The secret of Islamic patterns
This is the pre-edited version of my latest piece for news@nature. The online version acquired some small errors that may or may not be put right. But what a great paper!

Muslim artists may have used a sophisticated tiling scheme to design their geometric decorations

The complex geometrical designs used for decoration by Islamic artists in the Middle Ages, as seen in buildings such as the Alhambra palace in southern Spain, were planned using a sophisticated tiling system that enabled them to make patterns not known in the West until 20 years ago, two physicists have claimed.

By studying many Islamic designs, Peter Lu of Harvard University in Cambridge, Massachusetts, and Paul Steinhardt of Princeton University in New Jersey have decided they were put together not using a compass and ruler, as previously assumed, but by tessellating a small number of different tiles with complex shapes.

The researchers think that this technique was developed around the start of the thirteenth century, and that by the fifteenth century it had become advanced enough to generate complex patterns now known as quasiperiodic. These were 'discovered' in the 1970s by the British mathematical physicist Roger Penrose, and were later found to account for puzzling materials called quasicrystals. Discovered in 1984 in metal alloys, quasicrystals initially foxed scientists because they seemed to break the geometric rules that govern regular (crystalline) packing of atoms.

The findings provide a further illustration of how advanced Islamic mathematics was in comparison with the medieval West. From around the eleventh century, much of the understanding of science and maths in the Christian West came from Islamic sources. Arabic and Persian scholars preserved the learning of the ancient Greeks, such as Aristotle, Ptolemy and Euclid, in translations and commentaries.

The Muslim writers also made original contributions to these fields. Western scholars learnt Arabic and travelled to the East to make Latin translations of the Islamic books. Among the mathematical innovations of the Islamic world were the use of algebra, algorithms (both of which are words derived from Arabic) and the use of numerals now known as 'Arabic' (although derived in turn from Indian notation).

The mathematical complexity of Islamic decoration has long been admired. The artists used such motifs because representational art was discouraged by the Koran. “The buildings decorated this way were among the most monumental structures in the society, combining both political and religious functions”, says Lu. “There was a great interest, then, in using these structures to broadcast the power and sophistication of the controlling elite, and therefore to make the ornament and decoration equally monumental.”

Lu and Steinhardt now propose that these designs were created in a previously unsuspected way. They say that the patterns known as girih, consisting of geometric polygon and star shapes interlaced with zigzagging lines, were produced from a set of just a handful of tiling shapes ranging from pentagons and decagons (regular ten-sided polygons) to bow-ties, which can be pieced together in many different ways. The two physicists show how these tiles could themselves be drawn using geometric constructions with compasses that were known by medieval Islamic mathematicians.

Some scrolls written by Islamic artists to explain their design methods show tiles with these shapes explicitly, confirming that they were used as 'conceptual building blocks' in making the design. Lu says that they’ve found no evidence that the tiles were actually made as physical objects. “But we speculate they were”, he adds, “so as to be used as templates in laying out the actual tiling on the side of a building.”

Lu and Steinhardt say that designing this way was simpler and faster than starting with the zigzag lines themselves: packing them together in different regular arrays automatically generates the complex patterns. “Once you have the tiles, you can make complicated patterns, even quasicrystalline ones, by following a few simple rules”, says Lu.

The researchers have shown that many patterns on Islamic buildings can be built up from the girih tiles. The resulting patterns are usually periodic – they repeat again and again, and so can be perfectly superimposed on themselves when shifted by a particular distance – but this regularity can be hard to spot, compared say with that of a hexagonal honeycomb pattern.

The patterns also contain many shapes, such as polygons with 5, 10 and 12 sides, that cannot themselves be packed together periodically without leaving gaps. This property of the polygons means that scientists long believed that it was impossible for crystals to show five- ten- and twelvefold symmetries, such that rotating them by a fifth, tenth or twelfth of a full circle would allow them to be superimposed on themselves.

So when 'crystals' that appeared to have these symmetries were discovered in 1984, they seemed to violate the basic rules of geometry. But it became clear that these quasicrystals aren't perfectly periodic. In the same year, Steinhardt pointed out how patterns with the same geometric properties as quasicrystyals could be constructed from the tiling scheme devised by Penrose.

Steinhardt and Lu say that, while there is no sign that the Islamic artists knew of the Penrose tiling, their girih tiling method provides an alternative way to make the same quasicrystalline patterns. The researchers say that a design on the Darb-i-Imam shrine in Isfahan, Iran, made in 1453, is virtually equivalent to a Penrose tiling. One of the mesmerizing features of this pattern is that, like a true quasicrystal, it looks regular but never repeats exactly.

“I’d conjecture that this was quite deliberate”, says Lu. “They wanted to extend the pattern without it repeating. While they were not likely aware of the mathematical properties and consequences of the construction rule they devised, they did end up with something that would lead to what we understand today to be a quasicrystal.”

Reference
Lu, P. J. & Steinhardt, P. J. Science 315, 1106 - 1110 (2007).

Postscript
I have received some comments from Roger Penrose on this work, sadly too late for inclusion in the Nature piece but which provide some valuable perspective on the discovery. This is what he says:
"The patterns are fascinating, and very beautiful, and it is remarkable how much these ancient architects were able to anticipate concerning 5-fold quasi-symmetric organization. But, as Steinhardt (and, in effect, Lu) have confirmed directly with me, the Islamic patterns are not the same as my patterns (on several counts: different basic shapes, no matching rules, no evidence that they used anything like a "Penrose pattern" to guide them, the hierarchical structure indicated by their subdivision of large shapes into smaller ones is not strictly followed, and would not, in any case, enable the patterns to map precisely to a "Penrose tiling"). I do, however, regard this work of Steinhardt and Lu as a most intriguing and significant discovery, and one wonders what more the ancient Islamic designers may have known about such things. I should perhaps add that the great Astronomer Johannes Kepler, in his Harmonice Mundi (vol.2), published in 1619, had independently produced a regular pentagon tiling that is much closer to my own tilings than anything that I have seen so far in this admittedly wonderful Islamic work."

Peter Lu, incidentally, has indicated that he agrees with everything that Penrose says here. The relationship between the Darb-i-Imam pattern and a Penrose tiling is subtle - much more so, it seems, than media reports of this work have tended to imply.

When research goes PEAR-shaped

I’ve got a muse@nature.com column up today about the closure of the lab at Princeton that was investigating paranormal phenomena. Inevitably these things have to be chopped and changed before they appear, but here’s the pre-edited version. I feel scientists have no need to get too heavy about this kind of thing – if nothing else, it could serve as an interesting discussion point for students learning about how science is, and should be, done. To judge from the descriptions I’ve read of the PEAR lab and its ethos, we could probably do with a bit more of that in the scientific community. But why, oh why, do these people feel the need to come up with a ‘theory’ that is just a tangle of words? It is, in the time-honoured phrase, not even wrong. Sometimes you can’t help feeling that quantum theory has a lot to answer for.

There should be room for a bit of fringe science – but it's liable to suck you in.

It can't do a great deal for your self-esteem when media interest in your research project seems to catch fire only in response to the project's demise. But Robert Jahn and Brenda Dunne of the Princeton Engineering Anomalies Research (PEAR) laboratory probably aren't too bothered by that. For the attention generated by the closure of the PEAR lab – or rather, by the suggestion in the New York Times that this removes a source of ongoing embarrassment to the university – can surely only enhance the profile of Jahn and Dunne's longer-term vision of exploring "consciousness-related anomalies".

What "anomalies", exactly? With meticulous care, Jahn and Dunne avoid describing the phenomena they've studied using the more familiar words: telekinesis and telepathy. They have been studying people's ability to control machines and to transmit images from remote locations using only the power of the human mind. According to your perspective, that choice of language is a way of either promoting the paranormal by stealth or avoiding knee-jerk criticism.

The affair has inevitably ignited debates about the limits of academic freedom and responsibility. The NY Times quotes physicist Robert Park, a noted debunker of pseudo-science, as saying "It’s been an embarrassment to science, and I think an embarrassment for Princeton", while physicist Will Happer at Princeton says "I don’t believe in anything [Jahn] is doing, but I support his right to do it."

The university itself is trying to keep out of the fray. While stressing that the work done at PEAR was, like most other research at the university, privately funded, Princeton spokeswoman Cass Cliatt says that the lab's closure "was not a university decision". She adds that "the work at the lab was always understood by the university to be a personal interest of Professor Jahn's." Jahn, now an emeritus professor, was former dean of the engineering school and is an expert on electric propulsion.

Jahn and Dunne, a developmental psychologist, confirm that the decision was theirs. "We have accomplished what we originally set out to do 28 years ago, namely to determine whether these effects are real and to identify their major correlates", they say. With Jahn about to retire, "it is time for the next generation of scholars to take over." They hope that their work will be continued through the International Consciousness Research Laboratories, a network established in 1996 and now boasting members from 20 countries.

Some will surely share Park's view that this sort of thing gives science a bad name. But they'd be wrong to let the matter rest there, because PEAR's research reveals some interesting things about the practice and sociology of science.

