a particular environment? And the answer is we don't really know,  there don't seem to be any rules that allow us to predict biodiversity. There are some observations, such as biodiversity is greater in the tropics than elsewhere but no real understanding of why this might be.

C.P. Snow wrote about the two cultures, what is less well reported are his comments on the gulf between "pure" sciences and applied sciences. Philip Ball expands on this theme, and makes a plea for a better appreciation of the engineers and technologists, under whose aegis much essentially scientific work is done. One of his examples are plastics (or polymers), the field in which I am trained.

Paul Davies asks how special are we? In cosmology we hew to the Copernican Principle, the idea that there's nothing special about earth, nor the sun nor even the galaxy we find ourselves in: if we look around the universe we expect to find planets, suns, galaxies just like our own. It is only when we enter the highly speculative area of the multiverse that this part of the Copernican Principle starts to break down. Related to this questions is the more open one of "Are we, intelligent life forms, special?". We simply don't know whether life, or intelligent life is common in the universe.

I hope you're not getting bored of this machine gun delivery of chapter synopses!

Ian Stewart writes on the importance of mathematics, often hidden from view even to those in the know. He uses the example of the recent Mars missions, which fairly evidently use the mathematics of Isaac Newton (a fellow of the Royal Society), but less obviously the work of George Boole (another fellow living 1815-1864). Boole is responsible for providing the foundations of modern computing through his Boolean logic - the ones and zeros on which computers thrive. Compression and error-correction algorithms also make heavy but invisible use of mathematics. JPEG compression, in particular, uses the work of, foreign member of the Royal Society, Joseph Fourier (1768-1830).

John D. Barrow is up next, he is a cosmologist. He starts off explaining the underlying simplicity of physical laws, and the attempts to unify the theories of different forces into a single "Theory of Everything". The current best candidate for this theory of everything is string theory. He then discusses chaos and complexity: simple laws do not lead to simple outcomes. The behaviour of a pile of sand is not easy to predict.

The next three chapters have a a slight theme running through them. Oliver Morton starts off with the "blue marble" image captured from Apollo 17. This demonstrates, self-evidently, the spherical nature of the earth but beyond this it implies an isolation and stasis. There is little evidence of movement, or process taking place. Morton's point is that the Earth is not a static system: light from the sun enters and great cycles turn over carbon, nitrogen and water in the system, taking these chemicals through the earth and the sky. This leads into thinking about climate change.

Maggie Gee starts off by introducing about apocalyptic writing, fiction about the end of the world (or at least after a great disaster). Gee is an author of such fiction, including The Flood and The Burning Book. I must admit I've always seen this as a genre that doesn't really ask me to contemplate my own end, but rather selfishly imagine my survival in the aftermath. After this introduction she then moves on to discuss global warming and the part that writers might play in it's communication. I found this a very interesting perspective. Most of the authors in this volume I've read before, Maggie Gee is one I haven't read but aim to address this lack.

Continuing the global warming theme, Stephen H. Schneider is a climate scientist who has long been involved in the the Intergovernmental Panel on Climate Change (IPCC), as an normal author in the first two reports and a lead author in the second two reports. In this chapter he talks about introducing standardised language to describe uncertainty into the fourth assessment report, known as AR4. There is a clear need to do this because if the scientists writing the report don't communicate their assessments of uncertainty then others, less-qualified, will do it for them. It's not that uncertainty was unrecognised in previous reports, but it's communication was not clear. Schneider was involved in preparing clear advice in this area. Persuading scientists to use well-defined language to communicate uncertainty seems to have been a battle.

