BlueSci Issue 27 - Easter 2013

The Cambridge University science magazine from

Cambridge University science magazine

FOCUS

A World of Music

Easter 2013 Issue 27 www.bluesci.co.uk

Northern Lights . Open-Source . Cryptography Energy Saving . Mount Everest . Oliver Sacks

Curing ‘the bends’ 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

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

Easter 2013 Issue 27

Cambridge University science magazine

Features 6

Regulars

Have you Heard the Northern Lights?

Shane McCorristine examines the eerie sounds made by the glowing sky

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The Myriad Genes

Open for Everyone

Commemorating a Commission Felicity Davies celebrates the centenary of the Medical Research Council

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

About Us...

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.

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Away from the Bench

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Two weeks before he treks out, Elly Smith talks to Dr Andrew Murray about science on Everest

History

FOCUS

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Elizabeth Mooney reflects on the opening of the new Cambridge Science Centre

Cracking Codes Philipp Kleppmann deciphers the advance of cryptography throughout the centuries

3 4 5

Maja Choma discusses the environmental impact of biomedical research

Initiatives

Haydn King describes the open-source software movement and two of its most striking characters 12

On the Cover News Reviews Science and Policy

Chin-Chin Chen discusses the implications of a Supreme Court ruling on BRCA cancer gene patents 10

Contents

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Nathan Smith explains how the pre-antibiotic era could come back to help us

Behind the Science

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Robin Lamboll looks at the controversial career of a neurologist who works with music

Arts and Science

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Christoforos Tsantoulas explores the relationship between music and science

Weird and Wonderful

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Committee President: Nicola Love ���������������������������������������������������������������� president@bluesci.co.uk Managing Editor: Felicity Davies �������������������������������������� managing-editor@bluesci.co.uk Secretary: Beth Venus ���������������������������������������������������������������� enquiries@bluesci.co.uk Treasurer: Robin Lamboll �������������������������������������������������������� membership@bluesci.co.uk Film Editors: Letizia Diamante & Alex Fragniere ������������������������������������� film@bluesci.co.uk Radio: Anand Jagatia ..................... ��������������������������������������������������� radio@bluesci.co.uk Webmaster: James Stevens ���������������������������������������������������� webmaster@bluesci.co.uk Advertising Managers: Philipp Kleppmann & Deirdre Murphy ���� advertising@bluesci.co.uk Events & Publicity Officer: Martha Stokes �������������������������������������� events@bluesci.co.uk News Editor: Joanna-Marie Howes ��������������������������������������������������� news@bluesci.co.uk Web Editor: Aaron Critch ���������������������������������������������������������� web-editor@bluesci.co.uk

Contents

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Issue 27: Easter 2013 Editor: Jannis Meents Managing Editor: Felicity Davies

Striking a Chord?

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 LealCervantes, 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

Varsity Publications Ltd Old Examination Hall Free School Lane Cambridge, CB2 3RF Tel: 01223 337575 www.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 copyright remains with the original rights holder). To view a copy of this license, visit http://creativecommons. org/licenses/by-nc-nd/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.

2 Editorial

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 opensource 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 Meents Issue 27 Editor

Easter 2013

Electron Microscopy Nicola Love explains the technique used to obtain this issue’s cover image The Cambridge University science magazine from

Cambridge University science magazine

A World of Music

www.bluesci.co.uk

Northern Lights . Open-Source . Cryptography Energy Saving . Mount Everest . Oliver Sacks

A replica of the first electron microscope developped by Ernst Ruska in 1933

j brew

FOCUS

Easter 2013 Issue 27

Easter 2013

in the 1670s 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 distinguished 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 1920s 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 undergoing endocytosis 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 is a 3rd year PhD student at the Department of Physiology, Development and Neuroscience On the Cover 3

News cambridge scientists have discovered four-

JON HERAS

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

Check out www.bluesci.co.uk or @BlueSci on Twitter for regular science news and updates

Insulin—Bound to Help 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 RAUL654

New Twists in the Tale of DNA

Recipe for an Unstable Universe May Burst Our Bubble

4 News

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 NASA

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

Easter 2013

Reviews Bad Pharma: how drug companies mislead doctors and harm patients – Ben Goldacre “MEDICINE IS BROKEN”, Ben Goldacre fearlessly declares in his new book Bad Pharma.

