Easter 2013 Issue 27

www.bluesci.co.uk

The Cambridge University science magazine from

Cambridge University science magazine

Northern Lights . Open-Source . CryptographyEnergy Saving . Everest . Oliver Sacks

FOCUSA World of Music

Curing ‘the bends’

This breakthrough article included early research into decompression and the first ever dive tables.

It’s just one of the treasures in the Cambridge Journals Digital Archive

journals.cambridge.org/thebends

The University of Cambridge has access to the Cambridge Journals Archive, via journals.cambridge.org

Hill and Greenwood decompressed themselves, without any serious symptoms, after short exposures at excess pressures of as much as five and even six atmospheres.”From ‘The Prevention of Compressed Air Illness’, Journal of Hygiene, 1908

CP Dive Tables Ad.indd 1 15/03/2013 20:12

Have you Heard the Northern Lights?Shane McCorristine examines the eerie sounds made by the glowing sky

Contents 1

Cambridge University science magazine

Easter 2013Issue 27

Contents

BlueSci was established in 2004 to provide a student forum for science communication. As the longest running science magazine in Cambridge, BlueSci publishes the best science writing from across the University each term. We combine high quality writing with stunning images to provide fascinating yet accessible science to everyone. But BlueSci does not stop there. At www.bluesci.co.uk, we have extra articles, regular news stories, podcasts and science films to inform and entertain between print issues. Produced entirely by members of the University, the diversity of expertise and talent combine to produce a unique science experience.

President:� Nicola Love ................................................................ president@bluesci.co.ukManaging Editor:� Felicity Davies .......................................managing-editor@bluesci.co.ukSecretary:� Beth Venus ..................................................................enquiries@bluesci.co.ukTreasurer:� Robin Lamboll .........................................................membership@bluesci.co.ukFilm Editors:� Letizia Diamante & Alex Fragniere ..................................... film@bluesci.co.ukRadio:� Anand Jagatia..................... .....................................................radio@bluesci.co.ukWebmaster:� James Stevens .....................................................webmaster@bluesci.co.ukAdvertising Manager:� Philipp Kleppmann & Deirdre Murphy ...... advertising@bluesci.co.ukEvents & Publicity Officer:� Martha Stokes ...................................... events@bluesci.co.ukNews Editor:� Joanna-Marie Howes ................................................... news@bluesci.co.ukWeb Editor:� Aaron Critch ........................................................... web-editor@bluesci.co.uk

Committee

FOCUS

Features

The Myriad GenesKevin C-C Chen explores the implications of a Supreme Court ruling on BRCA cancer gene patents

6

8

Open for EveryoneHaydn King describes the open-source software movement and two of its most striking characters

10

Commemorating a CommissionFelicity Davies celebrates the centenary of the Medical Research Council

Cracking CodesPhilipp Kleppmann deciphers the advance of cryptography throughout the centuries

14

Regulars

On the Cover 3News 4

Reviews 5

Science and PolicyMaja Choma discusses the environmental

impact of biomedical research

22

HistoryNathan Smith explains how the pre-antibiotic

era could come back to help us

Away from the BenchTwo weeks before he treks out, Elly Smith talks to

Dr Andrew Murray about science on Everest

InitiativesElizabeth Mooney remembers the opening of

the new Cambridge Science Centre

Behind the ScienceRobin Lamboll looks at the controversial career

of a neurologist who works with music

Weird and Wonderful 32

26

BlueSci explores the phenomenon of music—what it is, where it comes from and why we do it

About Us...

28

A World of Music

12 25

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24

Curing ‘the bends’

This breakthrough article included early research into decompression and the first ever dive tables.

It’s just one of the treasures in the Cambridge Journals Digital Archive

journals.cambridge.org/thebends

The University of Cambridge has access to the Cambridge Journals Archive, via journals.cambridge.org

Hill and Greenwood decompressed themselves, without any serious symptoms, after short exposures at excess pressures of as much as five and even six atmospheres.”From ‘The Prevention of Compressed Air Illness’, Journal of Hygiene, 1908

CP Dive Tables Ad.indd 1 15/03/2013 20:12

Arts and ScienceChristoforos Tsantoulas explores the relationship

between music and science

30

Editor: Jannis Meents

Managing Editor: Felicity Davies

Business Manager: Michael Derringer

Second Editors: Sheenagh Aiken, Luke Burke, Laura Burzynski, Keren Carss,

Maja Choma, Aaron Critch, Kathrin Felder, Nicola Hodson, Robin Lamboll, Ana Leal-Cervantes, Shaun Lim, Nicola Love, Vicki Moignard, Deirdre Murphy, Laura Pearce, Laura Schmidt, Elly Smith, Nathan Smith, Caroline Sogot, Christoforos Tsantoulas,