Gregory Benford talks about time, firstly he talks about the Deep Time discovered in the 19th century by geologists such as Charles Lyell FRS. This was the realisation that the earth had been around rather longer that the few thousand years that a literal reading of the bible suggested. This change in thinking was based on an assumption that the changes in landscape seen in the present were largely all that was required to create the landscape, this is in contrast to the prevailing view of the time based on cataclysms like the biblical Flood. Also, Darwin was of the view that evolution would have required hundreds of millions of years to lead to the diversity of species seen today.  The great age of the earth was subsequently confirmed using radioactive decay measurements. Also discussed is time and it's merging into space which is central to Einstein's general theory of relativity. Benford is a scientist and science-fiction writer, I can recommend Cosm, a story about physicists who create a universe in a particle accelerator and drive it off in a pickup truck.

And finishing off with a chapter by Lord Rees, the current President of the Royal Society. Rees looks forward  to discoveries in the next 50 years; at various times in the past people have claimed we are coming to the end of science. Rees points out that each new discovery opens up new areas, so feels there's no risk of us running out of science to do. He also writes of the continuing role of scientists as advisers, a task that the Royal Society continues to coordinate and drive. And the finally on moral responsibilities of scientists, on which I wrote a little previously with regard to the atomic bomb.

All in all I found this a very enjoyable read, some of the philosophical and literary chapters I would not have read as full length treatments but enjoyed in shorter form. The links to the Royal Society are tenuous in many of the chapters, so perhaps it's best to approach this book as a sampler for fine science writing.

Sunday, March 21, 2010

The Green Scientist

This week I'm writing about my attitude to some green issues, and how I think my scientific background informs my approach. The reason I'm doing this is that when discussing green issues, it becomes obvious that I have some very different starting points compared to non-scientists. I can describe my own views, and I believe various of them are shared by other scientists for similar reasons. And it might get a little bit ranty.

First of all, I really like the idea of sustainability: the idea that after our lives we leave the earth in broadly the same state as we found it so that those that follow us have something to live on. I believe we should be trying to preserve our natural environment and the species in them, even the unattractive ones. How we achieve sustainability, and what we actually focus on are the areas of collision.

And so to "Chemicals": "Chemicals" which are always bad and must be excluded from things. From a scientific point of view this is frustrating: all things are chemicals - atoms joined up together. Even if we're slightly more sophisticated and claim that natural chemicals are good, and man-made chemicals are bad, we're still on tricky ground. Anyone for strychnine, belladonna or ricin? Really we can only say "good chemical", "bad chemical" by looking at the chemical in question. There is a Romantic view abroad that nature favours us and wishes to provide us with nice things: this simply isn't true. At best nature is indifferent, and in many cases it is actively out to get us.

There's a biological variant of this stance, in genetically modified organisms (GMO). I think there's real potential for GMO's in sustainable agriculture, but it is excluded for essentially ideological grounds and with ideological fervour. Misplaced genes can certainly be a problem but much more likely when introduced en bloc in introduced organisms (rabbits in Australia, rats in almost any island environment, Himalayan Balsam in UK), and we're surprisingly tolerant of crops that are toxic if prepared inappropriately (potatoes, rhubarb, red kidney beans, cassava). We're in the bizarre situation where one group can complain of the contamination of the genetic purity of their crops by GMO's for which there is no evidence of harm, and no expectation of harm. Where the detection of the contamination takes rather sophisticated scientific techniques. And beyond that even people are getting agitated by the thought of eating cattle fed with GMO's, when we have no way of detecting whether the cattle have eaten the GMO - there is no measurable effect.

The image at the top of this post is another example, I found it buy searching for "belching-pollution" it's the type of image you often see illustrating a story about pollution but those are cooling towers, the stuff coming out of them is water vapour - clouds. Not pollution at all.

The Food Programme on Radio 4 irritates me every week, and I really like my food. A typical script runs roughly like this:
Supermarkets are bad, lets do a taste test. Here's Mrs Miggin's hand-knitted pie, with Mrs Miggins who we've been talking to for the last 10 minutes, here's a supermarket pie, doesn't it look nasty? I don't think I want to eat that. Let's try them both, well Mrs Miggins pie is lovely, but I really didn't like the supermarket pie. The supermarkets are evil. What's that you say? "Mrs Miggins pie costs 5 times as much as the supermarket pie". Well I'm sure that isn't important.
I think I drifted off the point slightly with that last bit of rant, but it reveals something of my character. I'm actually in favour of people that do stuff, rather than the people that stand on the sidelines complaining that they're doing it wrong but don't really proffer a workable solution.