The PEAR project offers a glimpse of what scientists can expect if they decide to dabble in what is conventionally termed the paranormal. Reasonable scientists cannot rule out the possibility of telekinesis, telepathy and other such 'anomalies' of the mind, simply because there are still such huge gaps in our understanding of consciousness and the brain. But most will say, again reasonably enough, that because all previous attempts to study these putative phenomena have failed to establish anything like a consistent, reproducible and unequivocal body of data, the chances of doing any serious science on the subject are minimal. As John Webster said of witchcraft in the seventeenth century, "There is no greater folly than to be very inquisitive and laborious to find out the causes of such a phenomenon as never had any existence."

In short, they regard effects like these as examples of what American chemist Irving Langmuir famously called pathological science. Experience teaches us that these things, from N-rays to cold fusion and homeopathy, are will 'o' the wispshttp://www2.blogger.com/img/gl.italic.gif: too elusive for fruitful research, and probably imaginary if not downright fraudulent.

At least, this is the standard positivist position. But perhaps a stronger reason why scientists usually steer clear of such things is that it would be professional suicide not to. In a paper called 'The PEAR Proposition'1, published in the Journal of Scientific Exploration (a journal produced by the Society for Scientific Exploration, of which Jahn and Dunne are both officers), the PEAR duo describe the hostility they experienced at Princeton when the lab was set up. They found "covert ridicule,… grudging concession of academic freedom, and… uneasiness in public discussion of the subject." Most scientists find this sort of work not outrageous but simply embarrassing.

Predictably, Jahn and Dunne found it virtually impossible to publish their findings. Their papers, many of which reported the effects of subjects' mental and emotional states on a computerized random number generator, were returned with the comment that they treated an "inappropriate topic". One journal editor said that he would consider the text only when the authors were able to transmit it telepathically.

It is no wonder, then, that those from the academic community who swim in these murky waters are older and already established in their mainstream disciplines. The 'leaders emeritus' of the Society for Scientific Exploration are Peter Sturrock and Laurence Fredrick, emeritus professors at Stanford and Virginia respectively, both with secure reputations in space physics. Not only have such people earned themselves a bit of academic slack (as well as the ability to attract funding) but they cannot simply be cold-shouldered in the way that younger researchers would be. For the same reason, Nobel laureate physicist Brian Josephson has been permitted for years to pursue research on 'mind-matter unification' at Cambridge University amid what one senses to be a mixture of unease and resignation from his colleagues.

'The PEAR Proposition' contains many poignant notes. It shows how awkwardly the habits of academia sit with discussion of the everyday world of human interactions – an unavoidable issue in this line of work. The authors' talk of the "superficial jocularities" of their lab celebrations and the "spontaneous repartee therein" evoke a deeply uncool avuncularity, while Jahn and Dunne hardly do justice to their evidently relaxed working relationship by saying that it "constituted a virtual complementarity of strategic judgment that has triangulated our operational implementation in a particularly productive fashion." It's hard to doubt that the PEAR lab, with its artwork on the walls, its parties and its stuffed animals, was a lot more fun than most research labs. That the attempts to capture this atmosphere in the language of academese are so stilted says a lot about how routinely successful this language is in stripping the research literature of its humanity.

But in the end, this fascinating document undermines itself. When Jahn and Dunne talk about "the tendency of the desired effects to hide within the underlying random data-substructures", and the way their volunteers would often produce "better scores" in their first series of tests, they echo the way that other researchers of pathological science, such as cold fusion and the 'memory of water', betrayed their lack of objectivity with talk of "good runs" and "bad runs".

And perhaps that is the real worry in looking for marginal and unreliable phenomena. Jahn and Dunne are commendably honest about the "bemusing" and "capricious" nature of their measurements, but that only adds to the impression that they decided they were engaged in a battle of wits with nature, who did her darnedest to hide the truth of the matter.

It would be a poorer world that castigates and shuns any researcher who dabbles in unorthodox or even positively weird ideas. But the PEAR experience should be sobering reading for anyone thinking of doing that: it suggests that these things suck you in. You start off with random number generators and unimpeachable experimental technique, and before long you are talking about "an ongoing two-way exchange between a primordial Source and an organizing Consciousness." You have been warned.

Reference
1. Jahn, R. G. & Dunne, B. J. J. Sci. Explor. 19, 195 - 245 (2005).

Sceptical of the sceptics

Here’s the pre-edited version of my March Lab Report column for Prospect. In the course of writing it, I found it necessary to look at some of what has been written and said by the well-known climate-change sceptics, such as those named in the article. This has been interesting. No, let me rephrase that. By a monumental effort of will, I have suppressed the fury, frustration, stupefaction and despair that their comments are apt to induce, and found a precarious way to treat them as ‘interesting’. What I mean by that is that these remarks, coming from people who are undoubtedly smart, are so ill-informed, illogical, prejudiced and emotional that it makes little sense to approach them without trying to get some perspective on what the real issues are. The comments here by Melanie Phillips are a case in point – they are so dripping with furious contempt and scorn that there can be little doubt this touches on something rather personal to her. I suspect that in many of these cases, the issue is that warnings of climate change threaten to compromise a libertarian approach to life, because they imply that there are some freedoms we enjoy now that might have to be curtailed in the future. But I’m guessing, and frankly I don’t find it a very appealing prospect to try to analyse these people.

It would be a quixotic task to try to point out all the errors in the climate-sceptic rants – that would take too long, it would achieve little, and it would be rather boring. What is most striking, however, is that very often these errors are so elementary that they show that these people actually have no interest in trying to understand climate science, or science in general, but just want to find flaws and parade them. That is why the climate-sceptic position is rather repetitive, even obsessive: you just know that they are going to reel out the ‘hockey stick’ argument, even though, first, the criticism of Michael Mann’s work is still very contentious, and second, and most significantly, it is a laughable nonsense to imply that the whole notion of global warming rests on Mann’s ‘hockey stick’. Indeed, the sceptics’ arguments always depend on the notion that we assess global warming, and the anthropogenic contribution to it, by looking at global mean surface temperatures. It must be well over ten years ago now that scientists were explaining that the tell-tale sign of human influence is to be found in the fingerprint of regional differences in the warming trend (and the fingerprint is indeed there).

All the same, I cannot resist pointing out just a few of the idiocies in some of the sceptics’ arguments. This from Phillips has nothing to do with climate change, but tells us at once that this is not someone with more than a cartoon knowledge of the history of science. In lambasting scientists who have found higher than expected methane emissions from plants, she says:
“No doubt Galileo had the same problem when all medieval parchments agreed that the sun went round the earth; or Christopher Columbus, when all navigational maps agreed that the earth was flat.”
Yes, and newspapers print this stuff.
“People say ‘the ice caps are melting’. Well, some are; but others are growing.”
Hmm… aside from the north and south polar ice caps, where are these ‘others’?
“People say ‘the seas are rising’. Well, some are, but others are falling; and where they are rising, the cause often lies in the movement of land rather than any effects of climate change.”
Plain wrong, as simple as that.
“The earth’s climate is influenced by a vastly complex series of factors which interact with each other in literally millions of ways. Computer models, which have created global warming theory, simply cannot deal with all these factors. If over-simplified material is fed into the computers, over-simplified conclusions come out at the other end.”
Melanie Phillips has decided that computer models do not do a good job of modeling the climate system? She is an expert on this? She discounts the endless model verification checks that climate modelers run? On what grounds? Will the Daily Mail let her print any statement she likes (apparently it had no qualms in permitting her to say that most of the Earth’s atmosphere is water vapour).

Nigel Lawson is an interesting case, not least because he used to control the UK’s purse strings, and so you’d like to hope this is a man with a clear head for facts. But if his reasoning on the economy was like his reasoning on climate change, that’s a truly scary thought. Here we have a marshalling of the ‘facts’ that is so selective and so distorted that you wonder just what passes for normal debate in Westminster. Oh, and the occasional lie, such as that the Royal Society tried “to prevent the funding of climate scientists who do not share its alarmist view”. (They did nothing of the sort; Bob Ward of the RS asked ExxonMobil when it intended to honour its promise to stop funding lobby groups who promote disinformation about climate change. There was no suggestion of stopping any funds to scientists.) Lawson’s comment that “the new priests are scientists (well rewarded with research grants for their pains) rather than clerics of the established religions” is about as close as I’ve seen a sceptic come to aping the stock phrases of cranks everywhere, but is also revealing in its implication that Lawson seems to find the idea of experts who know more than him offensive – a common affliction of the privileged and well educated non-scientist.

Alright, enough. I’ll start despairing again if I’m not careful. Here’s the column.
*****************************************************************

The latest report by the Intergovernmental Panel on Climate Change has come as near to blaming global warming on human activities as any scientists are likely to, while adding that its extent and consequences may be worse than we thought. The IPCC has previously been so (properly) tentative that even climate-change sceptics will have a hard time casting them as scaremongerers. So where does this leave the sceptics now?

Many politicians and scientists are hoping they will now shut up. But that’s to make the mistake of thinking this is an argument over scientific evidence.

