Me, me, me

Well, what do you expect in a blog, after all? Here, then, is some blatant advertising of forthcoming events at which I’m speaking or participating. I’ve been trying to rein back on this kind of thing, but seem to have acquired a cluster of bookings in the near future.

You’ve already missed the seminar on new materials at King’s College, London, on 12 May – a very interesting collection of people assembled by Mark Miodownik, whose Materials Library is a very fabulous thing to behold. I hope to post my talk on my website soon.

On 27 May I am talking about my book Universe of Stone at the Hay Festival. And it seems that I’ll be participating in a discussion about science books for Radio 4’s Material World, which will be recorded at Hay the previous day. The other panellists are Sir David King and Steve Jones.

On 28 May I will be chairing a public discussion on synthetic biology at the Science Museum’s Dana Centre, called ‘Making Life’.

In June I have what is looking ominously like a residency at the Royal Institution, starting with a discussion of my novel The Sun and Moon Corrupted at the newly launched RI book club on 9 June. I will be coming along to face the critics after the discussion – do come and be gentle with me.

The following Monday, 16 June, I will be attempting to persuade the RI audience why human spaceflight is seldom of any scientific worth and is best left to private entrepreneurs (see here). The counter-argument will be ably put by Kevin Fong of UCL.

Then on 10 July I’ll be talking at the RI about my book Elegant Solutions, published by the Royal Society of Chemistry, which looked at the issue of beauty in chemistry experiments (details here). This is an event organized to mark the book’s receipt of the 2007 Dingle Prize for communicating the history of science and technology from the British Society for the History of Science.

Then I’m having a holiday.

Mixed messages

Last night I drove into the traffic hell that is Canary Wharf to see a play by the marvellous Shifting Sands in a rather nice little theatre marooned on the Isle of Dogs. (I would advertise it, but this is the end of their run. I’m collaborating with Shifting Sands on a production early next year based on the life of Paracelsus and funded by the Wellcome Trust.)

I’ve never ventured into E14 by car before, for good reason. Here is a traffic system that radiates sneering contempt, confronting you with a morass of flyovers, tunnels and slip roads labelled only with signs saying things like ‘Canary Wharf Depot A’. One wrong turn and I was in a tunnel that offered no escape until it spat me back out at the Rotherhithe Tunnel.

My point is this. You emerge, dazed, anxious and disorientated, from some underground cavern to find yourself on a busy roundabout, and in the middle is the structure shown above. Traffic lights point in all directions; some beckon in green, some prohibit in red, some tantalize in amber.

‘You can’t be serious’, I muttered, and several moments passed before I twigged that indeed this is not a serious device for directing traffic, but, can you credit it, an art installation. At least, I could only assume so, but I decided to quiz the bar attendant at the theatre. She professed ignorance of the roads, but a local bloke sitting at the bar chipped in. The installation cost £140,000, he said, and he was living in a flat that overlooked it when it was first installed. ‘I’ve never seen so many accidents’, he said.

The stupidity of it is so breathtaking that it is almost a work of conceptual art itself. I try to picture the local council meeting at which the design was proposed. ‘Yes, I want to use real traffic lights. By utterly confusing and bewildering the driver, you see, it will make a comment on the complexity of everyday life.’ ‘Well, that sounds like a brilliant idea. Here’s 140 grand.’

This is all merely a slender excuse to advertise this nice preprint by Stefan Lämmer and Dirk Helbing on self-organized traffic lights that replace central control with autonomy. A self-organized approach could in principle let traffic flow considerably more efficiently, as I’ve discussed some time ago in a Nature article.

But I fear that E14 is beyond any redemption that self-organization can offer.

When worlds collide

[This is the pre-edited version of my
latest Muse article for Nature News.]

Worries about an apocalypse unleashed by particle accelerators are not new. They have their source in old myths, which are hard to dispel.

When physicists dismiss as a myth the charge that the Large Hadron Collider (LHC) will trigger a process that might destroy the world, they are closer to the truth that they realise. In common parlance a myth has come to denote a story that isn’t true, but in fact it is a story that is psychologically true. A real myth is not a false story but an archetypal one. And the archetype for this current bout of scare stories is obvious: the Faust myth, in which an hubristic individual unleashes forces he or she cannot control.