Fourth Estate, 2012, £13.99

As the title suggests, Goldacre takes on the multi-billion dollar pharmaceutical industry and exposes the tricks they play to undermine the scientific process of drug development in favour of big profit. 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 profits 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 scientific journals and academic establishments. Although this book may seem a little unbalanced at times, Goldacre attempts to compensate for 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

Periodic Tales – Hugh Aldersey-Williams

Penguin, 2012, £9.99

IN PERIODIC TALES, Hugh Aldersey-Williams goes through the periodic table not following the atomic number order but his own logic, finding interesting stories and anecdotes, whether about the well-known oxygen or the less celebrated francium. The book provides a good mix of various cultural references, history and scientific trivia. Each element is presented in an eclectic, yet rather selective way—you will find 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 for 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 find each element. But perhaps this makes the book more enjoyable for geeks with a more artistic slant. MC

Born to Run – Christopher McDougall

Profile Books, 2010, £8.99

Easter 2013

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. The 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 figure Caballo Blanco. Although it reads as a pleasantly flowing 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. The 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 film 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 Reviews 5

Aleesha NANDHRA

Have You Heard the Northern Lights?

Shane McCorristine examines the eerie sounds made by the glowing sky the aurora borealis, or the Northern Lights, is a

PUBLIC

The English explorer David Thompson was the first to test for auroral sounds

natural luminous 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 other world.

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 19th 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

6 Have You Heard the Northern Lights?

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 wellknown 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 Easter 2013

PUBLIC

men blindfolded by turns, and then enquired of them, if they heard the rapid motions of the Aurora. They soon became sensible they did not, and yet so powerful was the Illusion of the eye on the ear, that they still believed they heard the Aurora. What is the cause that this place seems to be in the centre of the most vivid brightness and extension of the Aurora: from whence this immense extent of electric fluid, how is it formed, whither does it go. Questions without an answer.”

With the onset of the heroic age of British Arctic exploration in 1818, the Admiralty made it a high priority to provide answers to these questions.

The scientific members of John Franklin’s Arctic land expedition of 1819-22, however, could not “distinguish its rustling noise, of which, however, such strong testimony has been given to us, that no doubt can remain of the fact”. On occasions, they came tantalisingly close to this perception: “we imagined, more than once, that we heard a rustling noise like that of autumnal leaves stirred by the wind; but after two hours of attentive listening, we were not entirely convinced of the fact”. Unable to hear them, they did receive testimony of auroral sounds from a credible source. At Fort Chipewyan in 1821, a fur trader from the North West Company told them of an aurora so powerful that “the Canadians fell on their faces and began praying and crying, fearing they should be killed; he himself threw away his gun and knife that they might not attract the flashes, for they were within two feet of the earth [...] and made a rustling noise, like the waving of a flag in a strong breeze”.

In most scientific accounts of aurorae in the 19th century there was a distinct tension between describing the wondrous spectacle of the Northern Lights while disciplining the emotions and avoiding superstition.

Whereas British expeditioners could not hear the Northern Lights, they continued to collect strange stories from sources they generally trusted. For example, even a prominent sceptic like Captain George Lyon could describe the “air of magic” during one stormy night in the Arctic and write how he had “never Easter 2013

The aurora borealis is a natural light phenomenon, sometimes visible in the northern hemisphere

contemplated the aurora without experiencing the most awful sensations, and can readily excuse the poor untutored Indians for supposing that in the restless motions of the Northern Lights, they beheld the spirits of their fathers roaming in freedom through the land of souls”.

Given that scientific experts continued to profess profound uncertainties about the nature of aurorae up to the 1940s, why did testimony on auroral audibility not force a change in approach? Partly, this was due to the wider disciplining of the heavens that was associated with the rise of meteorology and the decline of folk weather knowledge and prognostication during the Enlightenment. But, it was also because most reports came from permanent inhabitants of Arctic Canada: fur traders and indigenous inhabitants.

