BlueSci Issue 03 - Easter 2005 by BlueSci

Cambridge’s Science Magazine produced by

Issue 3

Easter 2005

in association with

www.bluesci.org

Looking Beyond Crossing the great divide: the art of astronomy

Mars or Glory A giant leap or a distant view?

• Hollywood • Science & Subtext • • Synaesthesia • Mobiles • Proteomics •

Easter 2005

Issue 3

contents

Features

Giving Elephants Wings:The Science of Proteomics

Nicholas T. Hartman reports on the next big challenge for modern biology.............................

What Does F# Taste Like?

Andrew Lin examines the phenomenon of synaesthesia.................................................................

The Killer Within

Bojana Popovic goes hunting for superbugs.......................................................................................

Dude,Whereâ&#x20AC;&#x2122;s My Phone?

Ramsey Faragher pin-points the latest innovation in mobile phone technology.......................

The Quantum Conundrum

Peter Mattsson looks at Einsteinâ&#x20AC;&#x2122;s battle with quantum theory....................................................

Of Flies and Men

Zoe Smeaton explores how the fruit-fly revolutionized experimental biology..........................

Waters of the Mediterranean

Lila Koumandou discovers why the Mediterranean Sea is quite so clear..........................................

Regulars

Editorial .............................................................................................................................. 03 Cambridge News ............................................................................................................. 04 Focus ................................................................................................................................... 06 On the Cover ................................................................................................................... 20 A Day in the Life of... ...................................................................................................... 21 Away from the Bench ..................................................................................................... 22 Initiatives ............................................................................................................................ 23 History ............................................................................................................................... 24 Arts and Reviews .............................................................................................................26 Dr Hypothesis .................................................................................................................. 28 The front cover shows an aluminium sample imaged by polarized light microscopy. Individual aluminium crystals of a few microns in diameter can be seen.Turn to page 20 to find out more.

Next Issue: October 2005 Article enquiries: submissions@bluesci.org General enquiries: enquiries@bluesci.org

Contribute to BlueSci We are now accepting submissions for our Michaelmas Term issue, to be received by 5pm on 11 July 2005.We want articles on all kinds of science. Whatever your scientific passion, why don’t you seize the chance to share it with our readers?

Photograph Competition Would you like to see your photograph on the cover of BlueSci? With an extensive website and a print run of thousands, the cover of BlueSci is the best way to publicize your work throughout Cambridge. Microscopy, high-speed or satellite photography, views of the cosmos… Whatever your field, send your picture and a brief explanation to competitions@bluesci.org by 11 July 2005.

www.bluesci.org Subscribe to BlueSci Termly popular science from Cambridge If you’re outside the University of Cambridge but want to receive BlueSci, we are now offering a subscription service For an annual fee of £12, or £15 for subscribers outside the UK, you will receive three issues of the magazine direct to your door Please send your delivery address and a cheque for £12 or £15, made payable to 'Cambridge University Science Productions' to: BlueSci Subscriptions, Varsity Publications Limited, 11-12 Trumpington Street, Cambridge, CB2 1QA

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From The Editor Cambridge is teeming with fascinating research and, as ever, our amazing cover photograph shows an example of what’s going on. ON THE COVER will tell you all about it. If you’re a DR HYPOTHESIS fan, don’t skip to the back page just yet because there’s plenty more between here and there. In particular our enlarged FOCUS explores the science behind, and the competition between, Hubble Space Telescope and the increasingly prevalent missions to the planets. If exam season is getting to you and you can’t stop texting in the UL, then watch out: according to DUDE, WHERE’S MY PHONE?, that patrolling librarian may one day be able to track you to your desk.Take a break and read about Owain Vaughan LOOKING BEYOND the arts-sciences divide. With revision over, perhaps you’ll be jetting off to a sunny beach. Lila Koumandou reveals why the WATERS OF THE MEDITERRANEAN are so blue. If you’re in Cambridge this summer, there’s lots to read: I’ve always associated colours with particular letters of the alphabet, but it never occurred to me that taste could come into it. If you’re willing to take on a diet of musical notes, then

you must read

WHAT DOES F# TASTE LIKE? THE QUANTUM CONUNDRUM examines the

implications of some peculiar quantum effects that Einstein himself struggled to make sense of. A DAY IN THE LIFE OF… a Hollywood science advisor may persuade you to consider an alternative career next year. Or perhaps you’re going into research in the autumn. In SCIENCE AND SUBTEXT, Emily Tweed discovers why that could be an explosive option. Communication is crucial to scientific research. If you’re driven by enthusiasm for your field, as we are, you’ll want to tell people about it. BlueSci is your platform; I hope you’ll take advantage of it. If you just want to get on with your research, then send us your news and give others the opportunity to read about it.We’ve worked hard to put together a magazine for you. If you’re passionate about communicating science and think you can do better, we’d love to hear from you. I very much hope you enjoy issue 3. Jonathan Zwart issue-editor@bluesci.org

From The Managing Editor

The transition from issue 2 to issue 3 has marked an exciting period of evolution for Cambridge’s first popular science magazine. One of our goals from the last issue was to redress the balance of biological and physical sciences articles, which I hope you will agree we have markedly improved upon for this issue. Secondly, we hope that you have had a chance to visit BlueSci Online, launched in January.This term we plan to include extra material online — the latest news stories and up-to-date events listings — as well as all our print edition articles and PDFs of back issues. So bookmark our site in your browser: www.bluesci.org. We’ve also made some changes to the magazine team — we’ve amalgamated news

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and events and to give our news reporting a more ‘journalistic’ feel we’ve also recruited a small news team to report on events. So if you have something you’d like us to cover please email events@bluesci.org. Finally, we’ve also made it possible to subscribe to BlueSci, so that alumni and local schools — indeed, anyone interested in receiving their own hard copy of the magazine — can receive three issues straight to their door. For more information please see our website or email subscriptions@bluesci.org. Many thanks for all the positive feedback you have sent in, as well as technical corrections and comments — we are still striving for perfection! Louise Woodley managing-editor@bluesci.org

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Issue 3: Easter 2005 Produced by CUSP & Published by Varsity Publications Ltd

Editor: Jonathan Zwart Managing Editor: Louise Woodley Submissions Editor: Ewan Smith Business Manager: Eve Williams Design and Production Production Manager: Tom Walters Pictures Editor: Sheena Gordon Production Team: Victoria Leung, Helen Stimpson

Section Editors

News Editor: Laura Blackburn News and Events Team: Carolyn Dewey, Bojana Popovic, Alan Forster, Lucia Alonso-Gonzales Focus: Ewan Smith Features: Joanna Maldonado-Saldivia, Helen Stimpson, Owain Vaughan On the Cover: Victoria Leung A Day in the Life of…: Nerissa Hannink Away from the Bench and Initiatives: Tamzin Gristwood History: Emily Tweed Arts and Reviews: Owain Vaughan Dr Hypothesis: Rob Young CUSP Chairman: Björn Haßler

enquiries@bluesci.org

Varsity Publications Ltd 11/12 Trumpington Street Cambridge, CB2 1QA Tel: 01223 353422 Fax: 01223 352913 www.varsity.co.uk business@varsity.co.uk BlueSci is published by Varsity Publications Ltd and printed by Cambridge Printing Park. All copyright is the exclusive property of Varsity Publications Ltd. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, without the prior permission of the publisher.

World-renowned primatologist Dr Jane Goodall DBE visited Cambridge on 22–23 February to lecture on her current work and on the Roots and Shoots programme, an organisation that encourages young people to become more involved in their communities. Dr Goodall gained her PhD from Cambridge in 1965, unusually without having studied for an undergraduate degree beforehand. Roots and Shoots started in 1991 with 16 Tanzanian students and has since grown to a membership of around 6,000 groups in 87 countries. It helps young people to take an active role in their communities by undertaking projects that will benefit people and animals, and the environment they live in. The goal is to promote understanding and also to give people self-respect and hope for the future, fostering the belief that the individual matters and can make a difference. Whilst Roots and Shoots takes up most of Goodall’s time — she is on the move 300 days a year — her research station in Gombe, Tanzania, is carrying out vital research into chimpanzees in the surrounding area. There are many questions about the chimp family structure that have remained a puzzle up until now. “With new DNA profiling techniques, we can take DNA from faecal samples and this can tell us exactly who the fathers are, which we could only guess before,” says Goodall. “This opens up a whole new question of whether there is any kind of bond between a father and his offspring, and if there is, how do they know?” she says.The behaviour of known individuals is being monitored over a

Ice-shelf Melting The causes of polar ice melting, past and present, are being investigated by scientists working at the British Antarctic Survey (BAS).“In the past two decades a lot of the ice-shelves along the spine of the Antarctic Peninsula have been breaking up and disappearing,” says Dr Dominic Hodgson from BAS. By studying the marine sediments underneath and near current ice-shelves, and shelves that have recently broken up, the scientists can tell when they had previously broken up, and whether or not these were random events. “Previous breakups of both kinds of ice-shelf corresponded to periods of extended global warming,” says Hodgson. One of the break-ups occurred when an ice-shelf was being warmed from below by the ocean, and from above by an increase in atmospheric temperature. “When iceshelves break up completely, the flow of inland glaciers into the sea increases greatly, and this is what causes the rise in sea-levels.” These collapses can occur very quickly once the shelf becomes

Michael Neugebauer

Goodall in Cambridge

Dr Goodall, who does not handle wild chimpanzees, with a sanctuary chimpanzee

long period of time, so the researchers can find out what effect the type of mother and family experience has on young chimps. Goodall has been studying the chimps at Gombe for 40 years and in this time the relationship between scientists and the media has changed dramatically. “My first book, ‘My Friends the Wild Chimpanzees’, with National Geographic, made Robert Hinde [her PhD supervisor] furious! Everything in the book was accurate, just in a different format — scientists didn’t write popular books then.” She believes that the interaction between scientists and the media is important, but often misused.“The media can play a huge

role in the shaping of public opinion”, she says. It’s important that people have the knowledge to be able to make informed decisions about the science that is being presented to them, the danger being that they will choose charisma over substance if they don’t understand. “Also, scientists should keep an open mind, and be first a human being, and second a scientist.That’s really important.” LB www.janegoodall.org www.srcf.ucam.org/curas

unstable: in March 2002 the Larsen B ice-shelf collapsed in the space of a month. “By studying previous collapses, we can understand how ice-shelves responded in the past, and therefore predict how they might respond in the future.” It is clear that we are going to see significant effects on the Antarctic ice-shelves if global temperatures continue to rise. LB www.antarctica.ac.uk

The Male Brain

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BlueSci would like to thank the St Catharine’s College Amalgamated Societies and Cambridge University Roots and Shoots for their kind invitation to this event.

Dominic Hodgson

Cambridge News

On 28 February, Professor Simon Baron-Cohen presented his case for autism being an extreme form of the male brain, discussing the sometimes controversial issue of the differences between male and female brains. In a lecture hosted by the Cambridge University Scientific Society, he argued that males are generally more prone to ‘systematic’ thinking, showing a preference for toys such as Lego and cars, whereas females show a preference for more ‘emotive’ toys that involve social interactions. Autism sufferers have below-average empathetic (social) skills, but usually have above-average systemizing skills, which would indicate an extreme form of the male brain. According to Professor Baron-Cohen there are four males displaying autistic traits for every such female, and males affected by Asperger’s syndrome outnumber females by nine to one. One piece of evidence that points to male-female differences involves picking out a simple shape buried within a

Easter 2005

Spinning Out

patents being filed in 1992. CDT’s Polymer LED technology ‘PLED’ can be used to make thinner and more energy-efficient displays that are also brighter and have higher contrast than conventional LCD displays. In addition, they have superior video-imaging performance and give a very wide viewing angle. PLED technology is already available in many existing products including Philips mobile phones and MP3 players. Manufacturing licences have been granted to companies involved in information management, communication and entertainment, such as OSRAM and Seiko-Epson. AF www.cdtltd.co.uk

Cambridge Display Technology (CDT) is the first University of Cambridge spin-out company to be floated on the US-based NASDAQ exchange. Trading under the symbol OLED commenced in December 2004 and this initial public offering raised $30 million. CDT’s chief technology officer Dr Jeremy Burroughes discovered that Light Emitting Diodes (LEDs) could be made using conjugated polymers — materials which can conduct electricity and emit light when a current is passed through them — when he was working in Professor Richard Friend’s group in the Cavendish Laboratory; this led to the first of many

Huntington’s and Sleep

The properties of mysterious particles called neutrinos will soon be unravelled by a multinational collaboration based at Fermilab near Chicago, US. The Main Injector Neutrino Oscillation Search, or MINOS, will look at the phenomenon of neutrino oscillations, where neutrinos change between one of three flavours — electron, muon or tau — as they travel through space or matter.This has implications for the Standard Model, which determines how the different particles that make up matter interact with each other. Dr Mark Thomson from the Cavendish Laboratory has been looking at the distinctive patterns generated when neutrinos produced at Fermilab crash into two huge detectors at almost the speed of light.“We have written software to try and work out what these patterns mean, testing it using sophisticated simulations so we can make the best of the data.” Neutrinos rarely interact with matter, so to increase the chance of one hitting the detectors the latter weigh in at a massive 1000 and 5500 tonnes. “The experiment is very neat; we will be able to compare the energy spectrum of neutrinos at the first detector — before they have had a chance to oscillate — with the spectrum at the far detector.”This will enable scientists to work out the differences between the squares of the masses of the different types of neutrino, which could then be used for the Standard Model. LB www-numi.fnal.gov

Dr Jenny Morton in the Department of Pharmacology and her colleagues from the Brain Repair Centre and the MRC Laboratory of Molecular Biology have obtained breakthrough results in their study of Huntington’s disease (HD). They have identified sleep disturbances in human HD patients to be a pathological feature of the disease.This has significant potential for the treatment of HD and in improving the quality of life for sufferers and their carers. Sleep disturbances in neurological disorders are common, not only in HD, but for other disorders such as Alzheimer’s and Parkinson’s. Using mice carrying the HD mutation, the researchers found that HD mice had profound abnormalities in their circadian rhythms, reflecting those seen in HD patients. They also found that behavioural disturbances were accompanied by changes in the expression of circadian clock genes. These genes are involved in maintaining the internal biological clock fundamental to all living organisms, influencing hormones that play a role in sleep and wakefulness, in metabolic rate, and in body temperature.The researchers plan to follow up this work by studying circadian rhythms in HD patients and determining if sleep abnormalities contribute to cognitive deficits.The long-term goal is to find treatments and new drug targets for this devastating neurological disorder. BP