Theodosia Woo

Copy Editors: Luke Maishman, Laura Pearce, Martha Stokes, Theodosia Woo

News Editor: Joanna-Marie Howes

News Team: Mrinalini Dey, Joanna-Marie Howes, Toby McMaster

Reviews: Maja Choma, Yvonne Collins, Christoforos Tsantoulas

Focus Team: Matthew Dunstan, Nicola Hodson, Zac Kenton, Elly Smith

Weird and Wonderful: Jordan Ramsey, Joy Thompson, Theodosia Woo

Production Team: Philipp Kleppmann, Esther Lau, Shaun Lim, Louise Nicol,

Laura Pearce, Caroline Sogot, Christoforos Tsantoulas

Illustrators: James Conan Baker, Josephine Birch, Alex Hahn, Aleesha

Nandhra, Christos Panayi, Emily Pycroft

Cover Image: Dr Daniela Sahlender

ISSN 1748-6920

2 Editorial Easter 2013

Varsity Publications LtdOld Examination Hall

Free School LaneCambridge, CB2 3RFTel: 01223 337575www.varsity.co.uk

business@varsity.co.uk

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License (unless marked by a ©, in which case the

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Issue 27: Easter 2013

humans have been making music for thousands of years. The oldest musical instrument dates to 36,000 years ago, and it is possible that the Neanderthals were already able to make music long before that. In fact, music may even predate the development of language! But much has changed since the first notes were blown on a flute made of bone. From the prehistoric age, medieval minstrels, Mozart and Duke Ellington, all the way to the present day, music has become more and more universal. In today’s high-speed society, most of us could not imagine a world without music. Many people use it as a creative outlet that counterbalances their day-to-day life, and some just listen to it in order to relax. And yet, we are rarely consciously aware of the importance music has in our lives. Indeed, there are few human abilities that we have possessed for such a long time and that we know so little about.

In this issue of BlueSci, we try to decipher this omnipresent phenomenon. In the Focus, we look at what music actually is, where it comes from, and finally ask the question why we play music. Our Regulars and Features, deal with music in a more specific way: we examine its relationship with science and how these two disciplines can profit from one another. We look at the life of Oliver Sacks who uses music in the treatment of his neurological patients and we listen to the sound of one of nature’s most fascinating phenomena: the Northern Lights.

But of course, music is not all that puzzles us. This diverse issue will introduce you to the science of cryptography and to the un-encrypted world of open-source software. We look at Cambridge as a scientific hot-spot and some of the issues it faces and, finally, we celebrate extraordinary achievements that have brought us to where we are now: we talk about science conducted on Mount Everest, 60 years after its summit was first climbed; 85 years after Fleming published his work on penicillin, we remember what treatments were available before that; and we look back at 100 years of research funded by the Medical Research Council.

As you know, we at BlueSci are always looking for new faces to contribute to our next issue. You could be an author, an editor, a member of our production team, film or radio crew or many other things. If you find yourself interested, please get in touch. That would truly be music to our ears!

Jannis MeentsIssue 27 Editor

Striking a Chord?

Electron Microscopy

in the 1670’s Antonie Van Leeuwenhoek revolutionised science when he began to experiment with magnification. His curiosity to observe anything that could be placed under a magnifying lens led him to be the first person to describe many microscopic entities, such as bacteria, which he isolated from his own tooth plaque, algae, nematode worms, and sperm. Leeuwenhoek’s discoveries rightly earned him the title of the ‘Father of Microbiology’, and his descriptions of the fascinating microscopic detail of the world fuelled the development of microscopes like those still in use today.

Since the time of Leeuwenhoek and his contemporaries, we have been trying to engineer microscopes that will allow us to view increasingly small objects in ever more detail. Optical or light microscopes, like those you might see in any lab or science classroom, use light and a system of lenses to magnify small samples, allowing us to view them as if they were up to 2000 times larger. However, the wavelength of visible light limits these light microscopes in their resolution to around 200 nanometres (200 billionths of a meter); two objects that are closer together than this cannot be distinguisehd any more. While this is sufficient to clearly see plant and animal cells as well as bacteria, it is not suitable to study organelles within the cell, such as the nucleus, mitochondria or chloroplasts, or to see most viruses.