Consider this, for instance: “As most of you have heard many times, the consensus of climate scientists believe sin global warming. Historically, the claim of consensus has been the first refuge of scoundrels; it is a way to avoid debate by claiming that the matter is already settled. Whenever you hear the consensus of scientists agrees on something or other, reach for your wallet, because you're being had. Let's be clear: the work of science has nothing whatever to do with consensus. Consensus is the business of politics. In science, consensus is irrelevant.”

This is from Michael Crichton – for the author of Jurassic Park has been giving high-level speeches about the ‘myth’ of climate change, and has even been summoned as an ‘expert witness’ on the matter by the US Senate. We need only concede that the Earth orbits the Sun and that humans are a product of Darwinian evolution to see that Crichton is not so much indulging in sophistry as merely saying something stupid. But because he is a smart fellow, stupidity can't account for it.

That's really the issue in tackling climate-change sceptics. There is no mystery about the way that some critics of the IPCC’s conclusions are simply protecting vested interests – ExxonMobil’s funding of groups that peddle climate-change disinformation, or the US government's extensive interference in federally funded climate science needs no more complex explanation than that. But this isn't true 'scepticism' – it is merely denial motivated by self-interest.

The real sceptics – strange bedfellows such as David Bellamy, Nigel Lawson, Melanie Phillips, a handful of real scientists, and Crichton – are a different phenomenon. For them there is a personal agenda involved. It’s less obvious what that might be than in, say, the comparable case of the ‘sceptics’ who denied the link between HIV and AIDS in the early 1990s. But what is immediately evident to the trained ear is that the sceptics’ denials carry the classic hallmarks of the crank – a belief that one's own reasoning betters that of professionals (even though the errors are usually elementary), a victim mentality, an instant change of tack when convincingly refuted, and (always a giveaway) a historically naive invocation of Galileo’s persecution. Of course, some of them simply tell outright lies too.

Bjorn Lomborg is a slightly different matter, since his objections focus less on denying climate change and more on denying the need to do anything about it. Nonetheless, although the economic arguments are complex, Lomborg's rhetoric – for example, suggesting that because climate change is less pressing than, say, AIDS, we should ignore it – is simplistic to a degree that again does not equate with his evident intelligence.

Economics is indeed going to be the future battleground. Yes, the argument goes, so climate change is happening, but that doesn’t mean we have to do anything to prevent it. Far better to adapt to it. This line has been pushed by heavier hitters than Lomborg, such as the eminent economists William Nordhaus at Yale and Partha Dasgupta at Cambridge, who reject the economic analysis of Nicholas Stern. The argument has some force in purely economic terms – which is perhaps not the foremost consideration if you live in coastal Bangladesh or on the Marshall islands – but it will take a lot of either faith or foolishness to let economics alone guide us into uncharted waters where we cannot rule out mass famine, decimation of biodiversity and unforeseen positive feedbacks that accelerate the warming. That’s not what economics is for.

Yet economists are right to say that we need informed rather than knee-jerk responses, and that these will surely involve compromises rather than dreaming of arresting the current trends. But by turning now to economics, however, the celebrity sceptics will only betray their agenda. It’s time to seek more reasoned voices of caution.

*****

How long before we witness the rise of the bird flu sceptic? (Matthew Parris has already staked his claim.) They could be right in one sense – according to Albert Osterhaus, chairman of the European Scientific Working group on Influenza (ESWI), “Isolated outbreaks of avian influenza in Europe are a problem in terms of economy, animal welfare and biodiversity, but the threat to public health will probably be manageable.” But they’ll almost certainly be wrong in another. The H5N1 virus is all too often portrayed as a bolt from the blue, like a bit of really rotten luck. In truth it’s illustrative of a fact of life in the viral world, where, to put it bluntly, shit happens. Last November, leading US virologists Robert Webster and Elena Govorkova stated baldly that “there is no question that there will be another influenza pandemic some day.” The ESWI agrees, and warns that Europe is ill prepared for it. Even if H5N1 doesn’t get us (by mutating into a form readily transmitted between humans), another virus will. Flu viruses are legion, and unavoidable. Here, at least, is one threat for which mitigation, not prevention, is the only option. H5N1 seems less transmissible in warmer weather, but one hopes even climate sceptics won’t see that as a point in their favour.

Space wars

I have an editorial piece on news@nature on China’s recent missile destruction of a satellite. The commentary in the scientific press has had much to say about the possible hazards of the space debris this created, but less about the implications and significance of the act for space militarization. This is my take on that.

Published online: 24 January 2007; doi:10.1038/news070122-8

muse@nature.com: A dangerous game in space
Is China's satellite zapping simply old-fashioned sabre-rattling? Or is it a rational step to restrict the use of space weapons?

How do you reconcile China's shooting down of a satellite earlier this month with the subsequent insistence by its foreign ministry spokesman, Liu Jianchao, that China opposes military competition in space?

China has not yet explained its objectives. But the action makes perfect sense in the context of game theory, the conventional framework for analysing conflict and cooperation.

Put simply, if you want to spur nations to collaborate in curbing space militarization, good intentions are not enough. You need to show that you can get tough if the need arises.

A benign interpretation of China's action, then, is that it might accomplish what years of talking have not: force the United States to negotiate an international treaty on space weaponry. Does China have such a specific goal in mind? Or does it merely wish to leave its options open in dealing with rebellious Taiwan?

These are dangerous questions. But it is worth bearing in mind that the Chinese test is at least consistent with a completely rational approach to securing international enforcement of the peaceful use of space.

The classic scenario to explore cooperation between nations using game theory is the Prisoner's Dilemma. Here, two players are each given the choice of cooperating with each other or betraying the other person (defecting), with different rewards or penalties for each potential outcome. Mutual cooperation is more beneficial to both players than is mutual defection. But temptation gets in the way: the player who defects against a cooperator wins the biggest prize of all.

Although the rational strategy in a one-off bout of the Prisoner's Dilemma is to defect, it runs against self-interest in repeated rounds. Then, the most successful way to play is often a 'tit-for-tat' strategy, in which a player will initially cooperate, then respond in kind to the other player's previous choice.

Robert Axelrod, the political scientist at the University of Michigan in Ann Arbor who pioneered the study of Prisoner's Dilemma strategies, points out that in the real world, players who follow the tit-for-tat strategy need to cultivate a reputation for toughness. Other players must know that provocation will be met with retaliation. In the case of China, the message could be that the militarization of space will not be prevented simply by condemning it, but rather by showing that you can and will play the game if necessary.

The real world is, of course, not a computer simulation, in which the agents are rational. Although game theory is studied in defence-policy circles, no one denies that it gives little more than a cartoon picture of international relations.

But in this case the model fits. China and Russia have been calling for years for a treaty to constrain space weapons. Not only have these calls been ignored by the United States, but last year the White House issued perhaps the most aggressive policy statement about space since the chilliest days of the Cold War. It stated baldly that the United States "will oppose the development of new legal regimes or other restrictions that seek to prohibit or limit US access to or use of space."

The document not only asserted the United States' right to pursue its "national interests" (including "foreign policy objectives") by preserving its "freedom of action" in space, but also threatened to deny adversaries the same freedom.

Is China an 'adversary'? Friendly overtures between NASA and the China National Space Administration might suggest otherwise, but NASA is not the Pentagon. The United States is not only still pursuing its national missile-defence programme but is also developing laser-based weapons that can knock out satellites from the ground or aircraft. It is hardly surprising then, that anyone who is serious about stopping such a relentless and defiant pursuit of space weaponry through international agreement will deploy the bullish lessons of game theory.

This is not to say that the Chinese test is defensible. It is understandable that its neighbours, such as Japan and Australia, should be dismayed by it, and that Taiwan should regard it as an act of aggression. And there is every chance that the United States will interpret it as the opening shot of an arms race rather than as a summons to the negotiating table.

China might think that keeping a strong hand relies on not making its intentions too explicit. All the same, there is a difference between developing space weapons at the same time as opposing the militarization of space, and developing weapons while refusing to ban them. Which would you prefer?

Nanotech rolls on

There's a nice little paper about to appear online in Nature Nanotechnology (advance online publication, doi:10.1038/nnano.2006.210). Christian Joachim and his colleagues have made a molecule consisting of a two wheels 8 Å wide on an axle. The wheels are in fact three-bladed paddlewheels, which may rotate by a third of a turn when pushed with the tip of a scanning tunnelling microscope. This sounds rather like Jim Tour's nanocar, in which the wheels are fullerenes. That's altogether a more sophisticated contraption: a four-wheeler with a full chassis, shown in the picture above. But Jim could only infer rolling from the nature of the path that the cars took when pulled with the STM. It looked pretty persuasive to me, especially as tripod cars could only go in circles. But Christian's work has more direct proof of rolling. By looking closely at the way the two-wheeled molecule moves, he and his colleagues can distinguish between simple hopping between the grooves of the atomic corrugations on the metal surface, smooth pushing when the corrugation is very shallow, and jumps due to rotation of one wheel by 120 degrees. Only one wheel turns at a time, so in that case the molecule pivots as it is pushed.