The LHC is due to be switched on in July at CERN, the European centre for particle physics near Geneva. But some fear that the energies released by colliding subatomic particles will produce miniature black holes that will engulf the world. Walter Wagner, a resident of Hawaii, has even filed a lawsuit to prevent the experiments.

As high-energy physicist Joseph Kapusta points out in a new preprint [1], such dire forebodings have accompanied the advent of other particle accelerators in the past, including the Bevalac in California and the Relativistic Heavy Ion Collider (RHIC) on Long Island. In the latter case, newspapers seized on the notion of an apocalyptic event – the UK’s Sunday Times ran a story under the headline ‘The final experiment?’

The Bevalac, an amalgamation of two existing accelerators at the Lawrence Berkeley Laboratory, was created in the 1970s to investigate extremely dense states of nuclear matter – stuff made from the compact nuclei of atoms. In 1974 two physicists proposed that there might be a hitherto unseen and ultra-dense form of nuclear matter more stable than ordinary nuclei, which they rather alarmingly dubbed ‘abnormal’. If so, there was a small chance that even the tiniest lump of it could keep growing indefinitely by cannibalizing ordinary matter. Calculations implied that a speck of this pathological form of abnormal nuclear matter made in the Bevalac would sink to the centre of the Earth and then expand to swallow the planet, all in a matter of seconds.

No one, Kapusta says, expected that abnormal nuclear matter, if it existed at all, would really have this voracious character – but neither did anyone know enough about the properties of nuclear matter to rule it out absolutely. According to physicists Subal Das Gupta and Gary Westfall, who wrote about the motivations behind the Bevalac to mark its termination in 1993[2], “Meetings were held behind closed doors to decide whether or not the proposed experiments should be aborted.”

The RHIC, at the Brookhaven National Laboratory, began operating in 1999 primarily to create another predicted superdense form of matter called a quark-gluon plasma. This is thought to have been what the universe consisted of less than a millisecond after the Big Bang. Following an article about it in Scientific American, worries were raised about whether matter this dense might collapse into a mini-black hole that would again then grow to engulf the planet.

Physicist Frank Wilczek dismissed this idea as “incredible”, but at the same time he raised a new possibility: the creation of another super-dense, stable form of matter called a strangelet that could again be regarded as a potential Earth-eater. In a scholarly article published in 2000, Wilczek and several coworkers analysed all the putative risks posed by the RHIC, and concluded that none posed the slightest real danger[3].

But isn’t this just what we’d expect high-energy physicists to say? That objection was raised by Richard Posner, a distinguished professor of law at the University of Chicago[4]. He argued that scientific experiments that pose potentially catastrophic risks, however small, should be reviewed in advance by an independent board. He recognized that current legal training provides lawyers and judges with no expertise for making assessments about scientific phenomena “of which ordinary people have no intuitive sense whatsoever”, and asserted that such preparation is therefore urgently needed.

It seems reasonable to insist that, at the very least, such research projects commission their own expert assessment of risks, as is routinely done in some areas of bioscience. The LHC has followed the example of the RHC in doing just that. A committee has examined the dangers posed by strangelets, black holes, and the effects of possible ‘hidden’ extra dimensions of space. In 2003 they declared that “we find no basis for any conceivable threat” from the accelerator’s high-energy collisions[5].

These scare stories are not unique to particle physics. When in the late 1960s Soviet scientists mistakenly believed they had found a new, waxy form of pure water called polywater, one scientist suggested that it could ‘seed’ the conversion of all the world’s oceans to gloop – a scenario memorably anticipated in Kurt Vonnegut’s 1963 novel Cat’s Cradle, where the culprit was instead a new form of ice. Superviruses leaked from research laboratories are a favourite source of rumour and fear – this was one suggestion for the origin of AIDS. And nanotechnology was accused of hastening doomsday thanks to one commentator’s fanciful vision of grey goo: replicating nanoscale robots that disassemble the world for raw materials from which to make copies of themselves.

In part, the appeal of these stories is simply the frisson of an eschatological tale, the currency of endless disaster movies. But it’s also significant that these are human-made apocalypses, triggered by the heedless quest for knowledge about the universe.