Much of the problem here seems to be an elision over scientific issues and capitalism / globalisation. GMO's largely became "bad" because they were developed by very large corporations for reasons of profit. I don't see large companies as intrinsically malign, I see them responding to a set of circumstances which makes them appear malign. The trick for society is to make an environment that makes companies to act for our collective good because it's in their best interest to do so.

So there you are: I'm a frustrated green, I sign up to the principles but the implementation offends my scientific sensibilities. In a timely fashion, it would appear I'm not alone - see this interview with Stewart Brand in New Scientist.

Thank you for hearing my rant.

Saturday, March 13, 2010

On being a fellow of Pembroke college

For a period in my life I knew that if I ever ended up in the news the item would have started "Cambridge don, Dr Ian Hopkinson..." because I was a fellow of Pembroke College, Cambridge.

Oxford and Cambridge universities in the UK, are structured somewhat differently from other universities. In addition to the normal university departments that you would find in any university there are the colleges. The colleges have their own independent, and in many cases, very long existence. They are responsible for the housing and pastoral care of students (and academics), as well as teaching involving small groups. In some subjects they employ full-time lecturers but this is not generally the case in the natural sciences. Each college has a mixture of fellows and students from all subjects, in some ways the parallel is with members of a club. Other universities have apparent equivalents in their Halls of Residence and 'colleges' although these things are actually quite different in character.

Clearly Pembroke is the best of the colleges by any rational evaluation! Whilst I was in Cambridge it celebrated its 650th anniversary, although little if any of the original physical structure remains. The college features a chapel designed by Christopher Wren, behind some panels in one of the parlours are the scribblings and sketches by the workmen involved in the building. The ceiling of the Old Library is a fabulous, intricate 17th century plaster construction, I spent many long college meetings admiring it. Alfred Waterhouse was involved in some substantial re-building of the college in the late 19th century demolishing, with dynamite, the pre-existing medieval main hall in the process.

The list of alumni is rich with comedians (Peter Cook, Tim Brooke-Taylor, Eric Idle, Bill Oddie) and writers (Clive James, Ted Hughes), a little light on scientists although it does feature George Gabriel Stokes, Ray Dolby (inventor of the Dolby noise-reduction system) and John Sulston (Nobel Prize winner). Historically, there's William Pitt the Younger, and Nicholas Ridley (martyred by the old enemy in Oxford). The wiki page gives a summary of the history, and an extended list of alumni.

Pembroke college was somewhat different from anything I had experienced previously and it introduced me to a whole range of social gaffes. From my initial purchase of my MA gown, where I hastily thrust my arms down the sown-up sleeves rather than out through the exit slits; to confusing the Master of Pembroke, Sir Roger Tomkys, former High Commissioner to Kenya with my pointless statement that I had bought my cutlery from Argos (he thought I meant the Greek island); to turning up one summer evening in very crumpled linen for dinner only to discover that it was a celebratory meal for the Drapers' Company and I was under-dressed by at least an order of magnitude. Fortunately, as a fellow, I was allowed to walk on the grass, the public aren't. There are no signs to this effect, because senior fellows thought they looked untidy.

As a fellow I received little in the way of cash, I was employed by the university as an Assistant Director of Research* and paid by the college to do a few hours small group teaching each week. Pembroke mainly paid me in food, drink and company. A fairly elderly medieval scholar was the college wine buyer and did an excellent job. Dinners were particularly fine after college meetings, starting in the parlour, for pre-dinner drinks, five courses with a different wine with each course after which we returned to the parlour for port and so forth, Bath Oliver biscuits (Oliver was a former fellow) and fruit eaten with silver knives and forks.  Most junior fellows seconded to serve in the parlour.  For a long period I never drank port that was younger than I was and I got a taste for Sauternes which I can no longer support. Mrs SomeBeans has never forgiven them for the goat's cheese profiteroles.