Disease Diagnosis for All DiagnovIS, a recently established Cambridge start-up company, promises an inexpensive diagnostic tool with the potential to cure millions. The business idea sprang out of a research project headed by Dr Charles Pritchard and Dr David Rubin at the University of Witwatersrand, Johannesburg. At the time Nic Ross, a student of Dr Pritchard, was developing software algorithms that examine tissues under a digital microscope and then screen them for malaria. This technology is the basis of the business. The integrated, automated, diagnostic platform makes use of advances in

news@bluesci.org

Peter Ginter

Mystery of Neutrinos

computational mathematics, digital imaging, automated electron microscopy and proprietary optical recognition software. DiagnovIS has recently designed an innovative hardware unit, through participation in the IfM Design Challenge, as well as through inputs from Cambridge-based technology consultants and a local microscopy developer. The platform is currently being tested on a model system of four different strains of malaria and is almost ready for phase one clinical trials. In parallel, the method is being developed for the diagnosis of a wide range of infectious and parasitic dis-

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C a m b r i d g e N ew s

number of other shapes. Males — and to a greater extent autism sufferers — are on average quicker than females at picking the shape out, and this is due to the more ‘systematic’ style of thinking of people with autism. Research carried out by Baron-Cohen and others on foetal testosterone has provided a potential physiological explanation for autistic traits such as little eye contact at an early age and speech development problems. These correlate with the amounts of foetal testosterone present during pregnancy, adding further weight to the male brain hypothesis. AF www.autismresearchcentre.com

Further information can be found in Morton et al., J. Neurosci. 25: 157–163 (2005) eases including tuberculosis and STDs. DiagnovIS was founded in 2004 by Pritchard, Ross, Sonja Marjanovic and Ilian Iliev, after they entered the 2003 Cambridge University Entrepreneurs business plan competition, sponsored by The Cambridge-MIT Institute. They won the ‘People, Planet and Productivity’ category, and the prizemoney was used as start-up funding. Since then the company has gone from strength to strength. Its next aims are to secure further financial backing for broadening the disease software portfolio, and hardware development. BP www.diagnovis.com

Nasa, ESA and A.Zijlstra (UMIST)

Focus

Virginia Hooper, Alistair Crosby and Louisa Dunlop investigate the pros and cons of funding for manned exploration of the solar system versus continued support of the Hubble Space Telescope and other unmanned, space-borne observatories

A Giant Leap or a Distant View? Kennedy did it in 1961. George Bush Sr did it in 1989. Last year, George Bush did it once again, and heralded the start of a great journey to send men to the moon and then on to Mars. Just days later, it was announced that the famous Hubble Space Telescope would not receive its planned lifeline. We examine both Hubble’s achievements and the new plans for space exploration and ask: does Nasa have its priorities right? To many the most important scientific instrument of recent times, the Hubble Space Telescope has revolutionised our understanding of the universe and the processes that go on within it.Yet despite these impressive credentials, the future of this extraordinary telescope remains uncertain. In January 2004, the US government outlined an ambitious new space programme focused around manned exploration of the moon and eventually Mars.Although likely to capture the imagination of the taxpaying public, these bold endeavours will undoubtedly put pressure on other science projects. Already, seven missions including JIMO, Ulysses and Geotail have been cancelled in a bid to conserve funds. It is against this backdrop of a new vision for space exploration that the latest servicing mission for Hubble has been indefinitely postponed.The cancellation of manned shuttle servicing last year came amidst safety fears fuelled by the illfated Columbia service mission of 2002 when the shuttle disintegrated on re-entry, killing all on board. Nasa now requires shuttles to be within reach of the International Space Station (ISS), to provide a refuge for astronauts in the event of a technical emergency. Hubble, however, is in orbit above the ISS so any servicing mission would be in breach of the new guidelines. A safer but more technically demanding option would be robotic servicing, but this now looks increasingly unlikely given the recent announcement of Nasa’s budget, which made no provision for future servicing missions to the telescope, either manned or robotic.

Eye in the Sky Launched in 1990, the Hubble Space Telescope is a 2.4-metre optical reflecting telescope that operates from ultra-violet to near infrared wavelengths. It orbits the Earth every 95 minutes from its position 600 kilometres above the surface. The simple modular design of the telescope has helped it to keep pace with innovation by allowing new components to be added with ease. Regular servicing every few years means that astronauts can add instruments and replace or repair outdated equipment. If servicing stops then Hubble will rapidly fall into disrepair.The most pressing requirement is for new gyroscopes. These allow the telescope to orientate itself and point towards objects of interest. Hubble has six gyroscopes in total and uses three at any one time. Unfortunately, only four of these are now operational. In an attempt to extend the useful life of the telescope, programmers have experimented with using just two gyroscopes at a time. Initial tests have worked well, and this new measure should keep the telescope working for an extra year — until the end of 2008. Eventually, a robot will be dispatched to de-orbit Hubble, which will then crash safely into the ocean.

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tant part of the spectrum for viewing distant galaxies, because the further an object is from Earth, the more the light from it is ‘redshifted’ — shifted towards the red end of the spectrum — by the Doppler effect. Although Earth-bound telescopes can see in the infrared, they are at a disadvantage because at these wavelengths the atmosphere is relatively opaque and absorbs this radiation before it reaches the surface. For this reason, most Earth-based infrared telescopes are positioned on mountain tops, high in the atmosphere and above cloud cover, in order to reduce the opacity. Hubble’s ability to see more clearly and much further has numerous advantages, one of which is that it has enabled scientists to calculate the age of the universe. Because the universe is expanding, the further a galaxy is away from us, the faster it moves away and the redder its light becomes. To visualise this, imagine the surface of a balloon with dots drawn all over it.The galaxies in the universe move apart in the same way as the dots on the balloon move as it is being blown up. An equation known as Hubble’s Law relates the distance to and the redshift of a distant galaxy, in a way that depends on the age of the universe. Hubble measures the redshifts of certain objects called Cepheid

In January 2004, the US government outlined an ambitious new space programme focused around manned exploration of the moon and Mars

Hubble provides the deepest glimpses into our visible universe by virtue of its vantage point above the atmosphere. This frees it from the distortion caused by air motions at optical wavelengths, which also makes stars twinkle. Turbulence in the atmosphere causes packets of air of different densities to mix.These refract the light from stars by different amounts, producing the ‘twinkling’. Hubble’s position gives an uninterrupted view of the infrared spectrum. Infrared radiation is the most impor-

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Variables, whose distances astronomers can find straightforwardly. Cepheid Variables are pulsating stars that are so luminous — up to 10,000 times brighter than the sun — that they can be seen up to 65 million light years away. The pulsation is due to physical changes in the size and surface temperature of the star over the course of just a few days.The fluctuation period is roughly similar for all Cepheids of the same brightness. We know how bright a star should be by

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Nasa/KSC

Fo c u s

measuring how long it takes to pulse. If we compare the observed luminosity of a Cepheid as seen by Hubble with its modelled luminosity, we can calculate the Cepheid’s distance from the Earth. Hubble has been able to detect Cepheids up to 10 times further away than any ground-based telescope. Using its data, astronomers obtained an age of approximately 13 billion years for the universe. This new figure solves one of the great problems in astronomy as previous esti-

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objects behind the galaxies and focuses them into bright curves imaged by Hubble.The mass needed to produce such an effect is 10 times more than the mass associated with the visible galaxy, suggesting the presence of additional, dark, matter. Astronomers showed in 1998 that the expansion rate of the universe was increasing with time, using Hubble observations of exploding stars called ‘type IA supernovae’. It is thought to be dark energy that causes this acceleration.

Hubble has witnessed some remarkable events: Shoemaker-Levy 9 smashing into Jupiter, dust storms on Mars, and the birth and death of stars

mates had suggested that the universe was younger than its oldest stars! Hubble has also allowed research into ‘dark matter’, the most elusive but most abundant form of matter in space. This, together with the even more mysterious ‘dark energy’, makes up more than 90% of the mass of the universe. Exactly what they are remains uncertain, and it is only recently that Hubble has provided conclusive evidence for their existence, which can only be explained if there were more mass in the universe than can be accounted for by conventional methods.The presence of dark matter can be inferred from the gravitational lensing of far galaxies: gravity deflects passing light rays from

Nasa

Percentage of federal budget spent on Nasa: 0.6 Money requested for manned spaceflight in 2006: $6.76 billion Cost of manned upgrade of Hubble: $300 million Year Nasa first put a man on the moon: 1969 Year by which Nasa wants to put another man on the moon: 2020 Total hits to Nasa’s website during the first six weeks of 2004: 6.53 billion

www.bluesci.org

Return to the Moon

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With its incredible resolution and the far-reaching field of view of its ‘Near Infrared Camera and Multi-Object Spectrometer’, Hubble has witnessed some remarkable events.These include images of the Comet Shoemaker-Levy 9 smashing into Jupiter, dust storms on Mars, and recording the births and deaths of stars. This constant stream of information is of vital importance to astronomers trying to understand the universe. As we have seen, Hubble will fail within the next few years and its supply of data to the astronomical community will cease, making new research more difficult. Not only the purely scientific impact of Hubble will be missed, but also the inspirational and cultural influence of this modern icon. Images from Hubble have permeated into popular culture and increasingly define our mental picture of the cosmos. Hubble was never intended to last indefinitely and the scientific community welcomes the prospect of a new and more sophisticated telescope. But astronomers will have to wait until at least 2011 for the launch of Hubble’s successor, the James Webb Space Telescope.This significant gap after Hubble’s final years is due to a change in priority: the US is redirecting Nasa’s focus to manned rather than robotic exploration of the near planets with a view to eventually setting a man on Mars by

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2035. The first step will be to send men back to the moon by 2020 at the latest. This will be achieved by phasing out the much-criticized ISS and the space shuttle and concentrating resources on developing new technologies to allow manned explorations beyond the first few hundred kilometres of space (low Earth orbit). These plans come at enormous expense without any significant increase in the overall budget. Funds are to be squeezed from other areas; for instance, current plans are for Nasa’s research into the Earth’s environment to have its funding cut by $1.1 billion between 2005 and 2009. But it was Bush’s vision of sending men to the moon and thence to Mars that really succeeded in grabbing the headlines. However, can the White House really justify such a grand commitment? The official report of the President’s Commission on Moon, Mars and Beyond implies that crews carry out better science than probes, and that human habitation in space is both feasible and desirable. Is what it says true?

Hubble Space Telescope

First proposed: 1962 First cancelled: 1973 Eventually launched: 1990 Cost: $2 billion Manned servicing missions to date: 4 Papers published using Hubble over the same time period: 2,651 Proportion of proposals for using Hubble accepted: 10% The Commission advocates astronauts operating observatories on the moon, but it would surely be better — not to mention cheaper — to position those telescopes in space, well away from any human activity. In order to be as sensitive as possible, telescopes need to be kept cold and free from vibration, and it is difficult to see how an expensive and noisy manned presence nearby would help. Hubble’s successor, for instance, will be stationed 1.5 million kilometres from the Earth and will be kept at a temperature

Focus

just 35 degrees above absolute zero. It is true that astronauts would be much better than robots at making detailed investigations of the Martian surface, but robots are cheaper, safer, and improving rapidly in capability. Unmanned missions can be prepared much more quickly than manned

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At today’s prices, the Apollo Program cost $100 billion. Nasa’s current robotic Mars rovers cost less than one percent of that price

ones, and planners can then use data from previous missions to select new research priorities. A manned mission, by contrast, would be decades in the making and could be seen as redundant before it even left the ground. At today’s prices, the Apollo Program (1963–72) to send men to the moon cost $100 billion. Mars is much harder to get to, yet Nasa’s current robotic rovers cost less than 1% of the price of Apollo. They have been able to crawl more than 7 kilometres over the surface of Mars, and provide detailed field evidence of how parts

Mars Milestones 1964: First successful fly-by, by Nasa’s Mariner 4, shows parts of Mars to be desolate and cratered, far from the popular stereotype of an inhabited and fertile world. 1971: Soviet Union successfully lands a spacecraft on Mars, but transmissions stop after just 20 seconds. 1975: Nasa successfully lands the two Viking spacecraft on Mars. The Viking 1 lander returns data for over six years, whilst the orbiters map the whole of the Martian surface. For the first time, features caused by water — such as dried-up river beds — are photographed. 1989: George Bush Sr pledges to send men to Mars but, at a cost of more than $400 billion, Congress rejects the plans. 1996: Scientists make controversial claim that Martian meteorite ALH84001 contains fossilized alien bacteria (see History, pages 24–25). 1997: Nasa’s Mars Pathfinder mission successfully lands on Mars. It carries a small rover, which returns data for nearly three months. The Mars Pathfinder website gets 30 million hits in a single day. 2003: European Space Agency launches the Mars Express Orbiter, which provides the best evidence to date that water ice is buried beneath the Martian soil. The UK’s Beagle 2 lander is lost without trace. 2004: Nasa successfully lands two golf-buggy-sized rovers on the Martian surface, which have since crawled more than 7 km and provided conclusive evidence that the surface of Mars was once wet.

of it were once covered by water. The case for government investment in human habitation and mining in space is more shaky. Proponents of space exploration sometimes argue that we might one day run out of places to live on Earth, but living in space would be profoundly

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expensive. Presently, it costs $10,000–$30,000 per kilogram to put a load into space, a figure that has barely fallen in 20 years. Launching five space shuttles requires as much energy as released by the bomb that destroyed Hiroshima.A recent UN report estimated that by 2300 the world’s population will level out at about 9 billion — this is 50% higher than today, but does not necessarily mean that inhabiting space is the only, or the best, option. Finally, for those who still dream of space, we may soon see the emergence of a private market in space travel. In June last year, Burt Rutan, an American, became the first individual to reach space in a privately funded spacecraft. Richard Branson has ordered five: prices will start at about £100,000 for a 3-hour hop, but are expected to fall as demand increases and the technology improves. But to some extent such criticism misses the point. Government space programmes have never been just about science and they have certainly never been about economics. They are about exploration and the inspiration of national pride, and Bush is correct that Nasa’s current manned programme fails to do either. But there are cheaper, more novel, and more deserving sources of inspiration than sending men back to the moon, and they include attempting to answer the biggest question of all: are we alone?