In the 1920’s it was shown that accelerated electrons could behave like light waves when in a vacuum, and furthermore, the path of these electrons could be shaped by electric and magnetic fields in a similar way to how glass lenses focus light. In 1933, these discoveries lead the German scientist Ernst Ruska to build the first microscope that used electrons rather than light waves. It was named, rather unimaginatively, the ‘electron microscope’.

Ruska won the Nobel Prize for his work, but not until 1986. Initially, his invention didn’t impress the scientific community as it was impractical to use, had the tendency to burn samples and its resolution was no better than that of traditional light microscopes. It wasn’t until five years and several prototypes after his first one that the electron microscope gained popularity. This was in no small part due to the discovery that coating biological samples with heavy metals, such as lead

or uranium, helped separate electrons, thus giving better contrast.

Electron microscopes magnify by firing streams of electrons at an object. The electrons hit the object, bounce off and are focused by electromagnetism onto a screen or a photographic plate to make a visible image. As an electron has a wavelength around 100,000 times shorter than a visible light wave, the electron microscope has a much greater resolving power and can be used to reveal the structure of much smaller objects than can be seen with light microscopes. Modern electron microscopes can resolve something as small as 50 picometers (around one trillionth of a meter) and magnify it by up to 10 million times. This resolution is staggeringly high when you consider that the diameter of a hydrogen atom is just 100 picometers. Such high resolution allows scientists to study cellular compartments and gain a greater understanding of what goes on inside a cell.

This issue’s cover image illustrates the incredible detail that can be achieved when using electron microscopy. Taken by Daniela Sahlender from Margaret Robinson’s lab in Clinical Biochemistry, the image shows a sub-cellular structure called a clathrin-coated vesicle, which has been magnified 1.6 million times. Clathrin vesicles are small bubbles, around 100-200 nanometers in size that are used to transport molecules, such as nutrients and hormones within and between cells. The vesicles are able to pass from the outside of a cell into the cell, a process known as endocytosis. The vesicles have a membrane similar to the outer membrane of a cell and these two membranes can merge, allowing the content of the vesicle access to the inside of the cell. The cover image shows a clathrin-coated vesicle being endocytosed and budding out from the cell membrane.

Antonie Van Leeuwenhoek would never have believed that his work with lenses would lead to the discovery of microscopes so powerful that tiny intracellular structures could clearly be seen. As we continue to build ever more powerful microscopes, who knows what else we might discover about the microscopic world around us.

Nicola Love explores the technique used to obtain this issue’s cover image

On the Cover 3Easter 2013

Nicola Love is a 3rd year PhD student at the Department of Physiology, Development and Neuroscience

A replica of the first electron microscope

developped by Ernst Ruska in

1933

Easter 2013 Issue 27

www.bluesci.co.uk

The Cambridge University science magazine from

Cambridge University science magazine

Northern Lights . Open-Source . CryptographyEnergy Saving . Everest . Oliver Sacks

FOCUSA World of Music

j bre

w

the hormone insulin is best known for its defective action in diabetes; those with type one are unable to produce insulin and those with type two are unable to respond to it effectively. The insulin receptor has also been shown to be involved in several cancers, with its over-expression in malignant cells leading to an increased insulin response. However, new research has finally produced a structure for the interaction of insulin with its receptor. This may lead to the development of drugs able to simulate the effects of insulin. At the same time, the development of insulin-mimicking molecules that would block the insulin receptor could prevent its overexpression in cancer cells from being an issue. The structure of the binding was published in Nature by Dr Michael C. Lawrence and colleagues at the Walter and Eliza Hall Institute of Medical Research in Australia. It reveals that the binding of insulin to its receptor takes place in a way distinct from other similar receptors. This implies that molecules engineered to bind or block the insulin receptor would be less likely to inadvertently affect other receptors. Dr Lawrence described the discovery as “a fresh consolidation of knowledge...with the potential to feed through into a new generation of insulin therapeutics”.DOI: 10.1038/nature11781 tm

cambridge scientists have discovered four-stranded ‘quadruplex-helix’ DNA in the year of the 60th anniversary of Watson and Crick’s ground-breaking publication on the DNA double-helix. Led by