As part of my job as fellow I was engaged in admissions interviews: one nervous fellow (me) interviewed fifteen nervous potential students for the Natural Sciences course. I remember having wet feet for most the morning, since I'd cycled in to college in a downpour. All but a couple of the students were predicted at least four A grades at A level, ultimately we were to take one or possibly two of the group I interviewed.

The colleges go to some length to make the admission system fair in relation to the background of the student, but to be honest the problem starts well before application. A vignette: my flatmate at Bristol University went to Harrow he was one of very few in his year *not* to apply to Oxford or Cambridge (Oxbridge), to the displeasure of the masters. I, from my respectable state comprehensive, was one of a handful to apply to Oxbridge. For my school, entry to Oxbridge was not a key performance indicator, it didn't really have the knowledge or background to support applicants.

In a way the debate on access to Oxbridge misses the point: it takes outstanding students, has excellent resources in terms of cash and people and it produces excellent output. What can you learn from this setup? As a measure of pre-university performance it's not great, we depend on written record and a few brief interviews. A real challenge would have been to take average students and see what we could do with them.

The best thing about college was my fellow fellows: they were bright, passionate about their work, always keen to talk about it. We met for lunch: classicists, modern linguists, historians, computer scientists, chemists, physicists, biologists, naturalists, engineers, English scholars talking about our work, the world and the etymology of the swearing of the American students over for summer schools. And in the usual college way we could wine and dine in our departmental colleagues colleges where the circle widened. It's an oddity of most modern universities that the scope for meeting colleagues from different departments is actually rather limited. The college system in Cambridge satisfies that need in some style.

Top image from Wikipedia:
*The Assistant Director of Research is no where near as grand as it sounds, it is a position that lies between postdoctoral research assistant and lecturer and is filled in Cambridge by people who will be unrequited in their desire for a permanent position.

Friday, March 12, 2010

The Presidents of the Royal Society (reprise)

In my previous post I described how I downloaded and played with the data on the fellows of the Royal Society, including a plot of the presidents of the society and their terms of office. I was a bit unhappy with this plot, I felt like it could be a bit more interactive. So I've been busy. The plot below shows you who was in office when you wave your mouse over it, and highlights their term. On the face of it this looks like I've done very little, but it took me six hours of playing with Protovis (a Javascript visualization library) top achieve this! You can do lots of very neat things with Protovis, and having done it one visualisation it should be easier to do the next one.

Monday, March 08, 2010

The Royal Society and the data monkey

This year finds the Royal Society celebrating its 350th anniversary. The Royal Society is Britain's national academy of science, one of the first of such societies to be founded in Europe. My brief investigations suggest that only the Italian Accademia dei Linceis and the German Academy of Sciences are older, and then only by a relatively small margin. The goals of the Royal Society were to report on the experiments of its members and communicate with like-minded fellows across Europe.

The Gentleman Administrator is planning some historical blogging on the Royal Society this year, starting with this post on the founding of the society and the role that Charles II played in it. On the face of it this post is about the history of the Royal Society, but in truth it says more about me as a data monkey than it does about the Royal Society. I shall explain.

The Royal Society supply a list of previous members as a pair of PDF format files, these contain each fellow of the Royal Society with their election date, their membership type and, for some, the dates of their birth and death. The PDF is formatted in a standard way suggesting to me that it could be read by a computer and the data therein analysed. I suspect there is an easier way to do this: ask the Royal Society whether they can supply the data in a form more amenable to analysis such as a spreadsheet or a database. But where's the fun in that?