It’s life, but not as we know it In our own solar system, there are two candidates for life. The first is Mars. Mars may be cold (as low as -140°C at the poles) and have a surface atmospheric pressure one two-hundredth that of the Earth; but we know from probes in orbit that it has subsurface water ice, and it has been volcanically active within the recent geological past. There may well be hardy organisms living deep in the soil or in fractures flushed by hydrothermal fluids. Nasa’s next Mars rover, to arrive in 2010, will carry instruments to detect organic molecules in samples it collects. The second is Jupiter’s moon Europa. Europa is even colder than Mars, and has no atmosphere at all, but underneath its icy surface there appears to be an ocean: observations of Europa’s magnetic field taken by the Galileo probe in 2000 indicate a fluid conductor fairly close to the surface. Sending humans there is out of

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the question: one day sending a robot to slowly melt its way through the ice and look for life is not. Indeed, a working team is being set up to look at the possibility of a joint venture to Europa between the European Space Agency (ESA) and Nasa. But it is the idea of other Earths that really gets people excited. In the last few years, astronomers have realised that planets are both a lot more common and a lot more diverse than once thought: to date, 145 (decidedly non-Earth-like) planets around nearby stars have been identified. Imaging Earth-like planets around nearby stars would require unfeasibly large mirrors or lenses, because the resolution of a telescope depends on its diameter. However, instruments known as interferometers may be up to the job, and Nasa plans to start flying them in orbit within 20 years. Interferometry is a technique in which one recovers information about a source by combining several observations of the source taken far apart but at exactly the same time. It has been used by radio astronomers to produce images of bright radio sources with a hundred times the resolution of the Hubble Space Telescope. Achieving the same with light, which has a much shorter wavelength, is much trickier, but possible, as a recent experiment by the University of Cambridge’s Cavendish Astrophysics group, COAST, showed. Their interferometer, less than 100 metres across and costing just £850,000, was able to image the surface of a star for the first time: a task far beyond even Hubble. Unfortunately, Nasa has a history of wasteful investments and overblown rhetoric. It also has some of the best engineers in the world and no shortage of worthwhile projects that won’t demand that astronauts risk life and limb. The circus that surrounds sending humans into space is both inefficient and scientifically unrewarding; George Bush should give Hubble a few more years, and then have the courage to leave manned spaceflight behind. The astronaut is yesterday’s icon. Virginia Hooper is a fourth year Natural Scientist, specialising in Geology; Alistair Crosby is a PhD student in the Department of Earth Sciences; Louisa Dunlop is a PhD student in the Department of Physics

Further Reading Hubble Space Telescope http://hubblesite.org Jet Propulsion Laboratory www.jpl.nasa.gov President’s Commission on Moon, Mars and Beyond http://govinfo.library.unt.edu/ moontomars A Budgetary Analysis of NASA’s New Vision for Space Exploration www.cbo.gov/showdoc.cfm? index=5772&sequence=2

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Fo c u s

Ask the Experts

Would you advise that future missions to space should concentrate on understanding the cosmological history of the universe, or instead on exploring our planetary neighbours, perhaps by sending humans there?

Professor Monica Grady, Open University would hesitate to suggest that cosmology is completed, but that is the impression that I frequently come away with after listening to descriptions of the Big Bang and similar topics. We can only explore so far back in time (space), before the laws of physics, both classical and quantum mechanical, can no longer be applied with any realism. Theory then comes into play, with strings, branes, multiverses and the spectre of time travel through wormholes perhaps bringing us closer to science fiction than reality. So although understanding the cosmological history of the universe is an important goal, it is, at the moment, theoretically impossible to achieve. In contrast, human exploration of our solar system is, for the time being, technically difficult to achieve. But certainly practicable in the not too distant future. And there is certainly a huge amount that we still need to learn about our local neighbourhood.Was or is there life on Mars? What is below Europa’s icy ocean? What is the structure of Callisto? Why does it have a magnetic field? Why doesn’t Venus have a magnetic field? What is the other side of Mercury like? Is Pluto a small planet, or a large Kuiper Belt Object? These

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in sending people into space at all. But as a human being, I’m nonetheless an enthusiast for space exploration — to the moon, to Mars and even beyond — as a long-range adventure for (at least a few) humans. But this will only happen when costs come down drastically. Present launching techniques are as extravagant as air travel would be if the plane had to be rebuilt after every flight. Manned spaceflight will only be affordable when its technology comes closer to that of supersonic aircraft. The International Space Station is neither practical nor inspiring — more than 30 years after Apollo, it merely allows astronauts to circle the earth at inordinate cost.There is maybe just one argument for it: if one believes that in the long-run space travel will become

Nasa, J. Bell (Cornell U.) and M.Wolff (SSI)

Professor Sir Martin Rees,Astronomer Royal hose of us who are now middleaged can remember the murky live TV pictures of Neil Armstrong’s ‘one small step’ in 1969. We imagined follow-up projects: a permanent ‘lunar base’, rather like the one at the south pole; or even huge ‘space hotels’ orbiting the Earth. Manned expeditions to Mars seemed a natural next step. But none of these has happened. The year 2001 didn’t resemble Arthur C. Clarke’s depiction, any more than 1984 (fortunately) resembled Orwell’s. But the use of space for communications, meteorology and navigation has forged ahead in the last three decades — as of course has astronomy, and surveys of the planets. Space exploration for scientific purposes can be better (and far more cheaply) carried out by fleets of unmanned probes, exploiting the advances that have given us mobile phones and powerful laptop computers. The practical case for manned spaceflight gets ever weaker with each advance in robotics and miniaturisation. Indeed, as a scientist, I see little purpose

are just a few questions outstanding within our own solar system. Why send humans to explore, though, and not robots? Both types of mission are necessary. Robotic exploration must be a pathfinder before humans can venture onto other planets.This will give us the confidence that we understand the measurable properties (temperature, pressure, gravity, light level, wind speed and so on) of a planet before we suffer the psychological and physical problems of the journey. Why do humans need to go? Robots are only as clever as the program that controls them. Humans exercise judgement and make decisions.Without this, planetary exploration is likely to be limited to drilling holes in rocks and taking photographs. ESA and Nasa have announced ambitious plans for the human exploration of space. Russia, China, India and Japan are also investing in space exploration. It is likely, probably necessary, and certainly desirable that any missions involving human space exploration should be

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routine, it ensures that the 40 years’ experience of the US and Russia isn’t dissipated.The next humans to walk on the moon may be Chinese — only China seems to have the resources, the dirigiste government, and the willingness to undertake a risky Apollo-style programme. If Americans or Europeans venture to the moon and beyond, this will have to be in a very different style, and with different motives. Costs must come down to the level when the enterprise could be bankrolled by private consortia. And there must be an overt acceptance that the enterprise is dangerous. The US public’s reaction to the shuttle’s safety record — two disasters in 113 flights — suggests that it is unacceptable for tax-funded projects to expose civilians to even a 2% risk. And the first explorers venturing towards Mars would confront — and would surely willingly accept — far higher risks than this. Future expeditions to the moon and beyond will only be politically and financially feasible if they are cut-price ventures, perhaps privately funded, spearheaded by individuals who accept that they may never return. multinational, and undertaken in the name of humanity in general and not of one nation, or group of nations in particular. Only in that way would I be a whole-hearted and enthusiastic supporter of human space exploration.

Dr Michael Foale, Astronaut and Deputy Associate Administrator for Exploration Operations, Nasa pace science, including both cosmology and the study of our solar system, is part of human exploration, driven by curiosity and a need to master our environment, for security. When exploring space, both new understanding and vicarious personal exploration of planetary surfaces, oceans or atmosphere serve to motivate and inspire us. So when we have limited resources for exploration and scientific inquiry, immediate questions and economic possibilities involving the solar system need to be balanced with the potential of discovering fundamental laws through new understanding of cosmology and unification of physical theories. In simple language we should keep our options of discovery open, but concentrate on those areas providing nearterm results.This includes human exploration of the south pole of the moon, and human exploration of Mars.

Giving Elephants Wings: The Science

All images: Jon Heras

After the sequencing of the human genome, the next big challenge for modern biology is to uncover our ‘proteome’, the identity of the proteins in our cells. Nicholas T. Hartman reports In many ways a living cell is analogous to a computer. The DNA, or hard disk, stores the necessary programming codes to produce the proteins, or programs, found within the cell. Proteomics is the field focused on identifying all the proteins in an organism or cell type, what their functions are, how they interact with one another and how their expression level varies in response to environmental changes. Proteomics is considered one of the hottest areas of science today. A search of the scientific publications database PubMed for the terms ‘proteomic’ or ‘proteomics’ yielded 373 articles published prior to 2001. By comparison, in just the first two months of 2005, a staggering 393 articles have been published on the subject. This is the story of how the physical and biological sciences join forces to create such a dynamic field. Proteins consist of chains of amino acids strung together via peptide bonds. Most cells use a palette of around 20 amino acids to assemble each protein according to the instructions permanently encoded in the cell’s DNA. In addition to a common backbone that holds the long chain together, each amino acid contains a functional group featuring a wide variety of different chemical species. Just as a skilled artist can create a complex painting from a small set of basic colours, the cell can join together different amino acids in a precise order to create a set of complex biopolymers. These are essential for the wide range of chemical reactions that support life. An ‘operating system’ of specific proteins is

required by almost every cell for essential functions such as energy metabolism, DNA replication or cell division. However, different cell types can synthesise the other proteins that are required to perform more specialised tasks.

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allowed for better sensitivity and mass accuracy, the inability to form ions from high molecular weight species generally limited this technology to the analysis of smaller molecules. A ‘small’ molecule such as Vitamin C weighs about 176 Daltons

Proteomics is revolutionizing the process of drug discovery

The science of proteomics is grounded in the ability to identify a protein rapidly by analysing portions of its sequence. Historically, proteins could be sequenced through a chemical reaction called Edman Degradation, by which amino acids are removed and identified one by one from one end of the protein. Dr Kathryn Lilley, head of the Cambridge Centre for Proteomics, says that although this technology has been used successfully, it is very low throughput and does not work well for all proteins. However, the advent of mass spectrometry (MS)-based protein analysis in the 1990s set the stage for the explosion of proteomics as a field. In its most simplistic form, MS can be viewed as a very accurate balance capable of measuring the mass of individual molecules and even atoms.The first generation of MS instrumentation was designed by J. J. Thompson and his associate Francis Aston at the Cavendish Laboratory around the beginning of the twentieth century. MS relies on the ability to manipulate and detect electrically charged molecules, called ions, moving through a vacuum. Through the use of ‘ion optics’, a beam of ions can be pushed, pulled and focused by forces from magnetic fields and electrically charged plates. One of the most common designs of modern mass spectrometers is based on the principle of time-of-flight.A time-offlight instrument measures the time it takes an ion, accelerated with a specific amount of energy, to travel a set distance in a vacuum.When the same force is used to push a set of ions with the same charge but different mass, the lighter ions will travel faster.With a properly calibrated instrument, travel times can be used to calculate an ion’s mass-tocharge ratio and ultimately its mass. Ion creation is the first and most difficult step in analysing a molecule by MS. Although newer instrumentation has

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(Da), but a single protein can easily weigh upwards of 100,000 Da. Some of the original ionization techniques, which used harsh conditions such as heat or collision with energetic electrons to form ions, failed for molecules with a mass of more than around 1000 Da. In the 1980s there were several major advances including the development of two techniques called Electrospray Ionization (ESI) and Matrix Assisted Laser Desorption Ionization (MALDI) that increased, by several orders of magnitude, the mass range of molecules that could be ionized successfully. For the first time scientists could introduce very large molecules, including whole proteins, into the MS: John Fenn, the developer of modern ESI, commented that it was like “giving elephants wings”. Signifying the importance of these advancements, Fenn and Koichi Tanaka shared a portion of the 2002 Nobel Prize in Chemistry “for the development of methods for identification and structure analyses of biological macromolecules”. MS-based protein sequencing relies on the principle that ionized chains of amino acids in a vacuum can be fragmented in a predictable manner. In practice, samples for analysis are often first digested with the enzyme trypsin (left) in order to cut a protein (top right) into specific smaller sections (peptides, right) with masses in the optimal fragmentation range of 500–5000 Da. A mass spectrum is taken of the products and compared to a database of predicted spectra for peptide sequences from all the proteins in the organism being studied.These databases are compiled from a sequenced genome by identifying possible peptides through bioinformatic predictions. In the final analysis, sequences of the peptides are matched up with the proteins from which they originated to generate a catalogue of proteins, along with statistical scorings

The Dalton

The unit of measure for atoms. roughly equal to the weight of one proton or hydrogen atom. One Dalton weighs 1.066 x 10-24 grams.

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Proteomics

indicating the confidence of identification. Proteomic analysis ranges from identifying a single unknown protein to studying as many proteins as possible in a particular tissue sample. Most proteins live a very secretive life, and although scientists can predict the existence of novel proteins from genomic analyses, it is difficult to observe their presence experimentally and investigate their role in the cell without proteomics. With the sequencing of entire genomes now almost routine — mainly a matter of time and money — the next frontier in biotechnology is the identification of all the proteins in a cell: its proteome. Analysing the proteome is, in many ways, a much more challenging problem than analysing a whole genome.Through alternative splicing of the RNA template and post-translational modifications of the protein itself — which are not obvious by looking at the DNA sequence alone — a genome of 22,000 genes can produce over 500,000 different protein forms! A diseased state or other condition may involve only certain spliced forms of a gene or alterations in post-translational modifications. Thus, proteomic analysis is on the front line of identifying cellular changes that can be difficult, if not impossible, to analyse by genomic approaches alone. More recently the concept of ‘quantitative proteomics’ has greatly expanded our ability to study challenging biological questions not only by identifying proteins, but also by studying the relative abundances of two or more different samples, in order to ask questions such as what happens to the expression levels of specific proteins in response to environmental stress or when in a diseased state. According to Lilley,“the ability to measure dynamic changes in protein abundance provides much more information than just cataloguing which proteins are found in the cell”. You can’t fix something if you don’t know what’s broken. Understanding how cells respond to stress increases our general knowledge of how cells work, and can yield valuable clues towards developing treatment options for a wide variety of conditions.Thus proteomics is revolutionizing the process of drug discovery by providing researchers with tools to identify which proteins are at the core of the onset of disease. Once targets have been identified, novel drugs can be designed to interact specifically with these proteins. Several companies have successfully designed extensive profiling technologies to identify the expression and activity of proteins within a sample, often with drug discovery in mind. For example, the Canadian company Kinexus offers customers the ability

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to create expression and activity ‘fingerprints’ for different protein families, such as kinases. In one example of their work, Kinexus has developed assays to screen for molecules that interact with specific proteins as a route to identifying potential targets for future drugs. One promising but controversial area of proteomics research is focused on identifying ‘diagnostic biomarkers’. This is the identification of specific biological molecules, such as proteins, which have reproducible changes in abundance between diseased and normal patients, thus allowing a biomarker assay to make a diagnosis before any obvious symptoms appear. Although many experiments have successfully observed changes in protein expression in mutant or diseased cells, many scientists and investors have been skeptical of the technology’s ability to allow accurate and early diagnoses in patients. To date, many publicly traded biotechnology companies such as Ciphergen, Compugen, Icoria, and Luminex have had difficulty convincing investors of their visions for biomarker technology and consequently have experienced significant decreases in stock price since their initial public offering. Ciphergen produces protein chips integrated with MS analysis and software to analyse complex protein mixtures for biomarkers. Wall Street has certainly been wrong in the past, and with the development of these and other promising technologies across the board, only time will tell if diagnostic biomarkers have a longterm viable business future. Although the sequencing of a specific genome can be finished, it will be much harder to say when, if ever, the analysis of an organism’s proteome is officially completed. Some of the cell’s most important and complex proteins are only present at very low levels, and just as each new telescope unveils a whole new cosmos to astronomers, improvements in sensitivity will open up a whole new world of fascinating proteins never before observed experimentally. With continuing advances in MS technologies, ongoing genome sequencing projects and the ever-increasing number of labs using MS-based protein analysis in their research, the future of proteomics looks bright. Who would have ever thought that ‘flying elephants’ could tell us so much. Readers interested in a more technical explanation of proteomics should refer to Nature Reviews Molecular Cell Biology 5: 699–711 (2004) Nicholas T. Hartman is a PhD student in the Department of Biochemistry