Thinking about the Northern Lights, therefore, has historically involved assessing who is best qualified to observe them. This continues to play out nowadays in conversations between seasoned field scientists and aurora watchers who all know of someone who heard the Northern Lights.

Yet, recent data from Finland has reignited the debate on whether the Northern Lights can make sounds. In 2012, researchers from Aalto University recorded a series of cracking or whipping noises during an auroral manifestation. These, they claimed, were formed about 70 metres above ground level (rather than in the atmosphere) and were caused in some way by the geomagnetic disturbances associated with the aurora borealis. The researchers noted that auroral audibility was a rare phenomenon and that “details about how the auroral sounds are created are still a mystery”.

As 2013 heralds a period of solar maximum, it behoves travellers and scientists in the Arctic to remember what the fur traders said and continue to keep their ears, as well as their eyes, open.

Shane McCorristine is a Marie Curie/Irish Research Council Postdoctoral Fellow at NUI Maynooth and the Scott Polar Research Institute Have You Heard the Northern Lights? 7

Christos PANAYI

The Myriad Genes

Chin-Chin Chen discusses the implications of a Supreme Court ruling on BRCA cancer gene patents a century after Gregor Mendel proposed the idea of inheritance and nearly six decades since the structure of DNA was deduced, we have come to realise that many human diseases are linked directly to our genes. From infections to heart disease, scientists have revealed associations between many debilitating illnesses and the different versions of genes, known as alleles, that people carry.

Understanding the genetic basis of disease has revolutionised the way we diagnose, monitor and treat illness, but it has also raised the question of whether the scientists who discovered these genes and their disease associations own their discovery, and to what extent should they be rewarded for their work.

The idea of patenting human genes is one that has been the subject of much contention and controversy.

Pharmaceutical companies, as well as many academic scientists, have carried out the majority of the research into the molecular basis of disease in the hope of generating a profit from their discoveries. Scientific research is an expensive business, and patenting can give labs financial security in promoting innovation and funding future projects. But, many scientists, medical professionals and non-profit organisations argue that it is unethical to charge a fee to those who seek to know if they carry a disease-causing allele, and that such information should be freely available to prevent unnecessary human suffering.

dullhunk

The cycle path from Addenbrooke’s Hospital to Great Shelford in Cambridgeshire features the BRCA2 gene sequence

8 The Myriad Genes

Gene patenting is once again in the spotlight as the United States Supreme Court is set to rule on a lawsuit that has dominated the debate on human gene patenting and decide whether the molecular diagnostic company Myriad Genetics can patent the BRCA1 and BRCA2 (Breast cancer type 1/2 susceptibility proteins) genes, giving them the sole right to perform diagnostic tests.

BRCA1 and BRCA2 were discovered and sequenced in the early nineties, from a woman with a strong family history of breast and ovarian cancer. Normally, BRCA proteins repair DNA when damage is detected.

However, a small number of people have a form of the BRCA gene that is unable to reverse the DNA damage causing genetic material to accumulate within a cell leading to the development of cancer. Carrying an abnormal copy of either BRCA1 or BRCA2 increases the risk of breast and ovarian cancer development by up to 60 per cent. The discovery of the BRCA genes was a major scientific advance in genetics, enabling screening of high-risk women for susceptibility alleles and therefore allowing early medical intervention and ultimately saving many lives.

Myriad, a company founded by one of the scientists who initially discovered BRCA, was granted a patent in 1997 and holds the rights for detecting gene mutations to diagnose cancer, as well as using the genes to identify novel drugs directly targeting the BRCA proteins. The controversy surrounding gene patenting stems from the refusal of Myriad to licence its genes to labs wishing to use BRCAs for clinical testing. Although Myriad will allow other researchers to study the genes for free, it is the sole provider of BRCA1 and BRCA2 diagnostic testing in the US, allowing them to set a market price of around $3000 for a full analysis of the genes.