This is the template that became attached to the Faust legend. Initially a folk tale about an itinerant charlatan with roots that stretch back to the Bible, the Faust story was later blended with the myth of Prometheus, who paid a harsh price for daring to challenge the gods because of his thirst for knowledge. Goethe’s Faust embodied this fusion, and Mary Shelley popularized it in Frankenstein, which she explicitly subtitled ‘The Modern Prometheus’. Roslynn Haynes, a professor of English literature, has explored how the Faust myth shaped a common view of the scientist as an arrogant seeker of dangerous and powerful knowledge[6].

All this sometimes leaves scientists weary of the distrust they engender, but Kapusta points out that it is occasionally even worse than that. When Das Gupta and Westfall wrote about the concerns of abnormal nuclear matter raised with the Bevalac, they were placed on the FBI’s ‘at risk’ list of individuals thought to be potential targets of the Unabomber. Between 1978 and 1995, this former mathematician living in a forest shack in Montana sent bombs through the US mail to scientists and engineers he considered to be working on harmful technologies. A lawsuit by a disgruntled Hawaiian seems mild by comparison.

And yet… might there be anything in these fears? During the Manhattan Project that developed the atomic bomb, several of the scientists involved were a little unsure, until they saw the mushroom cloud of the Trinity test, whether the explosion might not trigger runaway combustion of the Earth’s atmosphere.

The RHIC and LHC have taken far less on trust. But of course the mere acknowledgement of the risks that is implied by commissioning studies to quantify them, along with the fact that it is rarely possible to assign any such risk a strictly zero probability, must itself fuel public concern. And it is well known to risk-perception experts that we lack the ability to make a proper rating of very rare but very extreme disasters, even to the simple extent that we feel mistakenly safer in our cars than in an aeroplane.

That’s why Kapusta’s conclusion that “physicists must learn how to communicate their exciting discoveries to nonscientists honestly and seriously”, commendable though it is, can never provide a complete answer. We need to recognize that these fears have a mythic dimension that rational argument can never wholly dispel.


References

1. Kapusta, J. I. Preprint http://xxx.arxiv.org/abs/0804.4806
2. Das Gupta, S. & Wetfall, G. D. Physics Today 46 (May 1993), 34-40.
3. Jaffe, R. L. et al., Rev. Mod. Phys. 72, 1125-1140 (2000).
4. Posner, R. A. Catastrophe: Risk and Response (Oxford University Press, Oxford, 2004).
5. Blaizot, J.-P. et al., ‘Study of potentially dangerous events during heavy-ion collisions at the LHC: Report of the LHC Safety Study Group’, CERN Report 2003-001.
6. Haynes R.D., From Faust to Strangelove: Representations of the Scientist in Western Literature (Johns Hopkins University Press, Baltimore & London, 1994).

Talking about Chartres

There’s a gallery of images and a vodcast for my book Universe of Stone now up on the Bodley Head site: you can find it here.

Buddha in oils?
[This is the pre-edited version of my latest news story for Nature.]

Painters on the Silk Road may have been way ahead of the Europeans.

Artists working in Afghanistan were using a primitive form of oil paint hundreds of years before it became common practice in Europe, a team of scientists has claimed.

Yoko Taniguchi of the National Research Institute for Cultural Properties in Tokyo and her coworkers have analysed samples of Buddhist paintings in caves at Bamiyan in Afghanistan, made in the mid-seventh and early eighth centuries AD. They say that the paint layers contain pigments apparently bound within so-called drying oils, perhaps extracted from walnuts and poppy seeds.

But Jaap Boon, a specialist in the chemical analysis of art at the Institute for Atomic and Molecular Physics in Amsterdam, the Netherlands, cautions that this conclusion must be seen as tentative until more detailed studies have been done.

The Bamiyan caves sit behind the gigantic statues of Buddha that were destroyed by the Taliban in 2001. The paintings, showing robed Buddhas and mythical creatures, were also defaced but not obliterated. The Bamiyan caves are now a designated UNESCO World Heritage site.

The researchers removed tiny samples of the painted surface (typically less than 1 mm across) for analysis using state-of-the-art techniques. These can reveal the chemical identity of the pigments and the materials used to bind them to a layer of earthen plaster on the cave walls.