Water in biology

I have started a new blog called Water in Biology, which does what it says on the can. My hope is that it will act as a forum for presenting and discussing new research on the roles of water in the living cell. It seems that barely a week passes without something new and interesting coming out in this area, and I’m sure I’m seeing only a fraction of it. This will hopefully be a way of keeping track of what is out there, and hearing some informed opinions about it. It’s a controversial area, and I’m well aware that there are risks in setting this up: the behaviour of water in biological systems has been something of a magnet for weird and often not so wonderful theories. I hope to keep them at a distance. No doubt it will seem terribly elitist to the likes of the homeopathy enthusiast who expressed such disappointment on amazon.com about my book on Paracelsus, but I’d respectfully suggest that if homeopathy, Jacques Benveniste’s digital biology, or Masaru Emoto are your bag, this site might not be for you. (I’m sure there are lots of others that are.)

Dark matter, memories and chimeras
[This is my Lab Report column for the forthcoming (February) issue of Prospect.]

Cosmic bones
The universe has had its first X-ray, and the skeleton looks much as expected. It is made of mysterious dark matter, which accounts for five sixths of the matter in the universe. It has been mapped out in a project called the Cosmic Evolution Survey (Cosmos), which pieced together more than 500 images from the Hubble space telescope to trace out the fine filaments of dark matter threading through deep space. These act like flypaper for ordinary matter, concentrating it into stars and galaxies.

In effect, Cosmos has revealed the hidden framework behind the entire visible world. Among other things, it’s another reason to be thankful that Nasa was persuaded not to leave the ageing Hubble to decay, rather than risk another shuttle-borne service mission.

Dark matter can’t be seen directly—that’s why it is dark—and isn’t made from any known subatomic particles. But we know it’s there because of the gravitational tug it exerts on visible matter. It was first postulated to explain why galaxies don’t fly apart as they rotate—but not everyone was convinced it existed until a study last year revealed it apparently balancing an otherwise lopsided spread of visible matter in a collision between two galaxies.

The Cosmos team mapped the distribution of dark matter over a big chunk of the universe by looking at the way it bends light from very distant galaxies behind it. The densest clumps of dark matter, where filaments intersect, mostly match the positions of visible galaxies and gas, as they should. But there are a few regions of dark matter without visible matter and vice versa—bones without flesh, and flesh without bones, so to speak. That wasn’t predicted and can’t easily be explained. Might there be entire galaxies made only of dark matter? It seems more likely that the discrepancies are just errors in the data, which depends on a tour-de-force of astronomical measurement.

It remains something of a scandal that we know nearly nothing about the stuff these cosmic bones are made from (our ignorance of the “dark energy” that outweighs dark matter by a factor of three is even more profound). But that’s modern cosmology for you: the harder you look, the more puzzling it gets.

Forgetful computers
Another well-hidden scandal lies in the guts of modern computers. Imagine that your piano had to be retuned from scratch every time you wanted to play, or your television set had to be retuned to the broadcast frequencies whenever it was switched on. This is the way computers work: you turn on and wait for minutes as the working memory, or random access memory (RAM), relearns how to work by reading the “manual” held on the hard disk. Actually, it’s even worse. The RAM then forgets everything you tell it within a microsecond—or would do if its memory cells were not refreshed thousands of times a second. That’s why, if the power turns off unexpectedly, all your unsaved data is lost.
It’s also why the RAM sucks all the juice from laptop batteries within hours.

All this could be changed with a technology that is already commercially available but still too expensive to go into your computer. Non-volatile RAM is a memory that, once loaded with data, holds onto it indefinitely without needing any power. With such a memory, a computer wouldn’t need a hard disk at all, and would be ready to use the moment you switched on. Various forms of non-volatile RAM are being developed, the most advanced being ferroelectric RAM (FeRAM), in which the memory elements are a little like magnets with poles oriented by electric rather than magnetic fields.

FeRAM is big in east Asia—the leaders include Samsung, Matsushita and Fujitsu. There’s even a small FeRAM in the Sony Playstation 2. But big, computer-style memories remain too expensive to make this way, and so FeRAM is currently relegated to low-tech applications such as smart cards for Japanese railways. They can be read from six inches away, however, so you don’t even need to get the card out of your bag.

Dr Moreau visions
The UK Human Fertilisation and Embryo Authority recently concluded that “there needs to be a full and proper public debate and consultation” about whether it should licence the creation of animal-human chimeric cells, for example with human DNA housed by nonhuman cells. The HFEA wisely avoided a snap decision in response to the opposition to such cells in a government white paper. The issue, as it says, is “far from black and white.” But the white paper’s recommendations seem to suffer from visions of Dr Moreau. Xenotransplants of animal organs and tissues into human patients have been happening for years, but the popular idea, peddled by the human genome project, that genes represent the sacred core of humanity has apparently created a sense that they are untouchable.

While there are ethical difficulties with chimeric cells, the medical benefits could be huge. Stem cells can be cultivated from embryos, but human eggs are hard to acquire for this. Animal eggs carrying human DNA would be more readily available, and could usher in all kinds of stem-cell therapies. The stem cells wouldn’t be “half-animal” in any meaningful sense, any more than a molecule taken from a human cell is different from an identical one taken from an animal. The HFEA aims to complete its consultation in the autumn. UK legislation in this area has been sensible and permissive so far, but stem-cell scientists are nervous that this time the yuck factor is about to kick in.

You couldn't make it up

"School chemistry ban for teen tartan terrorist". There I was all ready to sink my teeth into this great headline from the Scottish tabloid the Daily Record, only to discover that they made it up.

The story is that the "tartan terrorist" 16-year-old Jamie Hoggan, who has been placed in Polmont young offenders' unit for firebombing council offices in Alloa last August, was being denied chemistry and physics lessons while being sent his homework by his school, the Alloa Academy. Young Jamie apparently wants to "drive the English out of Scotland" (I know, but this is a 16-year-old lad who has presumably watched Braveheart thinking it was history). According to the Daily Record, a "source" said that "science was out of the question while he was in Polmont because of what went before." The notion that one can't make bombs without GCSE chemistry, and that one becomes an expert bomb-maker with it, was so silly that this seemed to demand some comment. (And what was the problem with physics? That he'd nuke the council instead?)

But it was all fabrication. A tired-sounding head at the Academy told me the story was "complete rubbish", before referring me to a nice woman at Corporate Affairs who said she only held back from writing to the Record to, er, set the record straight, by the understandable fear that the newspaper would then run the headline "School chemistry lessons for teen tartan terrorist". A victory for common sense, then, and a big boo to silly tabloids. And Jamie apparently hopes to become a forensic scientist – good luck to him!

Looking for ways to fill up your Christmas holiday?

Then why not heed these shameless plugs for my friends? John Whitfield’s book In The Beat of a Heart is a fabulous read – one of the best science books of 2006, though it’s not received the UK push it deserves. If this doesn’t get shortlisted for next year’s Aventis Prize, there’s no justice. It explains the notion of metabolic scaling in biology – the idea that one can develop a unified view of life by considering the way energy requirements depend on size. Like Nick Lane’s Power, Sex, Suicide, it’s a timely reminder that there’s more to life than genes.

And if you’re in the Lincoln area, pay a visit to Lindsay Seers’ exhibition The Truth Was Always There, which explores connections between magic and alchemy, Lincoln cathedral, Robert Grosseteste, Temple Bruer and John Dee. This is part of an ongoing project by Lindsay, comprising five ‘biographical’ films that document a strange past and an obsession with becoming a human camera. There’s a forthcoming book, called (I think) Human Camera, that records these films and narratives. Yes, I admit that I’m a contributor – but that’s because I think it is a wonderful project. The exhibition runs until late January.

Pushing protons around

[This is the pre-edited version of my Crucible column for the February issue of Chemistry World.]

Life is pretty simple, when you come down to it. It’s a matter of shovelling stuff from one side of a wall to the other – the ‘stuff’ being hydrogen ions, and the wall a cell membrane. The biochemistry that follows from this is fearsome, but at root life is driven by piling up hydrogen ions and then letting them flow, like water released from a dam.

This imbalance of protons across a membrane creates a so-called protonmotive force. It is generated by proton pumps: proteins that can actively move protons ‘uphill, against a concentration gradient. They need energy to do that, and in the light-harvesting chloroplasts of plants that comes ultimately from sunlight, which sets an electron jumping between molecules. In our mitochondria the energy is generated by reactions that break down carbohydrates. In either case, the protonmotive force is used to power the enzyme ATP synthase, which rotates like a water wheel as it lets protons flow through, producing energy-rich ATP in the process.

So if that’s life in a nutshell, these proton pumps clearly need to be efficient and smooth-running pieces of molecular machinery. Even so, the ingenuity life displays in conducting and controlling the movement of protons is breathtaking.