Giulia Biffi, the research group from Professor Shankar Balasubramanian’s lab at the Department of Chemistry reported in Nature Chemistry that these ‘G-quadruplexes’ exist within the human genome alongside their double-helical counterparts. Using antibodies to detect quadruplex-rich areas of the human genome, the group identified significant levels of quadruplex ‘hot spots’ during cell division and, more specifically, during DNA replication. Furthermore, the concentration of quadruplexes decreased when replication was inhibited. These findings may lead to improvements in cancer treatment. Cancers are caused by mutated genes, called oncogenes that lead to uncontrolled DNA replication, cell division and tumour growth. Consequently, the high rate of replication increases the concentration of quadruplexes. Targeting and trapping these excess quadruplexes with synthetic compounds could prevent cell proliferation in cancer. Even though the discovery that four-stranded DNA exists within human cells is a landmark achievement, much is still unknown about the function of quadruplex DNA. However, it is exciting that DNA continues to puzzle and amaze Cambridge researchers today.DOI: 10.1038/nchem.1548 md

4 News Easter 2013

News

the discovery of a ‘Higgs-like’ particle at the Large Hadron Collider (LHC) may allow scientists to determine the eventual fate of our universe. The Higgs boson is a theoretical particle, that, if proved to exist, would validate The Standard Model of particle physics and explain the relationship between force and matter. Atoms are comprised of protons and neutrons, orbited by electrons. Protons and neutrons consist of quarks whereas electrons are classed as leptons. Quarks and leptons are held together by bosons. Two bosons, the graviton and the Higgs, have so far eluded detection. Last year, physicists detected a Higgs-like particle, the mass of which spells bad news for our Universe. Calculations predict the formation of a ‘quantum bubble’ at lower energy than its surroundings, which

our higher energy universe will want to occupy. The result is a rapid expansion of the bubble; replacing the known universe as it grows. This discovery suggests the possibility of a

‘cyclical universe’, which would make our ‘big bang’ merely the latest of a history of expansions. Just as physicists were coming close to confirming the identity of the Higgs, the LHC shut down for maintenance and will start operating again in 2015. DOI: 10.1126/science.1232005 jh

Insulin—bound to help

Recipe for an unstable universe may burst our bubble

Check out www.bluesci.co.uk

or @BlueSci on Twitter for regular

science news and updates

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New twists in the tale of DNA

in PERIODIC TALES, Hugh Aldersey-Williams goes through the periodic table not following the atomic number order but his own logic, fi nding interesting stories and anecdotes, whether about the well-known oxygen or the less celebrated francium. Th e book provides a good mix of various cultural references, history and scientifi c trivia. Each element is presented in an eclectic, yet rather selective way—you will fi nd out where in the Bible sulphur got a mention and how lead was used as a metaphor for the human condition. You will also be treated to an 18th century recipe of how to obtain phosphorus from urine—from 50 pails of it. Luckily, the author follows this protocol himself, saving us all the trouble and the gross factor, while satisfying our curiosity as to whether it will work. In short, Periodic Tales is a feast for anyone who wants to be able to answer the questions on the comedy show QI. Personally, I could do with fewer quotes from Shakespeare and even more stories of discoveries, whether strikes of genius or just pure luck, and where to fi nd each element. But perhaps this makes the book more enjoyable for geeks with a more artistic slant. mC

Reviews

Reviews 5

in BORN TO RUN, American author and runner Christopher McDougall unravels the strangely appealing pleasures of running. Set in the remote Copper Canyon area in Mexico, the book introduces the elusive Tarahumara tribe, reputed to be the most remarkable endurance runners in the world. Th e story follows a group of iconic Western ultrarunners who, along with McDougall himself, set to compete against the natives in a 50-mile race organised by the mysterious fi gure Caballo Blanco. Although it reads as a pleasantly fl owing novel, the characters and events are all real and the book is subtly packed with intriguing facts on the history, physiology, and culture of running. One theme is the ‘endurance running theory’ of human evolution, according to which, many aspects of our physiology can be explained as adaptations for long-distance running. Th e author goes on to explain how the wearing of modern cushioned shoes alters the natural running posture, holding this responsible for the recent explosion in injury rates. Fascinating and informative, Born to Run is written with evident underlying passion; a fi lm adaptation is already planned. Fellow runners will instinctively indulge in its themes while others may well be enthused to put their trainers on, or perhaps to even go barefoot, and discover what makes running so popular. Ct

“medicine is broKen”, Ben Goldacre fearlessly declares in his new book Bad Pharma. As the title suggests, Goldacre takes on the multi-billion dollar pharmaceutical industry and exposes the tricks they play to undermine the scientifi c process of drug development in favour of big profi t. Using carefully collected evidence and a forensic attention to detail, Goldacre unearths examples where drug companies have suppressed data, distorted evidence and used poorly designed clinical trials to mislead doctors, make huge profi ts and expose patients to unnecessary harm. If this is not shocking enough, Goldacre also brings to light the failings of those responsible for assessing the science objectively: from the regulators, to scientifi c journals and academic establishments. Although this book may seem a little unbalanced at times, Goldacre attempts to compensate this by acknowledging the importance of the pharmaceutical industry as a whole, and outlining ‘obvious fi xes’ throughout. Even though the tone is much more serious and intense than in his previous book Bad Science, his witty writing style, indignant passion and ability to humanise the numbers brings the subject matter to life and makes this book a worthwhile read. YC