Taniguchi’s collaborators used X-ray beams produced by the European Synchrotron Radiation Facility in Grenoble, France, to figure out the composition and crystal structures of pigment particles, deposited in a series of microscopically thin layers. The synchrotron facility produces extremely bright X-ray beams, which are essential for getting enough data from such small samples.

Meanwhile, spectroscopic methods, which identify molecular structures from the way their vibrations cause light absorption, were used to identify the organic components of the paint layers. The findings are described in a paper in the Journal of Analytical Atomic Spectrometry [1].

The researchers found pigments familiar from the ancient world, such as vermilion (red mercury sulphide) and lead white (lead carbonate). These were mixed with a range of binders, including natural resins, gums, possibly animal-skin glue or egg – and oils.

Boon suggests that this variety in itself raises concerns about potential contamination – microogranisms on the rock surface, say, or the fingerprints of people touching the paintings (something encouraged in Buddhist tradition).

He says that other techniques that really pin down what the organic molecules are should be applied before jumping to conclusions. With spectroscopy alone, he says, it can be difficult to tell egg from oils, let alone animal from plant oils.

But Marine Cotte of the Centre of Research and Restoration of the French Museums in Paris, a coauthor of the study, is convinced of the conclusions. She says that oils have an unambiguous spectroscopic signature, and adds that their molecular components have been confirmed by the technique of chromatography.

Oil painting is commonly said to have been invented by the Flemish painter Jan van Eyck and his brother Hubert in the fifteenth century. But while the van Eycks seem to have refined this technique to create stunningly rich and durable colours, the practice of mixing pigments with drying oils is known to be considerably older.

It is first mentioned in the late fifth century by the Byzantine writer Aetius, and a recipe for an oil varnish (in which a drying oil is mixed with natural resins) is listed in an eighth-century Italian manuscript.

In the twelfth century, a German Benedictine monk named Theophilus describes how to make oil paints for painting doors. Oil paints are also known from this period on Norwegian churches.

Drying oils are relatively slow to dry compared with the common medieval binders of egg yolk and size from boiled animal hide, which initially led Western craftsmen to regard them as fit only for rather lowly uses.

So the use of oils in fine art as early as the seventh century is surprising – all the more so for painting on plaster-coated rock, where the translucency of oil paints would not be expected to recommend their use. ‘It doesn’t make a lot of sense to use oils’, says Boon. He says that it would be really difficult to keep the paint in good condition for a long time in an environment like this, exposed to damp, fungi and bacteria.

But Cotte says that the oils are found in deeper layers where contamination would not penetrate, while being laid over an opaque bottom or ‘ground’ layer.

It’s not clear who these artists were, the researchers say. They were probably travelling on the Silk Road between China and the Middle East, and may have been bringing with them specialist knowledge from China.

Cotte says that these studies should aid efforts to preserve the paintings. “It helps you do that if you know what is there”, she explains – this would identify the most appropriate cleaning procedures, for example.

Reference
1. Cotte, M. et al., J. Analyt. Atomic Spectrosc. (in press, 2008)

Journeys in musical space
[This is one of the most stimulating things I’ve read for some time (not my article below, published on Nature’s online news site, but the paper it discusses). The paper itself is tough going, but once Dmitri Tymoczko explained to me where it was headed, the implications it opened up are dizzying – basically, that music is an exploration of complex geometries, giving us an intuitive feel for these spaces that we probably couldn’t get from any other kind of sensory input.]

Researchers map out the geometric structure of music.

To most of us, a Mozart piano sonata is an elegant succession of notes. To composer and music theorist Dmitri Tymoczko of Princeton University and his colleagues Clifton Callender and Ian Quinn, it is a journey in multidimensional space that can be described in the language of geometry and symmetry.

In a paper in Science, the trio offer nothing less than a way of mapping out all of pitched music (music which is not constructed from unpitched sounds like percussion), whether it is by Monteverdi or Mötörhead.

Commenting on the work, mathematician Rachel Wells Hall of Saint Joseph’s College in Philadelphia says that it opens up new directions in music theory, and could inspire composers to explore new kinds of music. It might even lead to the invention of new musical instruments, she says.