That life exists in water is a boon from the outset – because one of the things water does that other liquids cannot is transport protons rapidly. The hydrogen ion travels faster than other small cations in water by hopping along hydrogen-bonded chains of water molecules: rather like a Newton’s cradle, a proton hits one end of the chain and almost at once (figuratively speaking) another proton pops off the other end. This hopping, called the Grotthuss mechanism after the nineteenth-century German scientist who proposed the basic idea, is exploited by biomolecules to shift protons. Some proteins, such as the light-powered bacterial proton pump bacteriorhodopsin and some cytochromes, are threaded by ‘water wires’, strings of water molecules that act as proton-conducting pathways.

A water wire also winds through the membrane protein aquaporin, which transports water across cell walls. But for aquaporin, letting protons through could be disastrous, as it would disrupt the delicate balance of pH and charge across the membrane. So it has to achieve the seemingly impossible feat of transporting water but not hydrogen ions. How it does so is still not fully clear, but one idea is that the water wire contains a defect: hydrogen-bonding to the amino-acid residues within the pore forces two waters in the chain to sit ‘back to back’, so that a proton can’t jump between them.

That would be an extraordinarily delicate feat of molecular manipulation. But it is possibly trumped by the latest revelation about why proton pumping works so well. Magnus Brändén of Stockholm University and his colleagues (Proc. Natl Acad. Sci. USA, doi:10.1073/pnas.0605909103) say that there are, in effect, little proton circuits written onto the surfaces of cell membranes that help guide protons from a transporter – a pump protein – to molecules that exploit the protonmotive force, such as ATP synthase. The image, then, is not that of a pump spouting out protons into the cytoplasm, where some gradually drift over to where they’re needed; instead, the protons pop out of the pump’s mouth and stick to the membrane before proceeding to hop across it. That way, fewer get lost.

In effect, then, the membrane lipids act as proton-collecting antennas – rather as accessory pigments serve as light-harvesting antennas to shunt light energy onto the photosynthetic reaction centre in photosynthesis.

This idea has been mooted for years, but Brändén and colleagues have pinned it down by looking at the protonation of a single fluorescein dye molecule embedded in the wall of liposomes (closed, cell-like assemblies of lipids). Protonation changes the dye’s fluorescence, and so fluctuations in its brightness can be related to the rate of proton exchange with the surroundings. The researchers show that this happens at a faster rate than would be expected if protons were just being exchanged with the water – so long as the lipid head groups can themselves be protonated. The lipids gather protons and pass them around.

It’s a reminder that molecular biology isn’t just about the cleverness of proteins and nucleic acids. Even the molecules often assumed to be just part of the background or the scaffolding, such as lipids and water, may have inventive roles to play.

Mining the moon for all it’s worth

It's one of the curious characteristics of space exploration that the usual stringent hurdles for science news stories are nowhere to be seen. Whereas normally science reporters, enthusing breathlessly about new insights into, say, the origin of the universe, face an editor's dismissive "why do we care?", with space stories it is enough that someone did something or other up in space – hit a gold ball, say, or flew a shuttle mission without blowing up. True, if the story involves an unmanned spacecraft doing something like landing on a comet, then there might be some sales work to be done. But if there's a human inside, it doesn't much matter what he's up to – just stick it on the page.

That principle even extends to stuff that hasn't actually been done, but "will" be. We're going to send people to Mars! We're going to build a moon base! Yes, it's true that we've not even managed to finish off a useless piece of manned space junk floating inanely in Earth orbit, but look, we've learnt from our mistakes. (What we've learnt, it seems, is simply to make the claims bolder.) When something is going to be done in space, all critical faculties vanish. We're going to grow crystals there, or plants – and no matter whether that's really going to tell us anything worthwhile. And now the latest fad for which the media seems determined to fall hook, line and sinker is mining the moon for helium-3.

Helium-3, you see, is a wonderful clean fuel that will power our planet through nuclear fusion. Just a shuttle-load will power the USA for a year. And it's just waiting up there in the lunar soil for us to go and collect it.

Well actually, it isn't – we'd have to strip-mine vast areas of the moon to get at it. And while discussions of remote oil resources on Earth routinely have to run the gauntlet of hard-headed economical cost-benefit analysis, no one seems to care very much whether there is any justification for thinking that sending trucks to the moon to pick up this 'fuel' is really going to save anyone any money. All you have to do is talk about lunar helium-3 as a "cash crop".

And on top of that, there's the small difficulty that no one has ever produced energy from nuclear fusion in a commercially viable and sustainable way, and that even the most optimistic estimates put that goal 50 years distant. There's a good chance that it might not happen before 2100 (although making technological projections that far ahead is a bit pointless anyway).

The point is, of course, that these bogus utilitarian rationales are routinely trotted out in defence of a programme of human space exploration that is at root ideological. It's fine to believe that there is an intrinsic value in sending humans to other worlds (I happen to disagree, at least in the present state of affairs in space travel); but let's at least be honest about it. The magic word "resources" was invoked the last time I questioned the value of manned spaceflight (see here and here). But as I'd expected, when it came down to it what that meant was stuff like silicon – as though we are currently facing a silicon shortage here on our rocky planet.

So please – no more helium-3 as the justification for a moon base. That’s truly grasping at straws.

Treacherous beauty

[This is a review of a book on the zoological art of Ernst Haeckel, to be published in Nature.]

Visions of Nature: The Art and Science of Ernst Haeckel
Olaf Breidbach
Prestel, Munich, 2006

When Nature’s millennial issue of 1900 listed the most important scientists of that age, there was only one German biologist among them: Ernst Haeckel, professor of zoology at the University of Jena. Reckoned to have been instrumental to the introduction of Darwinism in Germany, and responsible now for inspiring generations of scientists with his stunning drawings of the natural world, Haeckel still retains a claim to such recognition. He is perhaps most widely known now as the author and illustrator of Art Forms in Nature, a series of plates published between 1899 and 1904 that showed the marvellous forms and symmetries of creatures ranging from radiolarians to antelopes.

But few scientists of his time are more complicated. He was the archetypal German Romantic, who toyed with the idea of becoming a landscape painter, venerated Goethe, and was prone to a kind of Hegelian historical determinism that sat uncomfortably with Darwin’s pragmatic rule of contingency. Haeckel’s view of evolution was a search for order, systematization and hierarchy that would reveal far more logic and purpose in life than a mere struggle for survival. His most famous scientific theory, the so-called biogenetic law which argued that organisms retread evolutionary history as they develop from an egg (‘ontogeny recapitulates phylogeny’), was an attempt to extract such a unifying scheme from the natural world.

It can be argued that this kind of visionary mindset, when it creates strong preconceptions about how the world ought to be, does not serve science well. Haeckel supplies a case study in the collision between Romanticism and science, and that tension is played out in his illustrative work. Olaf Breidbach’s text to this lovingly produced volume never really gets to grips with that. It has a curiously nineteenth-century flavour itself, declining to grapple with the difficult aspects of Haeckel’s life and work.

Here, for instance, is a proposition: Ernst Haeckel’s influence on fin-du-siècle German culture was pernicious in its promotion of a ‘scientific’ racist ideology that fed directly into Nazism. That case has been made (by historian Daniel Gasman in particular), and while it can be debated, Breidbach goes no further than to admit that Haeckel became a ‘biological chauvinist’ during the First World War, and that ‘sometimes the tone of his writing was overtly racist.’ Breidbach admits that this is not a biography as such, but an examination of Haeckel’s visual heritage. Yet one could argue that Haeckel’s dark side was as much a natural consequence of his world view as was Art Forms in Nature.

The claim that Haeckel doctored images in order to make them fit with a preconceived notion of how biology works is harder to ignore in this context. Even in his own time he was accused of that (particularly by his rival Wilhelm His), and to my eye the evidence (see Nature 410, 144; 2001 and Science 277, 1435; 1997) looks pretty strong. But Breidbach skates over this issue, alluding to the allegations only to suggest that the illustrations ‘instructed the reader how to interpret the shapes of nature properly’. Well, indeed.

On the whole, though, Breidbach simply explains Haeckel’s reliance on image without assessing it. Haeckel’s extraordinary drawings were not made to support his arguments about evolution and morphogenesis; rather, they were the arguments themselves. He believed that these truths should be apparent not by analysing the images but simply by looking at them. ‘Seeing was understanding’, as Breidbach says. If that’s so, it places an immense burden of responsibility on the veracity of the images.

This is the nub of the matter. Breidbach suggests that Haeckel’s drawings are schematic and that, like any illustrator, Haeckel prepared them to emphasize what we are meant to see. But of course this means ‘what Haeckel has decided we should see’. Quite aside from whether he hid nascent appendages that challenged his biogenetic law, consider what this implies for the plates of Art Forms in Nature. They are some of the most beautiful illustrations ever made in natural history – but it seems clear now that Haeckel idealized, abstracted and arranged the elements in such a way that their symmetry and order was exaggerated. They are pictures of Platonic creatures, the ideal forms that Haeckel intuited as he gazed into his microscope. Their very beauty betrays them. They are, as Breidbach says (but seemingly without critical intent), ‘nature properly organized.’ In this way ‘the labour of the analyst was replaced by the fascination of the image’. Absolutely – for ‘fascinate’ used to mean ‘bewitch’.