The company relies solely on the patents to generate its profit. However, its patent is due to run out in 2014, although they hope to extend it, as in the US a patent has a 20 year term from the Easter 2013

Easter 2013

MIKE MITCHELL

filing date, but can be extended if it relates to a human or animal drug product. The American Civil Liberties Union (ACLU), a non-profit organisation that advocates individuals’ rights, together with the Public Patent Foundation (PUBPAT), has challenged whether the patent should stand and has brought a lawsuit against Myriad. The outcome of the judgement will determine the fate of genetic research and every one of us who may seek medical attention for diseases in the future.

In the US, like most other countries, patenting ‘natural law’ is not allowed. For example, the law of gravity can be observed anywhere in the world, and the usage of such law is not (and cannot possibly be) restricted by a simple patent. The patent for genes is a more complicated issue. Although patent law cannot protect natural phenomena, DNA historically has been regarded as a sequence of chemicals determined by humans, and therefore not seen to be natural. This is because as recently as the 1990s, to sequence just one gene was considered a mammoth task. The first complete human genome sequence was published in 2003 at a cost of billions of dollars and joint effort across the globe. As protection for their effort and financial investment, many companies and academics filed patents for the genes they discovered, so they could secure the financial benefits the genes might bring. This was the case for Myriad, who beat their European competitors to patent the BRCA genes and as a result enjoyed great success through the sale of diagnostic tests.

Biotech companies argue that having the patents does not just reward their hard work but also allows their labs to focus solely on mutations that might occur in the patented genes. Myriad suggested that their company studied the mutations more thoroughly before publishing them, in comparison with other laboratories that simply reported the mutation without showing how it causes cancer. They claimed that the company had invested in building their facility to constantly improve and maintain the quality of their testing kit. Furthermore, most biotech companies only pursue litigation for those who seek to profit, not the majority of scientists who work on the general studies of the genes.

The ACLU, however, argued that the patents have slowed the progress of understanding BRCA mutations. Although there are currently 8000 publications on the genes, according to the journal Nature, Myriad had prevented at least five researchers from testing women directly following the studies.

Moreover, a study carried out by Professor MaryClaire King of the University of Washington, whose group was involved in the initial studies of the BRCA genes’ linkage with cancer, suggested that Myriad’s test kit, ‘Comprehensive BRCAnalysis’, did not pick

Purified DNA, fluorescing orange under UV light, can be isolated and used for sequencing

up a number of mutations that are significant in the development of cancer. Additionally, Myriad’s figures show that the company made $402 million in revenue, of which 90 per cent was directly from the test kit, in the fiscal year ending June 2011.

ACLU argued that Myriad has already been rewarded financially for the discovery of the BRCA genes. If the restriction imposed by the patent had been lifted, progress in the understanding of how different BRCA alleles lead to cancer could have improved significantly.

Critics of Myriad believe that patients are losing out as a result of the patent. For many people in Europe, health care is provided freely. More importantly, the BRCA patents in Europe are held

by Cancer Research UK, a charity, which offers a different diagnostic kit than that from Myriad and free licensing to “any reputable laboratory that wants to use it”. For US citizens, however, the expensive price tag will have prevented many from accessing the test for BRCA alleles and any early disease intervention. More worryingly, Myriad’s own testing has suggested that for Latino women, an entire 20 per cent of all mutations can only be detected by its supplementary test, costing an additional $700 and not covered by many insurers in the US. Since 2009, the journal Nature has been following the progress of the lawsuit between Myriad and ACLU. In March 2012, the federal court ruled in Myriad’s favour. The Supreme Court then requested the court to reconsider, but in August the court ruled in Myriad’s favour once more. Since then, ACLU and the PUBPAT have asked the Supreme Court to reconsider certain aspects of the case. On 30th November 2012, the court decided to answer the question of whether the human genes are patentable.

The ruling is expected later this year. Whatever the decision, the Supreme Court will not just be deciding on the fate of one biotech company, it will be deciding on the future of gene patenting, and the implication it has for patients around the world and the scientific community as a whole.