Although the work uses some fearsome maths, it is ultimately an exercise in simplification. Tymoczko and colleagues have looked for ways of representing geometrically all the equivalences that musicians recognize between different groups or sequences of notes, so that for example C-E-G and D-F#-A are both major triads, or C-E-G played in different octaves is considered basically the same chord.

By recognizing these equivalences, the immense number of possible ways of arranging notes into melodies and chord sequences can be collapsed from a multidimensional universe of permutations into much more compact spaces. The relationships between ‘musical objects’ made of small groupings of notes can then be understood in geometric terms by mapping them onto the shape of the space. Musical pieces may be seen as paths through this space.

It may sound abstract, but the idea brings together things that composers and musicologists have been trying to do in a fragmentary manner for centuries. The researchers say that all music interpretation involves throwing away some information so that particular musical structures can be grouped into classes. For example, playing ‘Somewhere Over the Rainbow’ in the key of G rather than, as originally written, the key of E flat, involves a different sequence of notes, but no one is going to say it is a different song on that account.

The Princeton researchers say there are five common kinds of transformation like this that are used in judging equivalence in music, including octave shifts, reordering of notes (for example, in inversions of chords, such as C-E-G and E-G-C), and duplications (adding a higher E to those chords, say). These equivalences can be applied individually or in combination, giving 32 different ways in which, say, two chords can be considered ‘the same’.

Such symmetries ‘fold up’ the vast space of note permutations in particular ways, Tymoczko explains. The geometric spaces that result may still be complex, but they can be analysed mathematically and are often intuitively comprehensible.

“When you’re sitting at a piano”, he says, “you’re interacting with a very complicated geometry.” In fact, composers in the early nineteenth century were already implicitly exploring such geometries through music that could not have been understood using the mathematics of the time.

In these folded-up spaces, classes of equivalent musical objects – three-note chords, say, or three-note melodies – can each be represented by a point. One point in the space that describes three-note chord types (which is cone-shaped) corresponds to major triads, such as C-E-G, another to augmented chords (in which some notes are sharpened by a semitone), and so on.

Where does this musical taxonomy get us? The researchers show that all kinds of musical problems can be described using their geometric language. For example, it provides a way of evaluating how related different sequences of notes or chords are, and thus whether or not they can be regarded as variations of a single musical idea.

“We can identify ways chord sequences can be related that music theorists haven’t noticed before”, says Tymoczko. For example, he says the approach reveals how a chord sequence used by Claude Debussy in 'L’Après-Midi d’un Faune' is related to one used slightly earlier by Richard Wagner in the prelude to 'Tristan und Isolde' – something that isn’t obvious from conventional ways of analysing the two sequences.

Clearly, Debussy couldn’t have know of this mathematical relationship to Wagner’s work. But Tymoczko says that such connections are bound to emerge as composers explore the musical spaces. Just as a mountaineer will find that only a small number of all the possible routes between two points are actually negotiable, so musicians will have discovered empirically that their options are limited by the underlying shapes and structures of musical possibilities.

“Music theorists have tended to regard the nineteenth-century experiments in harmony as unmotivated whimsy”, says Tymoczko. But his geometric scheme suggests that they were much more rational than that, governed by rigorous rules that their new approach can now uncover.

For example, the scheme supplies a logic for analysing how so-called voice leading works in chord progressions. This describes the way in which a sequence of chords with the same numbers of notes can be broken apart into parallel melodic lines. For example, the progression C-E-G to C-F-A can be thought of as three melodic lines: the E moves to F, and the G to A, with a constant C root. Finding efficient and effective voice-leading patterns has been challenging for composers and music theorists. But in the geometric scheme, a particular step from one chord to another becomes a movement in musical space between two points separated by a well defined distance, and one can discover the best routes.

This is just one of the ways in which the new theory could not only illuminate existing musical works but could point to new ways of solving problems posed in musical composition, the researchers claim.

Reference
1. Callender, C. et al. Science 320, 346-348 (2008).

NASA loses its (science) head, Pfizer loses its case
[This is my Lab Report column for the May issue of Prospect.]

The resignation of NASA’s science chief Alan Stern in April is a symptom of all that’s wrong with the US space agency. Stern has given no official reason for his abrupt departure, which of course makes it seem all the more that the reason is one he’d rather not talk about. Many suspect his decision stems from a frustrating relationship with NASA’s leadership, specifically its head Mike Griffin, despite Stern’s assertion that Griffin is “the best administrator NASA has ever had”. Stern’s aim to keep projects on schedule and within budget – both persistent problems for NASA – is hard to fault, but it has sometimes caused a collision of priorities.