It is not as if Haeckel did not have the alternative of photography – for microphotography was used as early as the 1850s. Breidbach recapitulates the arguments against an over-reliance on the veracity of photography (these ideas have been much discussed by cultural critics such as Vilém Flusser), pointing out that what one sees is determined by the technology. That is true, and it is apt to give photography a false authority. But are hand-drawn images really any better – let alone those rendered with such apparent skill and realism that their schematic nature is disguised? Indeed, Haeckel felt compelled in 1913 to publish Nature as an Artist, a series of photographs of his subjects which, he said, demonstrates that ‘there can be no talk of reconstruction, touching up, schematisation or indeed forgery’ in his drawings of the same. It was a remarkable work in its own right, but leaves us wondering why Haeckel did not use photos in the first place.

Another danger of such imagery is that it is prone to reflect the artistic styles of the day. Haeckel’s drawings fed into the florid, nature-inspired designs of the Art Nouveau and Jugendstil schools – but he was more influenced than influence. His medusae look like William Morris prints precisely because they have had that visual aesthetic imprinted on them. Breidbach says that for Haeckel, as for Goethe, ‘aesthetics is the foundation of his view of nature.’ But is that a good thing? As Ernst Gombrich has pointed out, artistic styles create unconscious biases and errors: when Gombrich speaks of the artist who ‘begins not with his visual impression but with his idea or concept’, it might as well be Haeckel he is talking of. And what happens when the cultural aesthetic moves on – does nature have to follow suit? Breidbach points out that, by using the visual language of his age, Haeckel helped to make science accessible to the public. But 20 years later, modernism had rendered his arabesque style old-fashioned.

As director of the Ernst Haeckel Museum at Jena, Breidbach has unequalled access to Haeckel’s notes and sketchbooks, and he makes good use of them. But perhaps for that very reason he felt unable to dig too deeply into the problematic areas his subject raises. (Haeckel is clearly still very much a legend at Jena, where his brain was cast in silver.) So although this is undoubtedly a gorgeous book, and the questions it raises are fascinating, I can’t help feeling that it represents an opportunity missed.

Tainted by association?
[This is the pre-edited version of my latest muse column for news@nature.]

Richard Doll's links with industry are disconcerting but hardly scandalous. And they don't make him a villain.

Few things will polarize opinion like the defamation of a recently deceased and revered figure. So the tone of the debate (here and here and here and here) that has followed the accusation that Sir Richard Doll, the British epidemiologist credited with identifying the link between smoking and lung cancer in the 1950s, compromised the integrity of his research by receiving consultancy payments from the chemicals industry, should surprise no one.

On the one hand, the disclosure of Doll's contracts with the likes of Monsanto and Dow Chemicals have provoked howls of outrage and accusations that his studies of purported links between the companies' products and cancer were nothing less than a cover-up. Much of this is crude conspiracy-theorizing; but there are also more weighty critics. Andrew Watterson, a professor of occupational and environmental health at the University of Stirling in Scotland, has said that "Doll's work… has limited the capacity of the UK over decades to take action on occupational and environmental carcinogens as quickly as it should have… His lack of transparency on and financial relationship with companies have seriously damaged the credibility of aspects of his research."

On the other hand, voices that will be no doubt dismissed by Doll's attackers as those of the 'establishment' have risen to defend his reputation. An editorial in the Times calls the charges "a cheap shot" made by "grave robbers". This, the newspaper intones gravely, is "a sad act of character assassination by people who should know better." Several leading UK scientists have written to the Times saying that "we feel it is our duty to defend Sir Richard's reputation and to recognise his extraordinary contribution to global health."

The situation is perhaps best exemplified by a leader headline in the Observer newspaper: "Richard Doll was a hero, not a villain." All of which brings to mind the comment of Brecht's Galileo: "unhappy is the land that needs a hero."

Unhappy we are indeed, if we cannot accommodate in our pantheons the complexities of real people. And while the collaborations of academe and industry certainly create tensions and problems, it achieves nothing to pretend that they ought not to exist.

Doll's consultancy work is not immune to criticism even by the standards of his time. But the suggestion that his research is invalidated, and his character besmirched, by such conflicts of interest (as they would now certainly be regarded) is one that smells of piety rather than an evaluation of the facts.

Here, then, is the case for the prosecution. Doll proclaimed that Monsanto's Agent Orange posed no carcinogenic hazard while receiving consultancy fees of $1000-1500 a day from the company for nearly 30 years. He compiled a review on behalf of ICA, Dow Chemicals and the Chemical Manufacturers' Association in their defence against claims of cancer induced in workers by exposure to vinyl chloride, for which he was paid £15,000. (Monsanto was also a big producer of vinyl chloride). And he argued that there was little basis for the idea that asbestos is a major health risk, while pursuing a long-term consultancy relationship with the UK's leading asbestos manufacturer Turner & Newall, which later donated £50,000 to set up Green College in Oxford, a medical school of which Doll was a founder and the first warden.

All of this would indict any researcher today who failed to declare such conflicts of interest. Doll was in fact rather inconsistent about such declarations – he made no secret of some of his links to industry, but the Monsanto connection was not disclosed until a court case over vinyl chloride in 2000. In any event, until the 1980s there was no expectation that academics should make this sort of paid work public, and so no reason to expect Doll to have been systematic about doing so.

That is one of the main lines of defence for Doll's supporters: it is absurd to judge him by today's standards, a notorious way of vilifying historical figures and events. It's a fair point, although we have to remember that we're talking here about the 1980s, not the nineteenth century. It doesn't take a great deal of insight to see that being paid by a company while assessing their products is not ideal.

Yet there is no obvious reason to regard this as venal or cynical on Doll's part. Using contract money to help set up a college does not seem particularly blameworthy. Doll donated other fees to charities such as the Medical Foundation for the Victims of Torture.

He gives every impression of being a man conducting his business in an environment that had not thought very hard about the proprieties of industrial research contracts. If he did not think too hard about it either, that does not make him a villain.

And he seems very much a man who knew his own mind. Overcoming industry's resistance to the link between smoking and cancer is hardly the act of someone in the pocket of corporations. Yet his scepticism about the effects of secondary smoking speaks of a man who was not turned into an ideologue by his conclusions.

On this count, we must remember that no evidence has been presented that Doll's conclusions were biased by his contracts. It's hard to see how that could be established either way; but certainly it is unfair to turn Doll into a yes-man bribed by industry.

Indeed, if anything, the affair has served to remind us how manipulative these industries could be. Peto says that Doll came under pressure (which he resisted) from the asbestos manufacturers not to publish any evidence of the harmful effects of their product. They claimed it would damage the national interest by undermining this important industry, and even threatened legal action. The Asbestosis Research Council, founded by Turner & Newall and others in 1957, has been accused of suppressing evidence of the dangers of asbestos, for example by vetting and censoring research on the topic [1].

A curious aspect of this whole business, not mentioned at all in media reports, is that it is all yesterday's news anyway. Doll's links with industry were reported by British newspapers after being discussed in an article published online on 3 November by the American Journal of Industrial Medicine [2]. But the information in that article on Doll's connections with Monsanto, Dow, Turner & Newall and others had all been documented in 2002 by one of the authors, Martin Walker [3]. In that latter paper, Walker states that Doll "has never made any secret of the fact that he has been funded by industry for specific research projects."

Quite aside from demonstrating the media's ability to generate its own content, this fact is notable because the American Journal of Industrial Medicine paper aims not to denigrate Doll but to call for a tightening of policies governing disclosures of interest today. There's still plenty of work to be done (see here and here) in that respect. We should recognise the shortcomings of the past, and move on.

References
1. Tweedale, G. Am. J. Ind. Med. 38, 723-734 (2000).
2. Hardell, L. et al. Am. J. Ind. Med. advance online publication (2006).
3. Walker, M. J., http://www.dipmat.unipg.it/~mamone/sci-dem/contri/walker.htm.

Looking for Turing’s fingerprints

Here is the pre-edited version of my Crucible column for the January 2007 issue of Chemistry World.There’s considerably more on this issue in the forthcoming reworking of my 1999 book The Self-Made Tapestry. OUP will publish this as a series of three books, probably beginning in late 2007.

How did the leopard get its spots? Recent research supports an idea first suggested by legendary code-breaker Alan Turing.

After another long time, what with standing half in the shade and half out of it, and what with the slippery-slidy shadows of the trees falling on them, the Giraffe grew blotchy, and the Zebra grew stripy, and the Eland and the Koodoo grew darker, with little wavy grey lines on their backs like bark on a tree trunk; and so, though you could hear them and smell them, you could very seldom see them, and then only when you knew precisely where to look.

Kipling’s Just So story of how the animals of Africa obtained their distinctive marking patterns is a fine example of Lamarckism – the inheritance of environmentally acquired characteristics, in this case via what seems to be a kind of tanning process imprinted with the shadows of trees. But the explanation that his contemporary biologists would have offered, invoking Darwinian adaptation (the markings being assumed to serve as camouflage), was arguably little more than a Just So story too. It explained why a marking pattern, once acquired, would spread and persist in a population, but it could say nothing about how such a pattern came to be, either in evolutionary terms or during the embryonic development of a particular zebra, giraffe or koodoo.