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Jon Heras

What Does F# Taste Like? Andrew Lin examines the phenomenon of synaesthesia What colour is the letter D? To most people, this question is meaningless, but some would feel confident saying that D is yellow, or that F-sharp is spicy and sour. These people have synaesthesia — literally, ‘joined sensation’ — a rare and fascinating condition that mixes different senses, so that a perception that normally occurs in just one sense, like hearing, also triggers secondary perceptions in another such as taste. Though these mixed perceptions may seem simply like overextended metaphors, they are very real to synaesthetes, and may even provide insights into human consciousness. All combinations of senses are possible in synaesthesia, but the most common form, in two-thirds of cases, is letter-colour synaesthesia. For these synaesthetes, each letter or digit evokes a perception of colour: the letter K might be lime-green, or the number 6, sky-blue.Words can have colours too, usually determined by the first letter of the word. These colour perceptions might be elicited by either printed or, more rarely, spoken words. Less commonly, some synaesthetes see specific colours when perceiving musical pitches, everyday sounds like a car horn, or odours and tastes. In some cases, synaesthetic perceptions can be quite complex, combining shapes, colours and textures, so that one might say a sound “looks like red, jagged triangles”. There are plenty of more exotic combinations. For example, some people perceive numbers as existing in a highly spe-

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One man complained that a dish tasted wrong because ‘there aren’t enough points on the chicken’

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cific spatial pattern. Xavier Seron and colleagues at the Université Catholique de Louvain, in Belgium, described one man for whom numbers existed on a line, with 1–10 going 45° up to the right, then after 10 turning abruptly to proceed straight to the right. Neurologist Richard Cytowic revealed how one man complained that a dish he cooked tasted wrong because “there weren’t enough points on the chicken”.The man also described the taste

of mint as having the texture of “cool glass columns”. Cytowic even reported one teenager who adopted specific postures in response to the sound of different words. Given the difficulty of understanding someone else’s subjective perceptions, you might wonder if these sensations are ‘real’ or just especially vibrant metaphors. In fact, the perceptions are highly reproducible: synaesthetes immediately report the same associations when tested unexpectedly years later. Moreover, psychological experiments have established that synaesthetic perceptions occur automatically and strongly influence sensory processing. These experiments adapt a task called the Stroop test, where subjects see

to find the 2 in a field of 5s. The added colour feature on the numbers makes the visual search much more efficient. The causes of synaesthesia are still largely mysterious. There is likely to be some genetic component: synaesthesia runs in families, with an inheritance pattern that suggests that the genetic factor may be on the X chromosome. Also, though most synaesthetes report having their unique perceptions as long as they can remember — many, in fact, are surprised to find that other people do not share their perceptions — synaesthetic experiences can also be induced by neurological conditions such as epilepsy. Some researchers have speculated that synaesthetes may have extra connections between brain circuits that normally process different sensory modalities. Interestingly, babies have a large excess of neural connections that later get pruned as the circuits are refined. Professor Simon Baron-Cohen, working at the Autism Research Centre here in Cambridge, has suggested that all babies might be synaesthetic because of extra connections between sensory circuits, and that adult synaesthesia occurs when some of these connections are not pruned. Intriguingly, synaesthetic associations often tend to follow associations made by

A Stroop test: say each word out loud, then the colour of each word in turn

names of colours printed in coloured ink, and are asked to name the colour of the ink, not the name printed. For example, if the word red is printed in green ink, one would answer “green”. Ordinary people are much slower to respond when the ink colour does not match what is printed, because reading the printed word is so automatic that it interferes with the correct response. The Stroop test can be adapted for letter-colour synaesthetes: a subject is asked to name the colour of the ink of a single letter, where the letter is printed in a colour that either matches, or does not match, that person’s synaesthetic colour perception. So, if someone perceives the letter K as green, they will be slower to name the ink colour presented if K is printed in red than if it is printed in green. The result indicates that the synaesthetic colour perception associated with specific letters is automatic. Another experiment that shows that synaesthetic colour perceptions are genuine involves a ‘search’. For normal subjects, it is easy to spot a pink dot in a sea of yellow dots relatively quickly, but it takes a long time to search out the number 2 in a field of 5s. But for a synaesthete who sees 2 as pink and 5 as yellow, it is relatively easy

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non-synaesthetes. Sound-vision synaesthetes tend to see light colours and angular shapes upon hearing high-pitched sounds, and dark colours and rounded shapes for low-pitched sounds. If forced to choose, non-synaesthetes tend to do the same, and even show interference in the Stroop test — delayed reaction times to visual stimuli that don’t match an accompanying sound. These spontaneous biases suggest that there may be some unconscious connection between hearing and vision in everyone, which reaches consciousness only in synaesthetes. Indeed, synaesthesia puts a wrinkle in one of the main problems of human consciousness, the so-called binding problem. After sensory input has been split up by all the specialised processing areas of the brain, how does it all come together into a unified subjective perception? In synaesthesia, apparently extra sensory features are ‘bound’ to the normal set, so understanding what happens differently in synaesthetic brains could provide clues as to how conscious perception arises in ordinary brains. Andrew Lin is an MPhil student in the Department of Anatomy

Easter 2005

The Killer Within Bojana Popovic goes hunting for superbugs

S. aureus usually lives harmlessly in the noses of 20–30% of healthy people. It only poses a threat if it invades open wounds, where it will cause infections. The use of penicillin revolutionized treatment of S. aureus infections, but shortly after its introduction to clinical practice, penicillin-resistant strains of S. aureus emerged. Alternative antibiotics (primarily methicillin) were employed to fight these infections, but MRSA evolved soon after. During the 1960s, MRSA was relatively uncommon. More cases appeared in the 1980s, but the problem exploded in the mid-1990s when particular ‘epidemic’ strains of

MRSA became established in hospitals in the UK. These strains now represent over 40% of the S. aureus that cause bloodstream infections in England. Recently MRSA has acquired multiple antibiotic resistances, leaving its infections virtually untreatable.

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Experts have so far uncovered 17 strains of MRSA

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Resistance is transmitted genetically by a bacterium to its progeny. Importantly, genes that carry resistance can also be transmitted from one bacterium to another by plasmids — carriers of chromosomal fragments containing just a few genes. Evolution of resistance provides bacteria with a competitive advantage in the environment and better subsequent survival chances. Bacteria reproduce at a staggering rate, so antibiotic resistance spreads very quickly once it evolves. One of the main ways in which bacteria become antibiotic-resistant is through evolution of a mechanism that inactivates the drug, and it is in this way that S. aureus developed resistance to penicillin. S. aureus acquired the ability to produce β-lactamase — an enzyme that inactivates penicillin and other antibiotics such as ampicillin — by hydrolysing the β-lactam ring that is central to their structure. Most S. aureus strains are now β-lactamase producers and thus are resistant to penicillin and ampicillin. However, these strains are susceptible to some β-lactam antibiotics such as nafcillin, methicillin or oxacillin, which are all β-lactamase-resistant. Methicillin resistance in Staphylococci is due to the acquisition of the mecA gene which encodes for the penicillin-binding protein (PBP) 2A. PBP 2A has a low affinity for all β-lactams, and confers resistance to all β-lactam antibiotics, including those that are resistant to βlactamase such as methicillin.

MRSA in the UK

• Deaths from MRSA infections have doubled from 1999–2003: 487 deaths were attributed to MRSA in 1999, compared with 955 in 2003. This is in part due to better reporting. • Recording of MRSA infections in UK hospitals has been mandatory since 2001.

• More than 7,000 hospital patients have been affected by MRSA in the UK each year since 2001. • Recent reports show that infections in England and Wales dropped by 6% in the last 6 months, when compared to the same period last year.

Source: BBC News http://news.bbc.co.uk

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The antibiotics of last resort that can still treat MRSA are vancomycin (left) and teicoplanin (below). These are both glycopeptide antibiotics and members of a vancomycin-like family of antibiotics that inhibit synthesis of the bacterial cell-wall.Vancomycin was originally isolated from soil taken from the jungles of Borneo. The purified compound exhibited lethal properties against all tested strains of Staphylococci as well as other bacteria which share the same cell-wall structure. Vancomycin is produced by the fungus Amycolatopsis orientalis and was first used in the clinic in 1959, in response to the strains of Staphylococci that were becoming resistant to penicillin. Teicoplanin — very similar to vancomycin — was isolated in the mid-1970s as a fermentation product of bacteria Actinoplanes teichomyceticus. The introduction of methicillin reduced the use of vancomycin for some years, but it was reinstated as a therapeutic agent when methicillinresistant S. aureus, MRSA, strains appeared. The acquisition of resistance by S. aureus to virtually all antibiotics in clinical use has propelled the vancomycin group of antibiotics to the forefront in the fight against MRSA. Experts have so far uncovered 17 strains of MRSA, with differing degrees of drug resistance. Frighteningly, US scientists have isolated VRSA, a strain resistant even to vancomycin. Teicoplaninresistant strains have also been detected.

Bojana Popovic

Antibiotics, from the Greek words anti (against) and bios (life), are chemicals produced by microorganisms that are capable of killing bacteria or inhibiting their growth. They have enabled the effective treatment of once life-threatening infectious diseases such as tuberculosis. Over one hundred years after the discovery of penicillin, the role of antibiotics in the treatment of infectious diseases is still as important today. An unfortunate side-effect of widespread antibiotic use has been the appearance of bacteria that are resistant to most commonly used antibiotics. Very recent examples of this type of resistance are the methicillin-resistant strains of Staphylococcus aureus, the socalled MRSA superbugs.

The most obvious way to address the problem of antibiotic resistance is to develop new kinds of antibiotics. Unfortunately, wider antibiotic use could shorten the cycle time for development of resistance, making antibiotics into a finite resource.This makes the search for new antibiotics financially unattractive, and it may be that the only sustainable option for combating resistance in the short- to long-term is to return to old strategies of fighting disease, namely surveillance and education. Bojana Popovic is a postdoc in the Department of Biochemistry

Cell-ID tells the user the area they are in, determined by looking up which base station is currently serving them

Dude, Where’s My Phone? Ramsey Faragher pin-points the latest innovation in mobile phone technology

Abinand Rangesh. Figures: Ramsey Faragher

You have arranged to meet a friend in a busy high street in London. She isn’t answering her phone, and you haven’t got a hope of finding her just by wandering around.Wouldn’t it be handy if you both had mobile phones that could be instantaneously and accurately positioned? The applications for such a technology are endless: keeping a watchful eye on your children; tracking goods and deliveries; seeing exactly where the bus you are waiting for is (and being able to decide whether to wait for it any longer); navigating when you are lost; finding a cash machine, petrol station or hotel; and perhaps, crucially, enabling the emergency services to locate you immediately when you call them. Currently, any mobile phone can be positioned to within the cell it occupies, i.e. the area of coverage of the base station that is serving the mobile phone at a given moment (see figure below). This is called the Cell-ID method. In rural areas, where there are few tall buildings to block signals, powerful macrocell transmitters can be used to provide coverage for 35 kilometres or more. Within cities, where buildings are densely packed, macrocell coverage is enhanced by placing microcell transmitters every few hundred metres or so.There are even picocell transmitters in use inside buildings, in tunnels and on cruise-liners to provide coverage within a 50-metre range. However, Cell-ID determines only the position of the base station that is serving your phone, and so the accuracy is dependent on the range to the base station. If a person happens to be using the tube, being served by picocells, they can be located quite accurately, but in most cases you cannot rely on Cell-ID to give a useful position fix. It is only adequate for tracking goods and looking up information on the local area. Vodafone, for example, uses Cell-ID for their Find and Seek service, which is regularly used by the police to determine the last known position of an abducted person. Improved accuracy can be achieved by combining Cell-ID with further infor-

mation from the network.Whilst making calls on the move, your mobile is constantly monitoring the network, deciding when it needs to be handed over to a new serving base station. The changeover is determined by the signal strengths of the nearby base stations.The time it takes for signals to get to and from the base stations (the Timing Advance, TA) is also measured. Enhanced Cell Global Identity (ECGI) uses these measurements to make a more accurate estimate of the position of the mobile. The accuracy is better than Cell-ID, but is limited by the large error in relating signal strength directly to distance and by the resolution of the TA timings. Signal strength is strongly affected by the environment the phone is in: moving a few metres in open space outside will not change the signal strength significantly, but moving a few metres into a building from outside causes a noticeable reduction. Signal strength, therefore, can provide only a very rough estimate of the distance from the phone to a base station. TA allows your mobile to compensate for the time-of-flight of the signals to and from the base station. This is needed to prevent the signals from all mobiles using a particular base station at a given

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moment from arriving at different times depending on their distances from the base station, as these times would keep changing if the mobiles were moving. Each kilometre of distance delays the signals by a little over 3 microseconds, so a busy cell would have to deal with signal delays ranging from almost zero, for a caller right next to the base station, to 100 microseconds, for someone right at

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Wouldn’t it be handy if you both had mobile phones that could be instantaneously and accurately positioned?

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the edge of a rural cell. The additional processing performed by the base stations would increase costs and complexity considerably.To overcome this, the handsets are asked by the base station to advance their times of transmissions (by the TA value) so that everyone’s signals arrive when the base station is expecting them. These timing adjustments corre-

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Image used with permission of Cambridge Positioning Systems. Based on Ordnance Survey mapping © Crown copyright. Media 671/05

spond to an error of 570 metres on the ground — helpful for positioning purposes, but still not that accurate. Triangulation has always been a straightforward positioning method in navigation, but is not very practical in a mobile phone system. One must calculate the directions from which the signals arrive at the mobile or at the base station. A large antenna (or two smaller antennas fixed a long way apart) is needed in order to measure this. Such an arrangement is sensitive to the direction of arrival of a signal, and the larger the antenna — or the wider apart the two smaller ones — the finer the angular resolution. Large antennas are impractical for mobile phones and large antenna arrays on the base stations further increase costs and complexity.