As an experimental physicist, getting data in various formats into computer programs for further analysis is what I do. This arises when I want to apply an analysis to data beyond that which the manufacturer of the appropriate instrument supplies in their own software, when I get data from custom-built equipment, when I trawl up data from other sources. I received a polite "cease and desist" message at work after I successfully worked out how to extract the text of internal reports from the reports database, they shouldn't have said it couldn't be done! I will save you the gory details of exactly how I've gone about extracting the data from the Royal Society lists, suffice to say I enjoyed it.

First up, we can identify the Presidents of the Royal Society, and their terms of office from the PDF files - this information is in the name entry for each of them. We can look this data up too). I've plotted these below in a manner reminiscent of the displays of the earth's magnetic field reversal, each coloured stripe represents a presidency, and the colours alternate for clarity. The width of the stripe shows you how long each was president:

In the earlier years of the Royal Society's history the Presidential term varied quite considerably: Sir Isaac Newton served for 24 years (1703-1727), and Sir Joseph Banks for 42 years (1778-1820). Since 1870 the period of the office seems to have been fixed at 5 years.

Next, we can work out the size of the fellowship in any particular year, basically we go through each fellow in the membership list and see when they were elected to the society and when they died: between these two years they were members. These data are plotted below:

We can see that membership in the early years of the 19th century started to rise significantly but then after 1850 it started to fall again.

This fits in with historical records, in the earlier years of the 19th century some younger fellows pointed out that the Royal Society was starting to turn into a fancy dining club and that most of the fellows had published very little, in particular Charles Babbage published Reflections on the decline of Science in England, and on some of its causes. Wheels ground slowly but finally, in 1846, a committee was set up to consider the charter of Society and how to curb its ever growing membership. I've not found the date on which the committee reported but subsequent to this date, admission to the society was much more strictly controlled. Election to the Royal Society is still a mark of a scientist a little above the ordinary.

The data on birth and death dates starts getting sparse after about 1950, presumably since many of the fellows are still alive and were reluctant to reveal their ages. Doing analysis like this starts to reveal the odd glitch in the data. For example,Christfried Kirch appears to have died two years before being elected. At the moment I'm not handling uncertainty in dates very well, and I learnt that the letters "fl" before a date range indicate that and individual "flourished" in that period, which is nice.

If anyone is interested in further data in this area, then please let me know in the comments below. I intend adding further data to the set (i.e. hunting down birth and death dates) and if there is an analysis you think might be useful then I'm willing to give it a try. I've uploaded the basic data to Google Docs.

The illustration at the top of this piece is from the frontspiece of William Sprat's The History of the Royal Society of London, for the Improving of Natural Knowledge, published in 1722.

Thursday, March 04, 2010

And the winner is...

I thought I'd write about Nobel Prizes and rewards in science. Long ago I had an illuminating discussion about the subject with someone in publishing, I believe it was the night we were ineptly making Tequila Sunrises and drinking the mistakes so some of the recollections are a bit hazy. The core of the argument was around prestige and cash, my position was that the scientific prestige of the Nobel Prize could not be matched with any cash reward and that it was the Nobel Prize that I'd go for, over the cash, any time. My publishing friend had serious trouble understanding this position.

Despite this I'm ambivalent about the Nobel Prizes, it's a nice annual event that brings science a little up the news agenda and its always interesting to spot the Nobel Prize winners in your department (to be honest this isn't much of a game for most people, whilst I was at the Department of Physics in Cambridge there were two Nobel Prize winners in physics still attending: Brian Josephson and Neville Mott). Reading down the list of Nobel laureates in Physics, about two thirds are household names for any physicist whilst the remaining third are only recognised in their own sub-fields. One per year globally is an awfully thin sprinkling for any meaningful recognition of talent.