It seems clear that this is not merely a genetic painting-by-numbers: the markings on two animals of the same species are recognizably alike, but not identical. How do the melanin pigments of animal pelts get distributed across the embryonic epidermis in these characteristically blotchy ways?

The favoured explanation today invokes a mechanism proposed in 1952 by the British mathematician Alan Turing, two years before his suicide by cyanide. Turing is best known for his work on artificial intelligence and the concept of a programmable computer, and for his wartime code-cracking at Bletchley Park. But his paper ‘The chemical basis of morphogenesis’ was something else entirely. It was an attempt to explain how the development of a body plan kicks off.

The fundamental question is how a spherical ball of cells ends up as a shape in which different cells, tissues and appendages are assigned to different locations. How does the initial spherical symmetry get broken? Turing’s comment reminds one of the old joke about physicists over-simplifying biology: “a system which has spherical symmetry, and whose state is changing because of chemical reactions and diffusion, will remain spherically symmetrical for ever… It certainly cannot result in an organism such as a horse, which is not spherically symmetrical.”

Turing proposed a set of differential equations which explained how molecules determining cell fates, called morphogens, might diffuse through a spherical body and induce (bio)chemical processes. Such a scheme is now called a reaction-diffusion system. The patterning results from competition between an autocatalytic reaction, which amplifies random chemical inhomogeneities, and diffusion, which smoothes them out. Turing’s calculations performed by hand (his notion of a digital computer was then barely realized) showed that patchiness could emerge. But it wasn’t until 1972 that Hans Meinhardt and Alfred Gierer in Germany clarified the essential ingredients of Turing’s model. The chemical patterns arise in the presence of an autocatalytic ‘activator’ molecule, and an inhibitor molecule that suppresses the activator. If the inhibitor diffuses more rapidly than the activator, then the concentration of activator is enhanced over short distances but lowered by the inhibitor over longer distances. This gives rise to islands of activator surrounded by regions where it is suppressed.

Calculations showed that this ‘activator-inhibitor’ mechanism could create orderly patterns of spots and stripes, more or less equally sized and equidistant. That brought to mind the leopard’s spots and the zebra’s stripes. But is such a system anything more than a pretty mathematical fiction? That wasn’t clear until 1990, when a team led by Patrick De Kepper at the University of Bordeaux identified the first chemical Turing pattern, using a reaction that, when well mixed, oscillated between yellow and blue states. This was closely related to the Belousov-Zhabotinsky (BZ) reaction, which was known since the 1960s to generate travelling chemical waves. The BZ reaction is a reaction-diffusion system, but does not itself produce stationary Turing patterns, because the relative diffusion rates of the reactants don’t fit Turing’s model.

Are patterns in the living world really made this way? Theoretical activator-inhibitor systems have now been able to provide very convincing mimics of a wide range of animal markings, from the reticulated mesh of the giraffe’s pelt to the crescent-shaped rosettes of the leopard and jaguar, the spots of the ladybird and the stripes of the zebrafish. All this looks plausible enough, but the clinching proof – the identification of diffusing morphogens responsible for pigmentation – has yet to be obtained.

There does now seem to be good evidence that chemical morphogens of the sort Turing envisaged act in biological development. Several proteins belonging to the class called transforming growth factor b proteins seem to act this way in fly and vertebrate morphogenesis, signalling the developmental fate of cells as they diffuse through the embryo.

But does anything like Turing’s mechanism act to shape embryos beyond the question of marking patterns, as Turing suggested? In general, embryogenesis seems more complex than that, operating under close genetic control. However, Thomas Schlake and colleagues at the Max Planck Institute of Immunobiology in Freiburg have very recently discovered that there is at least one other biological patterning process that apparently uses the activator-inhibitor mechanism. They have found that the follicles of mouse hair are positioned in the epidermis by the protein products of two classes of gene, called WNT and DKK. The former appears to take the role of activator, inducing follicle formation, while several variants of DKK proteins act as inhibitors1.

Hair and feather positioning has long been suspected as an example of a Turing pattern – the equidistant, roughly hexagonally packed patterns are just what would be expected. Schlake and colleagues have made that case by looking at how over-expression of WNT and DKK alters the follicle patterns on mutant mice, showing that these match the predictions based on an activator-inhibitor model. It is probably the best reason yet to think that Turing’s intuition was sound.


Reference

1. Sick, S. et al. Science Express doi:10.1126/science.1130088.

Is there such a thing as a 'safe technology'?

[This is the pre-edited text of my latest muse for Nature, which relates to a paper published in the 16 November issue on health and safety issues in nanotechnology.]

Discussions about the risk of emerging technologies must acknowledge that their major impacts have rarely been spotted in advance.

In today's issue of Nature, an international team of scientists presents a five-point scheme for "the safe handling of nanotechnology"[1]. "If the global research community can rise to the challenges we have set", they say, "then we can surely look forward to the advent of safe nanotechnologies".

The five targets that the team sets for addressing potential health risks of nanotechnologies are excellent ones, involving the assessment of toxicities, prediction of impacts on the environment, and establishment of a general strategy for risk-focused research. In particular, the goals are aimed at determining the risks of engineered nanoparticles – how they might enter and move in the environment, to what extent humans might be exposed, and what the consequences of that will be. We need to know all these things with some urgency.

But what is a "safe technology"? According to this criterion, manufacturing nuclear warheads would be "safe" if no human was exposed to dangerous levels of radiation in the process that leads from centrifuge to silo.

To be fair, no one denies that a technology's 'safety' depends on how it is used. The proposals for mapping nanotech's risks are clearly aimed at a very specific aspect of the overall equation, concerned only with the fundamental issues of whether (and how much) exposure to nanotechnological products is bad for our health. But it highlights the curious circumstance that new technologies now seem required to carry out a risk assessment at their inception, ideally in parallel with public consultation and engagement to decide what should and shouldn't be permitted.

There is no harm in that. And there's plenty of scope for being creative about it. Some of the broader ethical issues associated with nanotech, for example, are being explored in the US through a series of public seminars organized by the public-education company ICAN Productions. Funded by the US National Science Foundation, ICAN is creating three one-hour seminars in which participants, including scientists, business leaders and members of the public, explore scenarios that illuminate plausible impacts of nanotech on daily life. The results will be presented on US television by Oregon Public Broadcasting in spring of 2007.

Yet history must leave us with little confidence that either research programs or public debates will anticipate all, or even the major, social impacts of a new technology. We smile now at how anyone believed that road safety could be addressed by having every automobile preceded by a man waving a red flag. In those early days, the pollution caused by cars was barely on the agenda, while the notion that this might affect global climate would have seemed positively bizarre.

Of course, it is something of a cliché now to say that neither the internal combustion engine nor smoking would ever have been permitted if we knew then what we know now about their dangers. But the point is that we never do – it is hard to identify any important technology for which the biggest risks have been clear in advance.

And even if some of them are, scientists generally lose the ability to do anything about it once the technology reacts with society. Nuclear proliferation was forecast and feared by many of the Manhattan Project physicists, but politicians and generals treated their proposals for avoiding it with contempt (give away secrets to the Russians, indeed!). It took no deep understanding of evolution to foresee the emergence of antibiotic-resistant bacteria, but that didn't prevent profligate over-prescription of the drugs. The dangers of global warming have been known since at least the 1980s, and… well, say no more.

In the case of nanotechnology, there have been discussions of, for example, its likelihood of increasing the gap between rich and poor nations, its impacts on surveillance and privacy, and the social effects of nanotech-enhanced longevity. These are all noble attempts to look beyond the pure science, but it's not at all clear that they will turn out to be the most relevant issues.

Part of the impetus for aiming to address the 'risks' of nanotech so early in the game comes from a fear that potentially valuable applications could be derailed by a public backlash like that which led to a rejection in Europe of genetically modified organisms – some (though by no means all) of which resulted from a general lack of information or understanding about the technology, as well as an arrogant assumption of consumer acquiescence.

The GMO experience has sensitized scientists to the need for early public engagement, and again that is surely a good thing. It's also encouraging to find scientists and even industries hurrying along governments to do more to support research into safety issues, and to draft regulations.

What they must avoid, however, is giving the impression that emerging technologies are like toys that can be 'made safe' before being handed to a separate entity called society to play with as it will. Technologies are one of the key drivers of social change, for better or worse. They simply do not exist in isolation of the society that generates them. Not only can we not foresee all their consequences, but some of those consequences aren't present even in principle until culture, sociology, economics and politics (not to mention faith) enter the arena.

Some technologies are no doubt intrinsically 'safer' or 'riskier' than others. But the more powerful they are, the less able we are to distinguish which is which, or to predict how that will play out in practice. Let's by all means look for obvious dangers at the outset – but scientists must also look for ways to become more engaged in the shaping of a technology as it unfolds, while dismantling the now-pervasive notion that all innovations must come with a 'risk-free' label.

Reference
1. Maynard, A. et al. Nature 444, 267 - 269 (2006).

Hooke: what came next?