Bad Pharma: how drug companies mislead doctors and harm patients – Ben Goldacre

Penguin, 2012, £9.99

Fourth Estate, 2012, £13.99

Periodic Tales – Hugh Aldersey-Williams

Born to Run – Christopher McDougall

Profi le Books, 2010, £8.99

Easter 2013

the aurora borealis, or the Northern Lights, is a natural luminous light phenomenon that occurs in the night sky at polar latitudes and is sometimes visible in the northern hemisphere. For centuries aurora-watchers have reported hearing strange sounds of hissing and flapping during an auroral manifestation, but most scientists think of these as an anomaly.

Before the emergence of geomagnetic theories, natural philosophers and scientists had various interpretations of aurorae: they thought they were caused by solar rays, sulphurous vapours, electric fluid, combustion of inflammable air or glaciers. Indigenous people of the North, on the other hand, interpreted them as the torches of the spirits of the recently deceased, its motions as spirits (or children who died still-born) playing football, and its sounds as voices coming from the otherworld.

During the Enlightenment natural philosophers sought to separate science from superstition, by establishing stricter boundaries between empirical expertise—the western savant—and folk beliefs, including those of indigenous inhabitants; although this process of ‘purification’ was unable to fully consign folk beliefs to the scrapheap. For instance, in the 1780s, while looking back at the famous appearance of the aurora in England of 1716, Thomas Pennant criticised the “vulgar” suppositions of the populace, and suggested instead the natural explanation of “a great abundance of electrical matter”. Pennant believed this theory was supported by the sounds the aurora was reported to make: “crackle, sparkle, hiss”.

However, while indigenous witnesses reported distinct sounds of rushing, hissing, rustling, and crackling during meteoritic auroral activity to western travellers—the Sami people call the aurora ‘guovssahas’ (the light that can be heard)—this became a contentious issue once the great age of Arctic exploration began in the nineteenth century. Even if descriptions of these sounds were remarkably similar across regions and cultures, there was no instrumental evidence of their existence, and therefore most British scientists and Arctic explorers did not believe it. Long and attentive

observation by expeditioners during successive winters, utilising the latest scientific instruments, all failed to prove the existence of auroral sounds. This fact meant that perceiving the aurora borealis became interrelated with issues of credibility and expertise.

One sceptic put forward the popular argument that as none of the most well-known Arctic explorers had ever heard the aurora borealis, it was likely that any sound “might easily be attributed to the aurora, when the mind is excited by the wondrous spectacle, and susceptible to every illusion”. Naturalistic explanations ranging from acoustic illusions to environmental noise (the sound of the wind, waves, and cracking ice) were deployed if sounds occurred.

However, narratives in the library of the Scott Polar Research Institute reveal a more complicated and indeterminate picture of beliefs at the time, showing that the typical disenchanted pose of the scientific traveller was affected by testimonies from permanent European residents in the Arctic regarding the sounds of the Northern Lights. Indeed, tales received from fur traders working for the Hudson’s Bay Company could destabilise the sceptical position on auroral audibility.

Writing of his travels through northern Canada from 1769-72, the fur trader Samuel Hearne affirmed that “in still nights I have frequently heard [the Northern Lights] make a rustling and crackling noise, like the waving of a large flag in a fresh gale of wind”. Hearne’s account, which accepted that many non-indigenous travellers had not heard such sounds, became well-known among later British explorers, but it did not have an adequate scientific theory to explain them. A scientific amateur, the English fur trader and explorer David Thompson was the first to specifically test for auroral sounds. He spent the winter of 1796-97 at Reindeer Lake, Saskatchewan, where he performed some basic experiments on the perception of the Northern Lights: “in the rapid motions of the Aurora we were all perswaded [sic] we heard them, reason told me I did not, but it was cool reason against sense. My men were positive they did hear the rapid motions of the Aurora, this was the eye deceiving the ear; I had my

6 Have You Heard the Northern Lights? Easter 2013

Shane McCorristine examines the eerie sounds made by the glowing sky

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The English explorer David Thompson was

the first to test for auroral sounds

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