A mobile tracked on a journey around Cambridge using Solo Matrix

Another idea is to equip mobile phones with small Global Positioning System (GPS) receivers so that you can use your phone like a ‘sat-nav’ device in a car. GPS works out your position via satellites orbiting the Earth.There are 24 active satellites in the GPS constellation, but at any one time a GPS device can generally only see about one-third of them. Positioning this way requires direct lines of sight to at least three satellites, as their signals are very weak by the time they reach the Earth’s surface. GPS works with high accuracy outdoors in rural and suburban areas where there is always a reasonably good view of the sky. However, if the phone is in your pocket or bag, or you are indoors or in an area where the sky is obscured by tall buildings, the system does not work — a serious limitation when considering the typical scenarios for positioning a call to the emergency services, or locating an abducted or lost person. This is partly ameliorated by adding ‘assistance’ to the system, in which the GPS receiver is told where to look for satellite signals by messages sent from a central point in the mobile phone network. However, even with assistance the reception is often very poor and the caller has to wait a long time for a position fix, if one is available at all. The most promising technique today is called Matrix and was invented here in Cambridge. Matrix was developed by Dr Peter Duffett-Smith of the Cavendish Laboratory as an offshoot of positioning

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The most promising technique today is called Matrix and was invented here in Cambridge

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work he did during a radio astronomy project. Dr Duffett-Smith was using a technique called aperture synthesis to study distant radio sources. The method involved simultaneously gathering data with two or more radio telescope antennas that were separated by some distance. The resolution of the images improves as that distance increases. However, for the method to have worked the distance between the antennas had to be known to the nearest metre, even when they were more than 1000 kilometres apart. DuffettSmith found that not only could he use public broadcast FM radio signals, such as BBC Radio, to position a radio receiver attached to his telescope, but that this technique could be adapted to position any mobile radio device. In order to develop this technique for mobile phones he established Cambridge Positioning Systems Ltd. However, mobiles just measure the intensity of the signals they receive on one channel, whereas Duffett-Smith’s original technique required phase measurements on multiple channels. Matrix gets around this problem by solving a set of non-linear simultaneous equations using timing measurements made by the handsets on signals received from the base stations.A derivative of this system is Solo Matrix: a single handset can be positioned as long as it is moving, building up its own network timing model with the data it gathers on the move. Another enhancement of Matrix currently under development is called Enhanced GPS (E-GPS), which combines the high accuracy of GPS in rural areas with the high availability of Matrix in urban areas. The timing data gathered during Matrix calculations can also provide assistance data for a faster GPS fix. The Matrix equations assume that signals travel in straight lines directly to the mobiles from the base stations, but in urban areas and indoors the signals can undergo reflections and diffractions before reaching the mobile, leading to longer, more complicated propagation paths. By determining what the dominant delay processes are, and when signals transmit straight through a building and when they do not, these extra time delays can be modelled and incorporated into Matrix and E-GPS in order to improve the positioning accuracy further. Truly, the Matrix revolution is coming. For more information on Matrix go to www.cursor-system.com Ramsey Faragher is a PhD student in the Department of Physics

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Rough measurements of the signal arrival times are possible using Timing Advance, but its timing resolution is poor, which in turn limits the positioning resolution.

Measurements of the Angle of Arrival of signals (triangulation) is not possible with current handsets and the current GSM network. This system could only be implemented with network changes or new handset technology.

Matrix builds up a database of timing measurements from a network of mobiles, or from a single moving mobile, in order to solve a set of nonlinear simultaneous equations and calculate the positions of the handsets. The dashed arrows represent the timing measurements of each base station at each mobile. Once there are enough timing measurements, the relative positions of all the handsets and base stations from any arbitrary point can be calculated (black lines). Since the exact positions of the base stations are known, and their positions relative to the handsets can be calculated, the exact positions of the mobiles can be determined.

Jonathan Zwart. All figures by the author

The Quantum Conundrum

Peter Mattsson looks at Einstein’s battle with quantum theory Einstein is most famous for his two theories of relativity — special and general — but he also made significant contributions to quantum theory. In fact, his Nobel Prize was awarded for his quantum explanation of the photoelectric effect in 1905. Despite his initial contributions, however, he came to be deeply concerned about some of the counterintuitive predictions of quantum theory. He became so disillusioned that he spent much of his later life devising thought experiments to show the apparent absurdity of quantum theory.

quantum effects are very unusual, but do not really break the speed limit; to see that, however, we have to go on a miraculous journey, beginning right back in 1905. Shining light onto a piece of metal causes electrons to be ejected from the atoms at the surface, generating a measurable current (below left). This ‘photoelectric effect’ was discovered by Heinrich Hertz in 1887. This in itself was not a surprise: light carries energy and transferring this to the electrons in the metal could have given them the impetus they needed to escape. The real surprise came when

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‘Non-locality’ is the apparent ability of some quantum effects to be transmitted instantaneously through space over arbitrarily large distances

In particular, he was concerned about ‘non-locality’: the apparent ability of some quantum effects to be transmitted instantaneously through space over arbitrarily large distances. To the man who discovered that the universe’s ultimate speed limit was the speed of light, this made no sense. As we shall see, these

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the electrons being ‘kicked out’ by individual photons. For sodium, photons of red light, which have relatively long wavelengths, have too little energy to eject any electrons, no matter how many photons there are. By contrast, photons of violet light, which have a shorter wavelength, do contain enough energy, so that even a few of them eject a few electrons. Put like that, Einstein’s idea seems very simple, but it had at its heart a radical idea: that light was a particle, not a wave. This was a problem. Einstein and Planck had both applied the idea to phenomena that could not be explained by a wave theory, but what about all the other phenomena that were well described in terms of waves? In particular, what about interference? Imagine what would happen if a beam of light was shone through a pair of narrow slits and onto a screen. With only one slit, the results would be rather dull: just a bright patch on the screen. With two slits, though, the result is a pattern of bright and dark bands, known as interference fringes (below). As with water waves, light waves have peaks and troughs, and when the peak of the wave from one slit encounters the trough of the wave from the other, the two extrema cancel out to create a dark band. Conversely, when a peak from one slit meets a peak from the other, a bright band is created. With a wave theory, interference seems ordinary and natural, but how do we square all this with the concept of photons? Particles cannot interfere with each other in this way; while they could possibly bounce off one another, this would be a rare event for such small particles. Any ordinary particle theory would predict that two slits would simply produce two bright patches, one per slit (below right). Indeed it was experiments such as this, performed by Young in 1803, that helped to establish the wave theory of light, overturning Newton’s earlier theory in which light was described as a stream of particles called corpuscles.

experimenters tried using light of different wavelengths: in the case of sodium, for example, red light would not cause any electrons to be ejected, no matter how bright it was, but violet light would, even if it was quite weak. This made no sense.The current caused by the light beam should have depended only on its brightness and not on its wavelength. Einstein’s insight was to consider light not as a wave, but as a stream of particles called ‘photons’. Max Planck had introduced this idea in 1901 to explain the spectrum of radiation given out by hot bodies and one of its key elements was that each photon carried an amount of energy that was inversely proportional to its wavelength. Applying this to the photoelectric effect, Einstein imagined

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Easter 2005

This awkward situation was eventually resolved, independently, by Heisenberg and Schrödinger in the mid-1920s, but the cure initially seemed worse than the disease. In the everyday world, objects have definite positions and speeds, and we might expect that what is true for sofas and cars should also be true for electrons and photons. Heisenberg and Schrödinger, however, said no to this. In their theories, it was not possible — even in principle — to know both where particles were and where they were going at the same time. Instead, they introduced a ‘wavefunction’ which described the likelihood of a particle having a given position or a given speed when measured. The truly radical part was that the particle had no definite position or speed before measurement. It made no sense to argue that we simply did not know where the particle was; it was genuinely spread out like a wave. This was the key to allowing particles to behave in ways that were previously reserved for waves. None of this pleased Einstein one bit. Despite helping to promote the case of photons, he was far from happy with the new theory. Whenever anyone looked at them, electrons and photons seemed real enough, making definite blips on detector screens, but in-between they seemed only to have a nebulous sort of half-existence, scattered through space. This did not seem at all right to Einstein and from then on he spent his time trying to demonstrate why it did not make sense. His most famous effort in this regard was the Einstein-Podolsky-Rosen (EPR) thought experiment. The aim was to show that quantum mechanics allowed for quantum effects to travel instantaneously from one place to another, violating the ultimate speed limit — that of light, an essential component of Einstein’s theory of special relativity.A simpler version of the experiment was later proposed by David Bohm and that is the one we will look at here. Bohm’s version of the experiment takes advantage of a property of all sub-

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atomic particles known as ‘spin’. At one point, it was thought that these particles were literally spinning like miniature planets; this later turned out to be wrong but is still a useful picture. Like planets, which can spin either clockwise or anticlockwise, most can have one of two spin values. These are usually known as ‘spin-up’ and ‘spin-down’ and are assigned values of +1/2 and -1/2. Spin is a conserved quantity in that the total value of the spins of a group of particles stays the same over time. Bohm imagined an unstable atom with a total spin of zero that decayed by emitting two electrons in opposite directions. The details of the decay process were such that the atom left behind still had a spin of zero, meaning that one emitted electron must have been spin-up and the other must have been spin-down, as shown above right. But nothing told him which one was which. In fact, quantum mechanics specifically told him that the electrons’ spins had no definite values: they were spread out between spin-up and spindown.The only thing that could be said

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Fortunately, this ‘action at a distance’ turns out to be a very unusual beast. At first sight, it might appear to be very powerful. However, that is not so: the second electron’s change in state cannot be used to transmit any sort of message. Before the experimenter measures the spin of the first electron, the second electron has no definite spin value; if its spin were to be measured at this point, there would be an equal chance of finding it to be spin-up or spin-down. After the measurement on the first electron, the second electron suddenly acquires a definite spin value, opposite to that of the first electron. However, there is no way to distinguish between these two states of affairs with only one measurement. Just as detecting a photon on a screen pins down its position, measuring the spin of a particle pins that down also,

If we could send signals instantaneously, information could be sent back in time

for sure was that if the spins of the two electrons were measured they would be found to have opposite values. This property of quantum systems is known as entanglement. Einstein was troubled because before measurement neither electron had a definite spin. As soon as the spin of one electron was measured, the experimenter would know the value of the other one — the opposite of the first. In other words, measuring the spin of one electron caused the other electron to fall out of its nebulous state and acquire a definite spin. Curiously, the effect was immediate, despite the fact that nothing in the experiment required the two electrons to be anywhere near each other when the first measurement was made. They could be on opposite sides of the solar system — or in different star systems entirely — and the effect would still have to be immediate. For Einstein, this was profoundly disquieting; it is no wonder that he felt the theory must be missing something crucial. Among the many strange things that would be possible if we could send signals instantaneously from place to place is that information could also be sent back in time. The reply to a letter could come back before the original message was even sent and normal causality would go out of the window.

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kicking it out of its previous state. Subsequent measurements will always find the same value. If we could make copies of the second electron before we measured it, we could do it — if the spins of all the copies came out the same, we would know the state of the first electron had been measured — but quantum mechanics tells us that there is no way to copy an unknown state. This is known as the no-cloning theorem, and is quite inescapable. The end result is that, although quantum mechanics appears to allow quantum states to change instantaneously over arbitrarily large distances, this mechanism can never be used to transmit information. Any scheme that is designed to allow the flow of information turns out to obey Einstein’s speed limit and causality is perfectly safe. Quantum mechanics remains a deeply counter-intuitive theory, but it works and despite the best efforts of Einstein and others no one has yet found a flaw. It just goes to prove the old adage that fact really can be stranger than fiction. Peter Mattsson is a researcher currently visiting the Centre for Quantum Computation as part of a ‘knowledge integration in Quantum Technology’ project funded by the Cambridge-MIT Institute

Thom Kaufam, Rudi Turner, Gary Grumbling and FlyBase

Of Flies and Men Zoe Smeaton explores how the fruit-fly revolutionized experimental biology The science fiction author Isaac Asimov once said: “The most exciting phrase to hear in science, the one that heralds new discoveries, is not ‘Eureka!’ but ‘That’s funny…’” In modern science’s quest for progress, experimentation undeniably takes centre stage and sometimes the results of even a single experiment can prove revolutionary. Classic examples aside, one of the most exciting experiments of recent years remains relatively unknown outside the scientific community. It involved the geneticists’ favourite pet, the fruit-fly Drosophila melanogaster (above), and the results fundamentally altered scientists’ attitudes towards the usefulness of ‘model’ organisms in studying primary processes such as development. The results also provided further evidence to support the theory of evolution. It all began in 1894 with the publication of Cambridge geneticist William Bateson’s book, Materials for the Study of Variation. Bateson catalogued a huge number of abnormal variations — caused, he thought, by genetic mutations — that he had observed in organisms. In particular, he was interested in mutations that caused a part of the body to appear in an abnormal location, which he termed ‘homeotic mutations’.

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Legs develop on the fly’s head in place of antennae

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A striking example of a homeotic transformation occurs when the Drosophila’s Antennapedia or Antp gene is mutated, causing legs to develop on the fly’s head in place of antennae (top left).At first, little was known about the Antp gene, but subsequent experiments revealed it formed part of a gene cluster now known as the Hox gene cluster, homologues of which have since been found in a huge variety of organisms including mice and humans. Hox genes are spatial awareness genes; it is their job to determine where in an embryo a certain cell is, and then to relay this information to other genes of the

cell. This spatial awareness is a crucial function in development. Cells must differentiate into different types corresponding to their position within the growing embryo, which is achieved by specifically regulating gene expression levels in any one cell. For example, in Drosophila the body is partitioned into segments from the head (anterior) to tail (posterior) of the fly. Cells must ‘know’ which segment they are in so that they may develop to form part of the correct organ. Simply put, different Hox genes are expressed at differing levels in each of the segments, thereby producing segments with different environments.This is controlled by varying levels of other key substances usually along a concentration gradient, in which the substance is secreted at either the head or the tail and so gradually decreases in concentration towards the opposite end of the larva. Edward Lewis conducted pioneering research into the nature of homeotic genes, sharing the 1995 Nobel Prize in Physiology or Medicine for discovering that these genes were arranged on chromosomes in the same order as the body segments they control, with the first genes regulating head structures and the final genes controlling tail features. Further experiments revealed that the Antp gene product prevents the formation of leg structures in the anterior segments, but allows them to grow nearer the tail end of the larva where it is not expressed as strongly. This explains the fact that when this gene is deleted, leg development is not suppressed in the anterior segments and hence leg structures grow in place of antennae. Armed with this knowledge, and aware of the apparent similarities between Hox gene clusters in various different organisms, Walter Gehring performed an experiment in which he replaced the Drosophila Antp gene with the corresponding gene of a mouse. Amazingly the mouse gene functioned exactly as the Drosophila gene would have done within the fly.Whilst this is not evidence that the proteins encoded by the Antp genes perform the same function in mice and flies, it does show that the protein structure itself is conserved within both organisms.

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The fact that a protein structure had apparently been so highly conserved in two organisms after 500 million years of evolutionary divergence was a huge discovery providing much support for the evolutionary theory.