I went to a nice talk by Lisa Jardine at the (peripatetic) Royal Institution last week, on the newly discovered notes of Robert Hooke. Lisa and her students have been studying this portfolio of notes taken by Hooke in his capacity as secretary of the Royal Society since they were rescued from auction and returned to the Royal Society earlier this year (see my earlier blog entry in May). She says that they have completely transformed her view of Hooke since writing his biography (The Curious Life of Robert Hooke, HarperCollins) in 2003. One of the hazards of being a historian, she pointed out, is that you can never be sure what may come to light and revise all your opinions, which have previously been presented to the world with such blithe authority. Well, that happens in science too, of course.

Lisa is now convinced that Hooke himself, not Newton, was his worst enemy: he was a terrible record keeper, and never finished anything. For all his protestations of priority over Huygens in regard to the invention of the spring-balance pocket watch, it seems that he may have sunk his claim himself. The new notes include a page taken from the private notes of Henry Oldenburg, written in 1670, in which Oldenburg relates how Hooke presented such a watch (Huygens’ version was patented in 1674), and then leaves a space for a description of the mechanism, apparently for Hooke himself to fill in the details. Hooke seems to have done this sketchily in pencil, but his words got worn away and he never amended them more permanently. So Oldenburg got no further in trying to transcribe them than a few lines before apparently giving up and crossing the whole lot out. But worst of all, Hooke seems to have filched the page from Oldenburg’s papers after the latter’s death, in the course of preparing his priority claim in obsessive detail – and then promptly left it buried in his own notes until it has surfaced now. So when Oldenburg’s papers were later checked to assess Hooke’s claim, there was no sign of this page!

I’m also interested to hear that the Hooke pages are shortly to be ‘conserved’ – which means that the book will be taken apart and each page placed inside plastic (Lisa says the pages are already literally falling apart beneath their fingers). So I’ll be one of the few ever to have touched the originals, and to have seen the book in its pristine form. Phew.

Economists as storytellers

Economist blogger Dave Iverson has written to me about my “tease” (his words, nice choice) in the Financial Times about neoclassical economics. Dave has previously commented in a way that I found insightful and fair on the exchanges and debates in the blogosphere, particularly those on Mark Thoma’s and Dave Altig’s sites. His latest post is another useful contribution, and here it is:

“Philip Ball's Financial Times' critique of economics, titled Baroque Fantasies of a Peculiar Science caused quite a stir recently in the economics blogs (particularly here here and here here.). But last week the bickering subsided with Dave Altig (macroblog) and Philip Ball seeming to have reached an accord.. At one point Altig said, "If you want, call economics an attempt to construct coherent stories about social phenomenon..." Sounds about right to me. We economists are indeed story tellers. Following this discussion, it seems clear that economists need to be much more open and honest about our assumptions and the linkages, such as they are and often are not to the real world of policy and action. No argument from me on that score. I've been arguing similarly for years.

“For more critique, see Steve Cohn's August 2002 Telling Other Stories: Heterodox Critiques of Neoclassical Micro Principles Texts, wherein Cohn attacks the "'rhetoric' of neoclassical theory, …critiquing many of the stories told, the metaphors used, the analogies drawn, and the framing language deployed."

“In addition, there have been many book-form critiques arguing that economists, particularly neoclassical economists have over-driven their headlights in much the same way that Bell argues. Here are six of my favorites (arranged by date of publication):
J. de V. Graaff. Theoretical Welfare Economics. 1957
Guy Routh. The Origin of Economic Ideas. 1975
Mark Blaug. The Methodology of Economics: Or How Economists Explain.
1980
Robert L. Heilbroner. Behind the Veil of Economics: Essays in the
Worldly Philosophy. 1988
Mark Sagoff. The Economy of the Earth: Philosophy, Law and the
Environment. 1988
Andrew Bard Smookler. The Illusion of Choice: How the Market Economy
Controls Our Destiny. 1993”

The Cohn paper is excellent – it says pretty much all of what I said in the FT article and much more, and in more depth, and frankly more persuasively. I particularly liked this, in relation to Paul Ormerod’s FT critique of how the textbooks tell the same old neoclassical story, despite what some of the practitioners are now doing to the contrary:

“We shouldn’t allow neoclassical economists to “run away” from their textbooks. The tracts educate well over a million students a year and lay the groundwork for much of educated opinion about economic issues. They should be defended or abandoned. In critiquing principles texts we should quote from the books themselves and if charged with attacking straw men, ask who is to blame: the textbook authors who built these scarecrows, or the photographers who took their picture?”

In any event, I offer the Cohn paper to those who say I’ve misrepresented the field (or have misused the word ‘neoclassical’). And I do so partly because Cohn seems to me to be very fair, acknowledging (in a way that I admit I could have done more explicitly) some of the ways in which modern economics has moved beyond the simplistic picture. This seems to me to be about dialogue rather than attack – which is absolutely what I’d like to see.

Was life inevitable?

Here’s the unexpurgated version of my latest story for news@nature. There’s a lot of really interesting back story here, which I hope to return to at some point. This is far and away some of the most interesting “origin of life” work I’ve seen for some time.

Life may be the ultimate in planetary stress relief, a new theory claims

The appearance of life on Earth seems to face so many obstacles that scientists often feel forced to regard it almost as miraculous. Now two scientists working at the Santa Fe Institute in New Mexico suggest that, on the contrary, it may have been inevitable.

They argue that life was the necessary consequence of the build-up of available energy on the early Earth, thanks to purely geological processes. They regard it as directly analogous to the way lightning relieves the build-up of electrical charge in thunderclouds.

In other words, say Harold Morowitz and Eric Smith in a preprint posted on the Santa Fe Institute archive [1], the geological environment "forced life into existence".

This view, the researchers say, implies not only that life had to emerge on the Earth, but that the same would happen on any similar planet. And they hope that ultimately it will be possible to predict the first steps in the origin of life based on the laws of physics and chemistry alone.

Their proposal is "instructive and inspiring", says Michael Russell, a specialist in the origin of life at the California Institute of Technology in Pasadena.

Morowitz and Smith admit that they don't yet have the theoretical tools to clinch their arguments, or to show what form this "inevitable life" must take. But they argue that it is likely to have used the same chemical processes that now drive our own metabolism – but in reverse.

They say that the young Earth would have been accumulating energy from geological processes much as a dam accumulates gravitational potential energy by piling up water. Sooner or later, something had to give.

One source of such energy would have been energy-rich compounds called polyphosphates, generated in volcanic processes. These are 'battery molecules', analogous to the compound ATP, the ubiquitous source of metabolic energy in living cells.

Another source would have been hydrogen molecules, which are likely to have been abundant in the early atmosphere even though they are almost absent today. Hydrogen would have been generated, for example, by reactions between seawater and dissolved iron.

Energy-releasing reactions between hydrogen and carbon dioxide (a volcanic gas) in the atmosphere can produce complex organic molecules, the precursors of living systems.

In our own metabolism, a series of biochemical reactions called the citric-acid cycle breaks down organic compounds from food into carbon dioxide. Horowitz and Smith say that the energy reservoirs of the young Earth could have driven a citric-acid cycle in reverse, spawning the building blocks of life while relaxing the 'energy pressure' of the environment. Eventually these processes will have become encapsulated in cells, which makes the 'energy-conducting' flows more efficient.

Life, agrees Russell is "a chemical system that drains and dissipates chemical energy." He has used similar ideas to argue that "life would emerge using the same pathways on any sunny, wet rocky planet" [2,3]. But he believes that the most likely place for it to occur was at miniature subsea volcanoes called hydrothermal vents, where the ingredients and conditions are just right for energy-harnessing chemical machinery to develop [4].

The biochemical processes of living organisms are highly organized. Scientists have long puzzled over how these 'ordered' systems can come spontaneously into being, when the Second Law of Thermodynamics suggests that the universe as a whole tends to generate increasing disorder.

The answer, broadly speaking, is that local clumps of order come at the expense of increasing the disorder in their environment. But Horowitz and Smith suggest a rationale for why such concentrations of order should happen in the first place. They draw on the idea, proposed in the 1980s by Rod Swenson of the University of Connecticut, that ordered states are much better 'lightning' conductors' for discharging excess energy.

Thus, they say, despite several major extinctions throughout geological time, when most of life on Earth was obliterated, life itself was never in danger of disappearing – because an Earth with life is always more stable than one without. They call this 'condensation' of life from the energy-rich environment a "collapse to life", which in their view is as inevitable as the appearance of snowflakes in cold, moist air.

References
1. Morowitz, H. & Smith, E. Santa Fe Institute Working Paper (2006).
2. Russell, M. J. & Hall, A. J. in Hiscox, J. A. (ed.) The Search for Life on Mars, 26-36 (British Interplanetary Society, 1999).
3. Russell, M. J. et al. in Ikan, R. (ed.) Natural and Laboratory-Simulated Thermal Geochemical Processes, 325-388 (Kluwer, Dordrecht, 2003).
4. Martin, W. & Russell, M. J. Phil. Trans. Roy. Soc. B online publication doi:10.1098/rstb.2006.1881 (2006).