Chin-Chin Chen is a 2nd year PhD student at the Department of Medicine The Myriad Genes 9

James Conan Baker

Open for Everyone

Linuxmag.com

Haydn King describes the open-source software movement and two of its most striking characters

Linus Torvalds is the creator of what has become one of the most important computer operating systems

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“i’m doing a free operating system (just a hobby, won’t be big and professional)...” announced a young Finnish PhD student to an internet message board on the 25th of August 1991. In the two decades since Linus Torvalds made this announcement, what started as a small and amateur operating system has revolutionised the IT world. Linux, as it is known, now runs over 60 per cent of the world’s internet servers, powers over 90 per cent of the world’s supercomputers and holds a significant share of the smartphone market through Android.

At the time of Linux’s conception there were several similar projects developing experimental operating systems for research purposes—either to directly research operating system design or as a platform for other research. However, Linux stood out from the crowd because it was made ‘open-source’. This means that as well as being given a copy of the compiled machine code that the computer understands, users are also given the human readable source code that they are free to modify and improve. These modifications are then submitted back to maintainers who test the changes and incorporate them into the official release. This model is very similar to the one used by projects such as Wikipedia, where anyone is free to edit and improve the content.

Torvalds found that this model for software development worked very well—a community of academics from other universities throughout the world could freely collaborate on his project through the internet. In particular, this meant that each contributor could work on the particular area that most interested them, and in which they were most highly skilled. People worked on Linux because they enjoyed doing so and because improving Linux would benefit their own work and the work of others across the globe.

Another pioneer of the open-source movement is Richard Stallman, the founder of the Free Software

Foundation, the FSF. Although Stallman shared Torvalds’ opinions as to the pragmatic benefits of the open-source development model, he had his own more philosophical reasons for despising the classical closed-source development model.

In the early 1980s, Stallman worked at MIT’s Artificial Intelligence Lab, where something of a hacker culture existed. In its true meaning, hacking is the digital equivalent of the car enthusiast tinkering with their engine to improve performance, so this wasn’t hacking in the popular sense, but was more about having a thorough understanding of a system in order to improve it. This geek culture was challenged when in 1980 the lab upgraded to the top-of-the-range Xerox 9700, the first commercially available laser printer and a technological breakthrough according to the manufacturer.

However, the new printer proved to be a step backwards as far as the MIT lab was concerned. In an effort to improve the usability of their previous printer, the group had modified it so that it would message the job owner when their print job was done or if an error had occurred. However, Xerox refused to make the source code available for the new printer, believing that doing so would put their intellectual property at risk. This made it impossible to edit the software of Xerox products and effectively made the process of technological development a sealed box.

Stallman was infuriated. He felt that as the owner, he should be able to do whatever he pleased with the printer, including modifying its source code. So, in 1984 he initiated the GNU project to develop an operating system that would put its end users in control, allowing them to modify their system as they pleased. Although the GNU project itself has not released a fully working operating system, its freely available suite of utility programs can be combined with the Linux kernel, the central core of the Easter 2013

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Haydn King is a 4th year undergraduate at the Department of Engineering

Beatrice murc h

However, despite numerous attempts, Linux has never broken into the mainstream PC market. There are several reasons for this. Linux still struggles with its image of being too complicated and difficult for the average user, even though user-friendly distributions such as Ubuntu are as simple to use as the alternatives in most cases. Competitors have been able to establish complete dominance by using aggressive marketing techniques, such that even with our current competition laws, buying a new PC without also having to buy a Windows licence is practically impossible.

An area in which Linux has been gaining ground quickly in recent years is in the software that is available on it. While Linux itself is still the largest single open-source software project, there are a number of other projects that have thrived under the open-source model. The Mozilla Firefox and Google Chrome internet browsers now have nearly 80 per cent of the browser market share between them, and both are entirely open-source and cross-platform projects.

An entire ecosystem of applications has been built using the model, from office suites such as LibreOffice to music players like Amarok, many of which are also available on multiple platforms besides Linux.

Just as the free software movement is bigger than Linux, the open-source ideals extend beyond software.