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The genes are arranged in the same order as the body segments they control

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The case of the Hox genes clearly illustrates the significance of even individual experiments. Professor Michael Akam, a developmental geneticist and Director of the University of Cambridge’s Museum of Zoology, says, “The discovery of the conservation of the Hox genes marked a complete turning point from the presumption that the development of different organisms is basically very different, with no specific equivalences between them.” The Hox studies highlighted the striking similarities in geographical control within the developmental processes of flies and vertebrates. These similarities mean that the study of model organisms such as Drosophila (which are easy to work with in laboratories) may be more insightful than we had first thought in understanding processes such as our own development which, as Professor Akam points out, has an “applied medical interest — lots of medical problems relate to abnormalities in development”. In today’s scientific community, in which many biologists spend their working lives studying model organisms, it is hard to imagine disciplines such as developmental biology being carried out in any other way.The use of model organisms is in fact a fairly recent approach, and the story of its emergence illustrates just what makes science exciting: the ever present prospect that even a single set of experimental results could have a dramatic, or even revolutionary, impact on the very nature of science itself. Zoe Smeaton is a second year Natural Scientist

Easter 2005

Waters of the Mediterranean

Have you ever wondered why the waters of the Mediterranean Sea are so blue and crystal clear? Is it because the sun is shining so brightly whenever you go on holiday there? Or because there is little pollution? These factors may have something to do with it, but the main reason is that the Mediterranean Sea is oligotrophic. The word ‘oligotrophic’ comes from the Greek for ‘little, or not enough, food’ and it means that the waters of the Mediterranean don’t contain enough nutrients to support massive growth of algae — or phytoplankton — leaving the waters clear.

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Nutrients required for growth by algae are constantly depleted from the waters

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The opposite effect (eutrophication, from the Greek for ‘plenty of food’) causes excessive algal growth, turning the water a turbid green. Eutrophication often occurs in lakes and coastal areas when high levels of fertilisers are discharged into the water as waste from nearby human activities. Fertilisers and other organic waste contain high levels of phosphorus and nitrogen which marine organisms need to grow. Algae, which form the basis of the marine food chain, grow by photosynthesis so, very much like plants on land, they need light and carbon dioxide. There’s always enough carbon dioxide present in the water, and enough light at least in spring and summer, for plankton to grow efficiently.Along with the light and carbon dioxide needed for photosynthesis, algae also require nutrients. The two most important, which are often in short supply in marine waters, are nitrogen and phosphorus, in the form of nitrates or ammonia, and phosphates, respectively. When nitrogen or phosphorus are in short supply, the organisms are limited in their growth, no matter how abundant light and

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carbon dioxide. In eutrophic lakes, fertilisers and other organic waste bring high levels of nitrogen and phosphorus into the water. The algae feast on these nutrients, grow and divide rapidly, and so the population expands.When the algae die as part of their natural life cycle, they sink to the bottom of the lake where they are broken down by bacteria. Many bacteria use oxygen to release energy from their food by respiration, and soon enough the bacteria use up all the available oxygen and the bottom of the lake becomes anaerobic — without oxygen. Many of the plants and fish that normally grow in the bottom waters can no longer survive in these anaerobic conditions. Anaerobic respiration by the bacteria also produces foulsmelling by-products, such as hydrogen sulphide and methane. The effects of eutrophication are dramatic and can only be reversed by massive cleaning efforts. The processes involved in eutrophication point to another factor important to oligotrophication: the water column is stratified both in lakes and in the sea. Most of the time the top of the body of water is effectively separated from the bottom.This is partly because the surface waters tend to be warmer, making them less dense than the colder bottom waters. Mixing of these two layers of water only occurs during severe weather conditions, and in areas of upwelling and downwelling; this respectively forces the bottom water layers up, or the surface waters down, due to a combination of geographical features and ocean and atmospheric circulation. So, how does this explain why the Mediterranean is so blue? We have seen that algae need nutrients to grow, and the lower waters are, for the most part, separated from the surface waters. Since algae need light to grow, they prefer to be in the top waters where the sun shines, but most of the nutrient supply is in the bottom waters, where bacteria decompose organic matter and release nutrients. Looking at a map of the Mediterranean Sea reveals that it’s really more like a big lake — almost landlocked — with very limited water exchange through the Suez Canal

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Nasa

Lila Koumandou discovers why the Mediterranean Sea is quite so clear to the Red Sea, or to the Black Sea through the Bosphorus strait. The main point of water exchange for the Mediterranean is through the Straits of Gibraltar to the Atlantic Ocean. The Atlantic has plenty of nutrients to offer, but these are mostly found in the deep waters because algae out in the ocean greedily consume the surface nutrients. The Gibraltar Straits are relatively shallow though, so very little deep-water exchange — and thus nutrient exchange — takes place. In addition, the Mediterranean surface waters are more salty than those of the Atlantic because the Mediterranean is relatively warm and its surface water tends to evaporate in the

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In lakes and in the sea, the water column is stratified

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summer leaving the salt behind. You can definitely taste this if you swim on a beach off the Atlantic coast, compared to Mediterranean waters. This more salty water ‘attracts’ freshwater, which means surface waters from the Atlantic rush into the Mediterranean at the Straits of Gibraltar, and in return bottom waters from the Mediterranean exit into the Atlantic. Hence the vital nutrients required for growth by algae are constantly depleted from the waters of the Mediterranean. This makes the waters of the Mediterranean oligotrophic, so they don’t support high growth of algae. In turn fewer predators that feed on these algae, such as zooplankton, can survive. Thus there are fewer zooplankton in the Mediterranean, and the fish tend to be smaller.With fewer plankton present, the waters of the Mediterranean don’t turn green and murky, and are crystal clear and stunningly blue instead.This affords good pictures and lovely swimming conditions! Lila Koumandou is a PhD student in the Department of Biochemistry

On the Cover

Illuminating Aluminium

The office of the Microstructural Kinetics Group is a spacious room in the otherwise labyrinthine Annexe of the Department of Materials Science and Metallurgy, and houses five researchers, piles of paper, computers and the odd microscope. This is home to Tom Quested (right), the materials scientist responsible for our cover image, who works on simulating the behaviour of liquid aluminium as it cools into its solid, crystalline form during the industrial process known as casting. Pure aluminium is not easily manufactured into goods as it breaks easily under stress.Aluminium, both in its pure form and as an alloy, has a stable, protective layer of aluminium oxide on its surface, which

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The layer of aluminium oxide on the surface of the crystals is only about 10 atoms thick

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Tom Quested

makes it highly resistant to corrosion and allows it to reflect heat and visible light. By adding small amounts of other elements, such as copper, aluminium can be made into strong, lightweight, malleable alloys while retaining its corrosion-resistant and reflective properties — very useful for aerospace, packaging and construction. Aluminium alloys typically contain less than 10% other metals, and are what Quested is interested in.

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Victoria Leung speaks to the materials scientist Tom Quested, who took our cover image

Casting is the first step in creating aluminium products: after extracted or recycled aluminium is melted and mixed with the other elements, it is poured into a mould where it cools from about 50°C above its melting point (typically about 650°C), to below it, where the metal solidifies. Sometimes this mould is in the shape of the final product, such as a car engine block, but in the sort of casting that Quested studies, the ingots produced are shaped later. In ‘direct chill casting’, water is sprayed onto an ingot in order to lower its temperature and hot, molten metal is poured in at the top of the mould as the solidified ingot below is lowered. In industry, a 10-metre ingot is produced after many hours, but a scaled-down, laboratory version of these industrial moulds can be used to produce palm-sized pieces of aluminium.The shape of the individual crystals in these pieces can be quite different depending on how they were cast, and Quested’s job is to explain how and why. Two cast pieces are pictured left. Quested explained that the right-hand sample is more useful, as the crystals have roughly the same size in each dimension, giving the alloy consistent material qualities in every direction across the whole sample; its small crystals also mean that the material is less likely to crack when deformed. For the same reason, large crystals make the material brittle and therefore undesirable if the aluminium is to be shaped further; for direct chill casting, the ingot will be rejected if the crystals are bigger than one fifth of a millimetre. When molten aluminium cools below its melting temperature, crystals of solid aluminium are seeded,or ‘nucleated’,and grow until they occupy the whole casting.As we have seen, they can take a number of shapes, and their size can range widely from a few micrometres to several centimetres. In the casting of the sample pictured, small titanium boride particles acted as sites of nucleation, as it takes less energy for a crystal to form there; instead of atoms clustering into seed crystals purely through random motion, titanium boride particles provide a solid surface for atoms to bond to

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and cluster on. Without these particles the variation in crystal size across the sample, due to the variation in cooling rate, would be larger.The fractions of other elements in the alloy also affect crystal formation. Quested’s computer simulations must take into account all these factors, as well as heat flow and solute movement,in order to forecast nucleation and growth and thus the microstructure of the cast aluminium. Photographs such as the one on the cover allow Quested to measure the size of the aluminium crystals.After grinding and polishing samples to form a flat, smooth surface, he puts the samples under a microscope and shines polarized visible light onto them. Usually, the layer of aluminium oxide that lies on the surface of the crystals is only about 10 atoms thick, and therefore cannot be seen with the eye. When the oxide is grown instead by a technique known as electrolytic anodising, its thickness becomes comparable to the wavelength of visible light.The colours in the picture arise when the polarized light beams reflecting off the top of the aluminium oxide layer interfere with those reflecting from the bottom of the layer. In exactly the same way, sunbeams reflect from the surface of a thin film of oil and interfere to make rainbows. Each crystal looks a different colour, although there is no difference in the material; the colour only depends on the orientation of the

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The colours arise in the same way that light reflects from a film of oil to make rainbows

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oxide layer relative to the direction of polarization of the light.The twist in the sample, seen on the cover, comes from cutting with scissors. Ultimately, the casting process determines only some of the properties of the final product. The many other stages that the aluminium goes through before being pressed into the form of the heat sinks that keep your computer circuits running will be equally important. Good casting practice makes the later processing steps easier. Although Quested plans to write up his work and then perhaps move into a career in teaching, he is still working towards being able to predict with confidence the microstructure of aluminium once the manner of cooling in the casting process and alloy composition are known. www.msm.cam.ac.uk/mkg Victoria Leung is a second year Natural Scientist

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What led you to become a technical advisor? I began my medical training and went on to do a PhD in molecular biology, but I’ve always loved film, so during graduate school I became a film critic for a leisure and topical magazine for physicians.Then I came to UCLA to do further medical training, partly so I could be closer to the movie studios. In the 10 years I worked for the magazine, I interviewed directors and actors and began to set up a network, so that when people had questions in my field they knew to call me. How would you describe your role as an advisor? To give advice on the storyline and special effects, so they are not too far from reality. I realise it’s not a scientific seminar, but I’d like to avoid something ridiculous where the audience comes away with a completely wrong view of science. I’m usually looking at the most egregious errors or assumptions and correcting those, but I’ll let some smaller details slip through. I write and change dialogue, but it’s very clearly spelled out that I am not a writer. And even if they use my lines I can’t share in the profits as writers do because I’m paid a flat rate. When do you find out if they have used your advice? It varies according to the personalities involved and how closely I work with the project. Sometimes I don’t know until I see the final production, and at other times I’m involved in every draft of the script.There was one TV movie called Condition Critical

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Jon H eras

Hollywood to needs continually deliver interesting stories in order to attract movie-goers, and what better source of gripping plots than science? To add some realism, movie-makers often employ scientists as advisors. The animators on Finding Nemo had 20 lectures from marine biologists, and Nasa has its own ‘Entertainment Industry Liaison’. Professor Wayne Grody is the director of the Medical Molecular Pathology Laboratory at UCLA, and also works part-time as a scientific technical advisor. He has contributed to the Nutty Professor movies and TV’s CSI: Crime Scene Investigation, for which he is currently devising his own storyline.

Nerissa Hannink talks to Wayne Grody about his work as a scientific advisor for film and television

that involved research on prions (a type of protein believed to cause mad cow disease). There was a scene of a technician walking through the lab with a tray of coffee that wasn’t in the script. I protested but there was nothing they could do at that stage. What stage of production are you involved in? It depends who I am first contacted by; it may be the writer, producer or director. For The Nutty Professor I was approached by the art department because they wanted me to design the professor’s lab. That was fun because I went through the same catalogues I use to outfit my own lab and chose whatever I wanted because money was no object. Then they invited me to help dress the set, putting in Post-it notes and details like that. Once I was onboard they gave me the scripts, so I also ended up critiquing dialogue. Do you show people how to use equipment, so it looks convincing? Yes, one of my jobs is to help actors with physical roles.You often have actors who are extras, just sitting there pipetting, but they don’t know how to do it.That part is fun too. Apart from the scientific accuracy, it seems advice isn’t taken about how long a scientific experiment would really take? No, I’ve given up even trying, especially in a comedy. They do experiments that would take years or decades in an hour, but they’ve got to keep the story moving along, it’s unfortunate. Do you think some of your work encourages people to go into research or forensics, say from your work on CSI? I don’t know if I can take credit for that because it’s the creators of the show who’ve done the framework. If I give them a story that intrigues people, maybe I’ve helped. But there’s no doubt that CSI has increased the number of people who want to be criminologists. With all of your jobs it sounds as if you don’t have a typical day but could you describe what happens during a day of consulting?

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A day of consulting may be as brief as a phone call to answer a question, which often happens with CSI, or it might be reading a script and marking it up. If it’s on set, it’s usually several hours to a whole day. Outside of medicine, they are the hardest working people I’ve ever seen. I liken the set to an operating room, with the director like the surgeon in charge. It’s fastpaced and there’s a lot of tension and unexpected events. It’s controlled chaos. But I love the excitement and professionalism. Don’t some scientists like consulting so much that they quit ‘day jobs’ to do it? Yes, it happens, but I don’t think I would want to be a technical advisor full-time. Aside from the good points there is a real sense of insecurity in the movie industry: people are employed for one project and, as soon as it wraps, they’re looking around for the next job and that could take months. I’m always refreshed when I come back to the medical centre and people are unpretentious. In academic medicine we consider it to be one of our primary roles to train our replacements, and teaching is a noble calling, whereas in Hollywood no one wants a protégé to replace them, so I find there’s not a lot of mentoring or collegiality. Research from David Kirby at the University of Manchester has shown that science in movies, produced with the help of scientists (e.g. Deep Impact and Jurassic Park) can increase public and even political awareness about a research area, which can in turn increase funding. Are you ever conscious or wary that your work can have such an effect? I don’t deny that some of that happens. I think some of the funding for AIDS in the US, which was originally pretty meagre, may have been increased due to the various dramatisations on TV and in movies. What response have you got from other researchers about contributing to the perception of science? In general my own colleagues have found it exciting. I had some nice feedback for the movie on prions. Stanley Prusiner, who discovered prions, happened to catch it on TV and he contacted me to say it was a good portrayal. It was quite an honour.