A highly respected planetary scientist, Stern has been seen as a true voice of science at NASA, favouring projects that actually teach us something about the universe. But increasingly, NASA seems compelled to support popular programmes that pander to the romanticised American vision of space exploration. Griffin has frozen the budget for fundamental science to fund a manned return mission to the moon – a political rather than scientific venture. Stern also tried to reduce the focus of planetary missions on Mars at the expense of the outer planets.

The crunch seems to have come over Stern’s decision in March to shut down Opportunity, one of the two Mars rovers currently exploring the planet’s surface. Griffin was not informed of that decision, and when he found out, he reversed it. Whatever the demands of etiquette, Stern’s decision made sense: the rovers have been an immensely successful testament to the power of robotic exploration, but they have long fulfilled their objectives. Opportunity and Spirit can still gather useful data, but the real problem was that the public loves them: the planned shutdown became headline news and provoked objections in Congress.

The rovers are now portrayed like pets: newspapers talked about Opportunity being ‘put to sleep’ rather than switched off. This pathetic fallacy is a projection of the longing to put humans on Mars. The irony is that a populist commitment to cripplingly expensive human spaceflight projects will ultimately give the taxpayer far less value for money than the kind of missions Stern supported. For now, that kind of absurd sentimentality has deprived NASA of a highly capable head of science.

*****

When scientists submit papers for publication, they usually enter into an unwritten contract of confidentiality with the journal: the paper will not be disseminated outside of the peer review process, but the reviewers will not be disclosed to the authors.

The pharmaceutical company Pfizer has decided that this arrangement should be subordinate to its own interests. During a lawsuit last year over alleged side effects of its painkillers Celebrex and Bextra, it subpoenaed the New England Journal of Medicine (NEJM) to release the reviews and reviewers’ identities for papers published on the drugs, along with details of the journals’ internal editorial deliberations. The NEJM’s refusal has now been upheld by a federal court in Massachusetts.

Pfizer’s lawyers say that the information could help to exonerate the company in deciding to put the drugs on sale. Bextra was withdrawn in 2005 after claims that it could cause heart attacks and strokes; Celebrex remains on the market.

“The public has no interest in protecting the editorial process of a scientific journal”, the lawyers have say. But the public has every interest in knowing that scientific claims will be checked out by independent experts who not only are guaranteed anonymity but do not expose themselves to the danger of litigation. The best reviewers might otherwise decline the task rather than take that risk. A counter-argument is that information relevant to public health should not be kept confidential – but drug companies are after all under no obligation to disclose their own tests and trials.

Besides, Pfizer has not specified what it hoped to find in the documents. One interpretation is that the company is simply fishing for anything that might help its case, rather than acting on a belief that the NEJM holds some pivotal evidence. The court’s decision is the right one, but will it persuade drug companies that they cannot rewrite the rules by which science is conducted?

*****

The new head of the Human Fertilisation and Embryology Authority (HFEA), Renaissance historian Lisa Jardine, has certainly begun her role during ‘interesting times’. The impending vote on the Human Fertilisation and Embryology Bill crystallizes several moral dilemmas about today’s research and practice in these areas, and threatens to heighten the polarization they induce. Whatever positions Jardine takes are sure to upset some vocal group or other.

Perhaps this is why the appointment of someone used to taking the long view, and accustomed also to the hard knocks of public life, makes sense. Certainly, Jardine’s popularizing instincts seem right for the HFEA just now: she considers public education about fertility issues (“something people need to know about”) as important as the regulatory responsibilities. The HFEA, while not exactly an opaque bureaucracy, has seldom previously shown an explicit commitment to inform.

And now is the time to do it. So far, it seems that the kind of misinformation about the bill spread by Catholic officials and other religious groups – talk of animal-human ‘cybrid’ embryos in research as ‘of Frankenstein proportion’ – has not significantly dented a public appreciation of the benefits such research could bring. (The ‘animal’ component here is a mere shell for human genes.) But it’s never a good idea to underestimate the determination of zealots.