Mar 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.

Mar 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.

Mar 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.

Footnotes
Top image from Wikipedia: http://en.wikipedia.org/wiki/File:Pembroke_College_Cambridge.JPG
*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.

Mar 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.



Mar 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.

Footnote
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.