A D ay i n t h e L i f e o f …

A Hollywood Science Advisor

For more information on the work of science advisors and science in film, see David Kirby’s website www.davidakirby.com Nerissa Hannink is a postdoc in the Department of Plant Sciences

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Sophie May gets involved in Siberian conservation Siberia has long had the reputation of being a cold, inhospitable wilderness. Nonetheless, it is to be my destination for the summer of 2005. I, along with six other Cambridge students, will be travelling to the Tomsk region of central-southern Siberia to carry out ecological monitoring of the area’s taiga forest. Fred Currie, Wildlife and Conservation Officer with the Forestry Commission, and our Senior Leader, Kevin Hand, from the Tree Council, will accompany us. Our work will mark the beginning of a 3-year project aimed at securing Forestry Stewardship Council (FSC) status for a region of the Tomsk taiga forest. The Siberian taiga forms part of the largest tract of unbroken forest in the world, stretching more than 1,500,000 square miles.The word ‘taiga’ describes the mix of tree species found in the forest.The freezing temperatures and seasonal droughts favour coniferous forests of larch, spruce, fir and pine. Despite Siberia’s reputation as a hostile wilderness, the region is actually bursting with life. The taiga is home to elk, wolves, lynxes, red foxes, reindeer, sable and Russia’s largest population of brown bears. Many rare birds also inhabit the taiga, including white-tailed eagles and ospreys; both of which are ‘Red Data Book’ species (see box). Unfortunately, there is a dark side to Tomsk.The region has gained notoriety as a location of highly polluting chemical factories, nuclear weapons testing, oil and natural gas plants and extensive coal mining. Also, along with the rest of Siberia, illegal logging and poaching are rife. WWF estimates that at least 30% of all logging in Russia is illegal.This is believed to result in an annual state loss of over $1 billion. Another potential cause for concern is President Putin’s closure of the Federal

Glenn Vice

Lucy Taylor

Away from the Bench

Saving the Taiga

Expedition members Katie Marwick, Sophie May, Lucy Taylor and Wing-Sham Lee, to be joined by Kate Cochrane, Sarah Parker and Hannah Allum

Forest Service in 2000, passing its responsibilities to the Ministry of Natural Resources. Thus, one agency is now responsible for both protecting and harvesting the forest! FSC, founded in 1993, is an independent, not-for-profit organisation. FSC’s mission is to promote environmentally appropriate, socially beneficial and economically viable management of the world’s forests. Products certified with the FSC trademark are guaranteed to meet these criteria, opening up new ‘socially responsible’ consumer markets for the producers, and thus adding value to an intact, FSC-managed forest compared with an illegally logged one.

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Part of the largest tract of unbroken forest in the world

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One stipulation of FSC certification is that 10% of the forest is managed solely for conservation. This is where our summer research will be particularly valuable. On arrival in Siberia, we will be joining students and scientists from Tomsk State University.Together we will travel deep into the Tomsk taiga and use techniques such as transects and quadrats to monitor birds, mammals, plants, lichens and butterflies. This information will be used to assess the region for biodiversity and for the distribution of rare and endemic species. This is vital to determine which specific areas should be designated as conservation zones. We shall be collaborating with members of a team who, in 2000, helped achieve FSC certification of the Kosikhinsky forest in Altai, southern Siberia. Subsequent inspections of Kosikhinsky have demonstrated the benefits that can be achieved through FSC status. Since FSC certification, botanical surveys have been carried out in Kosikhinsky.These have identified eight regional Red Data Book species, and specific protection areas have been established for them. Areas maintained solely for conservation now exceed 15% of the managed forest.The forest is protected by guards who restrict inappropriate hunting and fishing, and the

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FSC believes that illegal logging is now virtually impossible in the region. Local people in Altai have also seen benefits.To maintain FSC certification — and hence the use of the FSC trademark — the logging company must follow rigorous rules concerning the local community.The company is a major employer in the region and all the staff are local. National legal requirements are met with regard to health and safety issues. Workers are better paid and receive their wages on time. Another FSC stipulation is that the forest provides non-timber benefits; locals are free to collect berries and mushrooms, and use the forest for honey production and grazing. We are very excited to be visiting Tomsk and are committed to doing our part in gaining FSC certification for the Tomsk taiga forest.This has the potential not only to protect the plant and animal life for future generations, but also to improve the current living and working conditions of local people. If you are interested in sponsoring the trip, please visit www.tomsktaiga.com www.fsc.org www.panda.org Sophie May is a second year Natural Scientist The Red Data Book • The ‘Red Data Book’ (now also known as the ‘Red List’) contains a list of species whose continued existence is under threat. • The list is produced annually by The World Conservation Union (IUCN). • The IUCN Red List is the most comprehensive, apolitical, global approach for evaluating the conservation status of plant and animal species. • There are 15,503 species on the IUCN 2004 Red List of Threatened Species. • 882 species are listed as Critically Endangered including the Chinese Alligator, Brazilian Guitarfish and Philippine Eagle. • In the Tomsk taiga, Red-Listed species include Juniper (Juniperus communis), several Lady’s Slipper orchids, Black Stork (Ciconia nigra), Osprey (Pandion haliaetus, pictured on the left), White-tailed Eagle (Haliaeetus albicilla) and the butterfly Erebia cyclopia. www.redlist.org

Easter 2005

I n i t i at i ve s

Back to School

For the school-child, the word ‘scientist’ tends to conjure up images of mad, test-tube-waving old men whose bubbling cauldrons may contain the elixir of life or the ability to reduce the world to dust. In an effort to counter such opinions, the scientific research councils are keen to involve PhD students in Researchers in Residence (RinR), a scheme to encourage interaction between children and genuine researchers. RinR involves putting real researchers, preferably young trendy specimens, into classrooms to speak to students about their research. It is hoped that such exchanges will break down stereotypes and so inspire the future generation of scientists. Before a RinR placement, volunteers attend a training day; mine took place at Brunel University. The post-apocalyptic landscape that is the Uxbridge Campus contrasted with the enthusiastic delivery of the organiser. He aimed to inspire us to go bravely forth unto classes of raucous children who only like science because they get to set light to each others’ hair with Bunsen burners! We also gained some practical examples of how science is taught in schools and ideas for projects we could do with the students. For my RinR placement, I decided to return to my former Glasgow secondary school. Before arriving, I had discussed

Deirdre Hoyle

Lucy Adam goes back to the classroom to inspire the next generation of scientists

lesson ideas with the science teachers there.With the older students I shared my own research experiences and helped them choose topics for their final-year science projects. With younger classes I helped make crystals (being a crystallographer) by evaporation, and took a class on extracting DNA — probably with the rest of the cell contents — from fruit with washing-up liquid. A major challenge was deciding what I wanted the class to learn from my talks. I was careful to remember that not having prior knowledge of a subject doesn’t mean the person is stupid, and recalled my exasperation at speakers who used too

simplistic a tone for my liking. I found it vital to make talks visually interesting and to maximise my interaction with the children.The students were happy to have any sort of distraction from their normal timetable and really liked the practical elements. I enjoyed the RinR experience and it made an interesting change to the lab routine. Oh, to be back in the days when you were told to “pick up the beaker and pour carefully…” http://extra.shu.ac.uk/rinr Lucy Adam is a PhD student in the Department of Biochemistry

Walking with Scientists

Tamzin Gristwood investigates a new way to explore science in Cambridge We ’ v e all heard of famous Cambridge scientists such as Isaac Newton, Henry Cavendish and Ernest Rutherford — to name but a few. But do we really know what they did, and where their ground-breaking research took place? In a twist to the standard Cambridge tour, SeeK (Science and Engineering Experiments for Kids) is hoping to address such questions by developing ‘walking and doing science’ tours of Cambridge scientists past and present. SeeK was founded in 1997 by Dr Rob Wallach (Senior Lecturer, Department of Materials Science and Metallurgy) with the aim of promoting the fun of science and engineering to children, their families and teachers. However, it is hoped that the walking tours will reach an even wider audience. “The idea came about as a result of comments made by tourists. Many

initiatives@bluesci.org

were keen to find out more about the university buildings and the people who worked there, rather than just trailing in and out of the colleges”, said SeeK Director Lianne Sallows. The prototype ‘walking and doing science’ website, which it is hoped will be officially launched later in the year, currently offers five themed walks; topics include ‘Human Evolution & DNA’ and ‘Atomic Physics’. For example, on the ‘Historic Highlights’ walk, sites visited include the Eagle pub, legendary for its role in the story of Watson and Crick’s discovery of the DNA double helix, and the Hopkins Building, named after Frederick Hopkins who opened the building when he founded the University’s Department of Biochemistry in 1914. For each walk, the website includes links to biographies of the featured scientists and in keeping with the handson spirit of SeeK, tours will be accompanied by activities relevant to each scientist’s work. SeeK intends to provide

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activities to be done both during the walk and at home, thereby making them accessible to children unable to visit Cambridge. The tours and activities will be linked to the current National Curriculum making them particularly pertinent to school groups. If you’re interested in getting involved, SeeK is now looking for volunteers with ideas for the activities to help write biographies and take photographs. The work available will be extremely flexible, with the degree of commitment up to each volunteer. For more information, to volunteer, or to sponsor the walking tour website, please contact Lianne Sallows through the Seek website, www.msm.cam.ac.uk/seek. So, get your walking boots ready and keep an eye out for the official launch of Cambridge’s first ‘walking and doing science’ tours. Tamzin Gristwood is a PhD student in the Department of Biochemistry

History

Science and Subtext

Emily Tweed talks to Hugh Aldersley-Williams about subtext in great scientific publications

of literary criticism have more power than they might think. There has been much talk in the humanities about subjecting science literature to this kind of treatment, but no-one really seemed to have done it properly. So the main aim is to show that these are intrinsically human documents, not utterly dispassionate, objective accounts. Some scientists still believe the latter, but the meanings are in there and they will be there in all scientific papers, as they are in anything we write. The idea that the author can rise above personality is a myth, even in science literature. For example, the animosity that James Chadwick — whose 1932 paper established the particulate nature of the neutron — felt for his French rivals Irène and Frédéric Joliot-Curie is clear in his text from the way that he refers to them, even getting their names wrong. The French were convinced the neutron was a ray-like phenomenon, whereas Chadwick and his mentor Ernest Rutherford at the Cavendish Laboratory in Cambridge believed it was a particle [although nowadays it is thought that it can be both, a paradox known as waveparticle duality]. It’s clear from reading the papers by both groups that either group might have made the discovery sooner if they’d been a bit less dogmatic. How did you choose the papers featured in the book? I tried to pick papers announcing major, and to some extent familiar, discoveries. Readers might have read accounts of them, but probably won’t have read the actual papers. For example, Watson and Crick’s discovery of the structure of DNA has been described many times in popular books, including by the scientists themselves, but Findings deals directly with their original paper. Personally I was struck by the authors’ cleverness: in Findings I argue that they use literary artifice to disguise their debt to the crystallographer Rosalind Franklin while pretending a grand rivalry with Linus Pauling, and repeatedly switch between descriptions of DNA in nature and the molecular model they have built of it, so as to confuse (and fuse) the two in readers’ minds. What value do you think the history of science has to the student of science and to the research scientist? Scientists should definitely know the history of their field, and the broader history that gives it a cultural context.They would avoid some embarrassing pitfalls. My best example of this is the 1996 paper in Science by the Nasa team that claimed to have found evidence of fossil life on Mars. I think there was a major flaw in the scientists’ logic; they build

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their claim for life on the formation of certain carbonate globules, but these globules they first state as having been formed by ‘biogenic activity’ — a com-

Abinand Rangesh

Journals, papers and articles are the day-to-day battleground of the sciences; places where discoveries are announced, debates rage and reputations are made. What can they reveal to us about the personal motivations and preconceptions of their scientist authors? In his new book, Hugh AlderseyWilliams, who studied Natural Sciences at the University of Cambridge, takes a seminal paper from each decade of the twentieth century and subjects them to a scrutiny worthy of any literary critic. Beneath the precise formulae and specialist terminology he finds a world of rivalry, prejudice and political bias. Also in this section, BlueSci takes a look at some of the scientific events featured in Findings, with expert opinions on each paper’s impact. Where did you get the idea for Findings, and what is your aim in analysing scientific papers in this way? It began with my previous book, The Most Beautiful Molecule, which described the Nobel Prize-winning discovery of the carbon molecule buckminsterfullerene. I found that the paper in Nature announcing this new molecule was full of unexpected treats: the scientists’ glee and good humour at their discovery, veiled references to arch-rivals, errors made in haste and so on. In Findings, I try to show that this was not a one-off and that any scientific paper is liable to contain its own subtext. By approaching the idea fairly rigorously, i.e. by performing the deconstruction many times over for key twentieth-century breakthroughs, I hope to convince scientists that the analytical techniques

pletely circular argument. What’s really astonishing though is that this is exactly the same false logic that was used by the American astronomer Percival Lowell in the 1890s when he used Giovanni Schiaparelli’s discovery of so-called ‘canals’ on Mars to claim them as evidence of intelligent life there. Nowadays Lowell’s claims are a notorious example of circularity, but the 1996 paper makes exactly the same mistakes. If the Nasa team had known this story, they might have constructed their own argument more carefully. Do you have a particular favourite among the papers you discuss in the book, one whose style, content or subtext you find especially interesting? I think the 1910 paper by the American zoologist Thomas Morgan, who discovered the link between sex and heredity in his experiments on fruit flies, is beautiful. Its logic is incontestable, the writing is spare but highly literate, and its pace is perfectly judged. And because of this it succeeded in a larger, rhetorical way, sending a signal that biology was coming of age, maturing from an observational pastime of gentleman naturalists to a rigorous experimental science. In the introduction to your book you mention the gulf that exists between nonscientists and the scientific literature: why do you think this exists? A lot of non-scientists are intimidated by the initial appearance of scientific literature. You certainly can’t pick up Nature and read it like The Times. And too many scientists rather enjoy the mystique.

Easter 2005

Geoffrey R. Hutchison

Seminal papers from this era include Rowland and Molina’s 1974 analysis of the harmful effects of chlorofluorocarbons (CFCs) on the atmosphere; James Lovelock’s proposal of the Gaia hypothesis, in which the environment on earth behaves as a huge self-regulating organism; and a new trend towards using mathematical models to describe the processes of evolution at the level of the population. In a nutshell: Throughout this decade scientists became increasingly involved with issues of human impact and sustainability, giving birth to the discipline of ‘environmental sciences’. What Findings says: “These papers of the 1970s show scientists awakening to a desire to express themselves in new ways when their research is stimulated by, or raises, concerns beyond the purely scientific.We have seen these writers hesitate on the brink, clearly uncertain whether or how to broach fears and feelings that find no outlet amid the strict and impartial reporting of scientific data. Some dare to take the plunge and marry scientific reporting with political persuasion, even to the extent of making specific policy recommendations, which is no part of the scientist’s traditional task in writing a paper for publication in a journal of the field.”