There are anomalies: Rosalind Franklin potentially missed out on a share in the 1962 award for the Nobel Prize in Physiology for "... discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material", this is the award to Crick, Watson and Wilkins for the discovery of DNA. She had died at the age of 37, and Nobel Prizes are not awarded posthumously. Jocelyn Bell Burnell was not awarded for her part in the discovery of pulsars. In fact wikipedia has a whole page of Nobel Prize controversies. Any award of this type must ultimately be subjective, and given the further constrains of the prize rules, a degree of controversy is inevitable.

Perhaps more pernicious is the idea that discoveries are made by three people or fewer. Isaac Newton said "If I have seen a little further it is by standing on the shoulders of Giants.": scientific discoveries make use of the discoveries that have come before, and these days discoveries may be made by the collaboration of very large groups of people.

I've never had the feeling, as a scientist, of flocking around an individual, rather more of flocking around an idea that has been developed by a number of individuals. You never find scientists in groups asking "What would Einstein do?". You rarely find scientists making references to "the school of X", where X is some famous scientist. There are no gurus in science.

Practically speaking I believe that my contribution to science in future years will be considered exceedingly minor; epsilon as numerical analysts would call it: the smallest thing you can have without being zero. For me the reward in science has always been the thrill of personal discovery, a sudden realisation that you have learnt just a little more about the way things work, something that no one else knows.  The desire that other people recognise that only comes later, and in the first instance the thrill is in showing the neat thing you have found (not your role in the discovery).

In truth I'd do science for no payment, and I think it's true to say most scientists would say the same. Before my employer gets excited by this revelation, I should point out that I charge for attendance at meetings and the amount of money you pay me to interact with various poorly designed IT systems is no where near enough! Similarly, as an academic, I required payment to write grant applications, attend examiners meetings and so forth.

And to end with my favourite Tom Lehrer Nobel Prize quote: "Political satire became obsolete when Henry Kissinger was awarded the Nobel Peace Prize."

Wednesday, March 03, 2010

A letter to the Institute of Physics

Dear Sir/Madam

As a member of the Institute of Physics I would like to register my extreme displeasure and unhappiness at the IOP submission to the House of Commons Science and Technology Committee regarding the leaking of e-mails from the Climate Research Unit at the University of East Anglia (reproduced here) . In my view this submission will damage the scientific reputation of the Institute amongst scientists and other learned societies. This submission will prejudice my future confidence in any policy statements that the IOP makes.

My specific complaints of the submission are as follows:
1. Item 2 mis-represents the current scientific practice of sharing of data and methodologies. Currently methodologies are generally shared by publication in scientific journals not by the explicit sharing of computer source code. Raw experimental data from third parties is not routinely shared. To imply that the researchers at CRU are acting out of step with current practice is false. 
2. Item 4 specifically casts doubt on the historical temperature reconstructions based on proxy measures whilst not acknowledging that such reconstructions have been repeated by a range of research groups using a range of methodologies, as described in the IPCC 2007 report.
3. Item 5 accuses the researchers at CRU of "suppression" of the divergence between proxy records and the more recent thermometer based record. This is ridiculous, the CRU has published on this very divergence in Nature.
4. Item 6 makes no recognition of the un-usual circumstances that CRU found themselves in, subjected to a large number of Freedom of Information requests, culminating in the publication of a substantial fraction of their private e-mail correspondence.

The subject of climate science and it's relationship to anthropogenic climate change is an area subject to political interference, in my view the IOP's submission is a political attack on the CRU at East Anglia University dressed in a flimsy scientific cover.

I expect the Institute to fully withdraw this submission to the Science & Technology Committee. I feel that the subsequent explanatory statement by the IOP is insufficient in addressing the shortcomings of the original submission. It also takes no cognisance of the fact the IOP position will be taken publicly to be the sum of all it's published statements, and indeed that this submission will be preferred, over all others, as a presentation of the IOP's policy by those who wish to deny the position on climate science that the IOP claims to hold.

I will be cancelling my direct debit mandate to the IOP now, I may decide to continue with my membership when it comes up for renewal.

yours sincerely,

Dr Ian Hopkinson

8/3/10: update, corrected some typos