Those who speak for science in the media, for example, often say that the public isn’t qualified to comment on the latest scientific developments. But this is a dangerous and disturbing misunderstanding of the way democratic society works: the public is ‘qualified’ to comment on anything it damned well wants to. So these scientists need to change their attitude. But then, so do those nonscientists who think it a badge of honour to reveal how totally fazed they are by the slightest bit of science! What are you working on at the moment? In June I am co-curating a contemporary design exhibition about ‘Touch’.

www.bluesci.org

Who,What,Where and When? The key publications from three decades 1980s

H. Kroto, J. R. Heath, S. C. O’Brien, R. F. Curl and R. E. Smalley,‘C60: Buckminsterfullerene’, Nature 318: 162–163 (1985). In a nutshell: Scientists working on the synthesis of large organic compounds in the atmosphere of red giant stars discover a new crystalline form of carbon. What the experts say: “The most famous molecule discovered by this group is the almost spherical footballlike C60 structure named ‘buckminsterfullerene’ after Robert Buckminster Fuller, an engineer who designed giant geodesic domes, but other fullerenes differing in the number of carbon atoms also exist.The discovery of fullerenes was quite unexpected and caused a sensation in the staid world of chemistry, but some time had to pass until gram quantities of pure C60 (and other fullerenes) became available for research purposes at a reasonable price. Fullerenes have been chemically derived in various ways, guest elements were placed inside the cages and superconducting complexes of fullerenes have been prepared by the addition of potassium and rubidium. C60 and its derivatives may even be of value as therapeutic agents in medicine; researchers are investigating their potential as inhibitors to enzymes specific to HIV. Finally, by-products of the mass production of fullerenes include carbon needles (‘nanotubes’) which, in view of their potential applications for composites and electronic components, have attracted as much interest as C60 itself.Who knows what the future will bring.” Professor Jacek Klinowksi, Department of Chemistry It’s at the Victoria and Albert Museum, but it is also funded by the Wellcome Trust, so it has a certain scientific underpinning. I am also writing a book about science and nationalism, a set of biographical sketches based on four scientists whose lives overlap with national interest in very different ways. The idea is to go from the beginning of modern nationalism in the second half of the nineteenth century up to the present day. It begins with Alexander Borodin, a Russian composer and renowned chemist, then moves onto Fritz Haber, the German chemist responsible for Germany’s use of poison gases in the first world war.Then I look

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1990s

D. S. McKay et al., ‘Search for past life on Mars: possible relic biogenic activity in Martian meteorite ALH84001’, Science 273:924–930 (1996). In a nutshell: A paper claiming to provide evidence for life on Mars captures the media’s attention but draws criticism from the scientific community for its line of reasoning. What the experts say: “This paper had a huge impact on its field when first published and stimulated an enormous amount of often acrimonious debate.The authors took five separate research findings regarding the formation and composition of certain carbonates found on Mars and linked them together as a chain of evidence to argue that they had found a fossil of a primitive Martian organism. I think it would be fair to say that hardly anyone in the scientific community was convinced that the final conclusion of the paper was true. However, the paper galvanised the community into action. This was mostly directed towards showing that one aspect or other of the findings was incorrect and hence that the whole chain of evidence would collapse. After this there was a huge increase in the amount of research into the possibility of life on Mars and how it might be recognised.This led to advances in the study of extremophile microorganisms and, indirectly, to a consolidation of the study of astrobiology. It also served as an additional impetus for space missions to Mars. Professor Monica Grady, Open University

History

1970s

at Chaim Weizman, a fermentation biologist who became the first president of Israel, and finally Carl Sagan, who was a spokesman for the US space race but was also very critical of other aspects of American political life and used his science to inform that criticism. For example, he was heavily involved in publicising the idea of ‘nuclear winter’. I think this is interesting as it shows science as a critical tool as well as an instrument of the state.. Finally, as a former Natural Sciences student at Cambridge, is there any advice you would give to current NatScis? Get a sense of the bigger picture. Go to lectures outside the subject that fill in the context.You can luxuriate in the fact that you don’t have to take notes, and won’t be tested on it. www.luloxbooks.co.uk References for all the papers mentioned in this article can be found at BlueSci Online. Emily Tweed is a second year Natural Scientist

Owain Vaughan talks to artist Martha Fleming about her journey across the great divide Artists and scientists, so the story goes, stand at opposite ends of a cultural playground, crossing over only to call each other names. The scientist, devoid of soul and imagination, sets about dissecting nature in pursuit of cold hard facts. The artist, unhindered by such niceties as facts, sets about understanding the world with their head in the clouds. The story is mostly fiction, but for some a mutual incomprehension pervades, stalling any chance of a constructive relationship. Enter Martha Fleming. As Research Artist in Residence at the Institute of Astronomy (IoA) here in Cambridge, her life’s work has been intent on making this divide irrelevant.

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If you think those pretty pictures from Hubble are amazing, wait till you see how they do it

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Fleming is a curatorial advisor for the latest exhibition at the Design Museum in London, You Are Here. The exhibition offers a journey through humanity’s endeavours to communicate information by visual means. The show’s breadth is vast, ranging from such instantly recognisable designs as Harry Beck’s 1933 Tube Map of London to a peculiarly angular map by Buckminster

Fuller — an effort to express the links between the landmasses of the Earth, rather than their divisions by oceans — and even to a colour-coded map of the emotional states in Shakespeare’s Macbeth by Fang Leo. Fleming’s section COSMOS begins the show. “COSMOS is about how astronomers extract information from the physical laws which govern light,” she explains. It is an engaging collection comprising a diverse range of pieces: an exquisitely simple diagram of the evolution of the cosmos by artist Agnes Denes; a NOAO solar spectrum complete with absorption lines marking the elemental composition of the sun; stark black-and-white images from a section of the Southern Sky Survey, where the simplistic pictures conceal hidden swathes of raw numerical data for astronomers. As Fleming reveals, “My basic message is: if you think those pretty pictures from Hubble are amazing, wait till you see how they do it!” In an artistic career spanning more than 20 years, Fleming has been involved in numerous projects, including architectural work, large-scale site ventures and gallery exhibitions. Science, and the similarities that exist between artistic and scientific pursuits, have frequently been an influence in her work. In 1984 she began a largescale site project with fellow artist Lyne Lapointe called Le Musée des Sciences. Created in an abandoned post office in Montreal, it explored the split between the arts and the sciences during the Enlightenment. For Fleming the proj-

Martha Fleming

Arts & Reviews

Looking Beyond

ect was “the first public articulation of the long-term interest I have in bringing the methodologies of artists and creative people together with the methodologies that scientists in a variety of disciplines use”. In 1997 she became Artist in Residence at the Science Museum, London, where she worked for two years on a highly successful museum-wide collection entitled Atomism & Animism. This project questioned how it is that science sees and how we see science, and incorporated, amongst other things, an attempt to relate the quantum and classical worlds through an examination of historical objects. Having spent many years researching science from a historical perspective, Fleming became increasingly fascinated by contemporary science, and in 2004, supported by NESTA and the Canada Council for the Arts, joined the IoA.

Owain Vaughan

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Solar spectrum showing the absorption lines which mark the presence of individual elements

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Science, and the similarities between artistic and scientific pursuits, have frequently been an influence in her work

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“What first attracted me to astronomy was that, essentially, what astronomers are working with is light, and as an artist this is one of the primordial elements you work with.” Though Fleming had been interested for some time in the scientific detection of light and the act of observation, her collaboration with the IoA gave her the

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opportunity to take this further. Whilst still working at the Science Museum, Fleming was introduced to the Scanning Tunnelling Microscope, an instrument that can image and even manipulate individual atoms. This discovery drew her attention to what lies beyond that which is visible to the tool artists employ most, the naked eye: “I realised I wanted to look not just at things such as refraction, reflection and perspective, but also at what light is actually made up of.” Fleming embarked upon this analysis at the IoA, and proceeded to investigate the actual practice of astronomy: the methodologies and the instrumentation of obser-

MSc in Creative Non-Fiction Writing This is a new course offered by the Science Communication Group at Imperial College. It is designed for anyone who aspires to write creative non-fiction, defined as writing at length on factual themes requiring analytical expertise, factual research, and explanatory skill. Popular science writing is one large sub-category of such writing. The course contains academic components on popular science writing and publishing, together with further relevant option courses, and extensive practical writing development exercises. Students also produce an extended piece of writing as an assessed project. For more information contact Paul Wynn Abbott, Science Communication Group Administrator, Room, 313C, Mech. Eng. Building, Imperial College, London, SW7 2AZ. Tel: 020 7594 8753 Fax: 020 7594 8763, email: p.wynnabbot@imperial.ac.uk web: www.imperial.ac.uk/sciencecommunication The closing date for applications is 27th May 2005 Valuing diversity and committed to equality of opportunity

Owain Vaughan

Fleming hopes to communicate the skills she possesses that could be of intellectual service to science as well as art

A r t s & R ev i ew s

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vation and detection. COSMOS represents an early opportunity to express some of the information she has garnered from the experience. However, Fleming’s work and her time spent at the IoA are not just about acting on behalf of the astronomers to explain their research to the general public. Not wanting to be a mere science tourist, she hopes to communicate to scientists the skills she possesses that could be of intellectual service to science as well as to art.This all forms part of Fleming’s long-term vision, “an understanding of shared methodologies between the arts and sciences as a basis for productive collaboration”. As she elaborates, “Whether it is in terms of conflict resolution or of understanding what consciousness might be, there are many complex cultural issues that need to be approached by an interdisciplinary team.” This will be no easy task, but Fleming is hopeful. “The thing that really holds me is a future interdisciplinary practice that is prodigious and productive, rather than divisive and destructive.” Scientists, take note.

Section of the Southern Sky Survey: Orion

You Are Here, sponsored by Microsoft and the Wellcome Trust, runs until 15 May 2005 at the Design Museum, Shad Thames, London SE1. For further information, visit www.designmuseum.org Owain Vaughan is a PhD student in the Department of Chemistry

Dr Hypothesis

Dr Hypothesis If you have any worries (purely of a scientific nature, obviously) that you would like Dr Hypothesis to answer, then please email him at drhypothesis@bluesci.org He will award the author of the most intriguing question a £10 book voucher. Unfortunately, Dr Hypothesis cannot promise to publish an answer to every question, but he will do his very best to see that the most fascinating are discussed in the next edition of BlueSci. Dear Dr Hypothesis, I have just arrived in Cambridge and have been greatly appreciating the city, especially the Backs. I really love the splendid architecture of buildings such as King’s College Chapel, which looks wonderful above the fields of daffodils and crocuses. However, in cold weather I don’t like to stay out too long to appreciate it. How long will the flowers stay, and why? Visiting Vivian

Lizzie Phillips

Dr Hypothesis needs your problems!

Dear Dr Hypothesis, I don’t like to think of myself as a sheep that always follows the crowd, but I’ve become aware that I have a tendency to unwillingly copy others when I’m in their company. This is a particular problem with yawning; when one person yawns I always seem to find myself yawning straight after them. I’ve tried a number of things to avoid this, including caffeine binges, but nothing seems to work. Could you tell me what’s wrong with me? Individual Irene

DR HYPOTHESIS SAYS: I’m afraid the flowers on the Backs are a speciality of spring-time Cambridge and they won’t last long. It’s all down to competition. The daffodils and crocuses use their flowers to attract pollinators, but the plant needs a lot of energy to make these flowers. They obtain this from the sun via photosynthesis, and therefore have evolved to complete this stage of their life cycle early in the season, before they are outcompeted for light by the leaves on the trees overhead. The only good news I can give you is that they will be back next spring. http://experts.about.com/q/709/ 3442061.htm

DR HYPOTHESIS SAYS: There’s absolutely nothing wrong with you Irene. It is common knowledge that yawning can be contagious. Physicians tell me that there are many possible cues that can set off yawning — including fatigue, boredom or, more seriously, conditions such as anaemia — so a disposition to yawn is present in most of us most of the time. Alternatively, yawns could have been used at one time in our evolutionary history to co-ordinate the social behaviour of the group, so when one person yawned so did everyone else. They seem to be contagious today because we might still have this left-over response which we simply don’t use any more. http://webperso.easyconnect.fr/baillement/ texte-yawning-lehmann.pdf http://faculty.washington.edu/chudler/ yawning.html

Dear Dr Hypothesis, I was recently listening to a documentary on a well-known radio station, when I was surprised to hear that Lucy was the first human known to have walked on two legs. Now, I have a very good friend Lucy who has no problem walking upright. I know for a fact that I am older than her and am also perfectly capable on foot. Come to think of it, so are my parents, and hers, and many other people… Who was this Lucy, as she surely can’t be my friend? Bipedal Brian

DR HYPOTHESIS SAYS: One of the oldest human skeletons thought to have walked erect, at 3.2 million years old, was discovered in Ethiopia in 1974 and given the name Lucy. On the night of the find, the archaeologists had a party which seems to have involved rather too much alcohol and The Beatles’ song Lucy in the Sky with Diamonds was played several times. No-one knows exactly who nicknamed the skeleton that night, but the name has stuck ever since. I think there is a clear message from this Brian — don’t drink and dig. www.asu.edu/clas/iho/lucy.html

luesci

Sorry Fiona! DR HYPOTHESIS APOLOGISES: In the last issue I answered Flightpath Fiona’s question as to why planes can fly but unfortunately did not explain it correctly. I have since been reliably informed that wings are constructed so that the path of the air travelling underneath a wing is curved more than that of the air travelling over it. This means that there is a greater change in the momentum of the air passing under the wing, causing a greater force to act on the underside of the wing than on the top. This results in a lifting of the aircraft. Many thanks to all those observant readers who noticed my mistake. In the last issue Dr Hypothesis asked you, the reader: Can men park cars better than women, and if so, why? Read some of the answers given below… “My experience of car parking is that with practice and studying the theory, the movement of the car is very predictable, and so, with elementary mechanical knowledge, it becomes second nature. However, when parking a woman these rules no longer apply. On the few occasions I have tried, the women refuse to move in the way I expect them to, and more importantly don’t stay there!” At the risk of enraging Dr Hypothesis’ better half, Professor Hypothesis, Dr Hypothesis shares this reaader’s concerns, although it wasn’t quite the answer he was looking for! Another reader commented on a recent study on the relationship between foetal testosterone and finger length: “Spatial skills such as map-reading and parking may be difficult for some women because they had too little testosterone in the womb… Low testosterone levels are also linked to shortened wedding ring fingers.”

Think you know better than Dr Hypothesis? He challenges you with this puzzle: Is there life ‘out there’? Please email him with answers, the best of which will be printed in the next edition.

Easter 2005