From the ideas of Stallman and his contemporaries came the notion of the ‘copyleft’ licence, the most famous of which are the Creative Commons licences.

These licences can be applied not just to software, but to all forms of creativity—writing, media, art and scientific works—and allow authors to share their work with others, who can build on it without fear of copyright infringement.

Open-source focuses on making applications as good as they possibly can be rather than on selling as many units as possible, and so the software produced is often far more flexible than closed alternatives. That is the open-source ethos.

Argonne national laboratory

operating system, to create what is often referred to as GNU-Linux, or just Linux.

In a video to mark the 25th anniversary of the GNU project in 2009, Stephen Fry publicly supported the project, saying “why can’t the community at large alter and improve [an operating system] and share it, that’s how science works after all—all knowledge is free and all knowledge is shared in good science. If it isn’t, then it’s bad science and it’s a kind of tyranny.”

So, how did a loosely knit group of academics with lofty ideals put together an operating system in their spare time to rival that of Microsoft and Apple?

Linux’s decentralised and ad-hoc methodology made contributing to the project straightforward and allowed each part of the system to be written by an expert. But even this cannot explain how such an outfit has won 60 per cent of the server market given the vast resources of its competitors.

The truth is that Linux is no longer only worked on by academics in their free time. Although Linux continues to rely upon the work of its community of users, over 70 per cent of the work is now carried out by paid developers. Some of these developers are paid by hardware giants such as Intel who see that the improvements made to Linux software will in turn improve the operation of their products and services, which rely on the Linux operating system.

Other companies that pay their workers to improve the Linux operating system include Red Hat and Novell, both of which make money by selling accredited Linux distributions and support contracts. This may seem strange; why would anyone be willing to pay for something they can get for free? Furthermore, neither company is allowed to keep any of their modifications secret. This means that they are essentially selling exactly the same thing as can be obtained from any of several entirely free distributions.

When asked why companies come to him and pay for what they could get for free, Red Hat cofounder Bob Young likened the question to one about ketchup: “Ketchup is nothing more than flavoured tomato paste. Something that looks a lot like Heinz ketchup can be made in your kitchen sink without so much as bending a copyright rule... so why don’t we, as consumers, make ketchup in our kitchen sink?”

The answer is obvious: it is cheaper and more convenient to buy ketchup from the local Sainsbury’s than to make it yourself, in the same way as it is cheaper to pay Red Had or Novell to fine-comb and provide technical support for Linux distributions.

Reliability is key when companies and organisations buy software, and you cannot guarantee the security of a piece of software unless you can see exactly how it works. NASA even have an expression that says: “software is not software without the source code”.

Richard Stallman, promoter of the free software movement and founder of the Free Software Foundation

Linux-based operating systems are used to run most of the world’s supercomputers, such as Blue Gene/P

h Josephine Birc

Commemorating a Commission

Felicity Davies celebrates the centenary of the Medical Research Council

George Hodan

The heptagonal shape of our 50p coins was introduced to make them more deistinguishable

Francis Crick (right) and James D. Watson (middle) with famous scientist Maclyn McCarty (left)

Research Council (MRC). Many have heard of this iconic institution, but few might realise the impact its research has had on our daily lives. This year, the MRC will be opening its doors to members of the public to reveal some of the life-changing research programmes that it funds. An emphasis on collaboration is a running theme, with many of their most recent discoveries being carried out in collaboration with the Welcome Trust, Cancer Research UK, or with one of the many other funding bodies in the UK. But it hasn’t always been this way.

The MRC grew out of the Royal Commission to research the most pressing medical problem in the UK in the early 20th century: tuberculosis.

Funds came from the 1911 National Insurance Act. The money was to be spent on research carried out by investigators in approved institutions, the first science institutes in the UK. The first of these continues today in North London as the National Institute of Medical Research. In 1913, 100 years ago, the Medical Research Committee and Advisory Council was established. This was the single research organisation for the UK, developing and funding their own research programmes and providing funding for research by other individuals or institutions that complemented their own.

Today, the MRC is a non-departmental public body funded through the government’s science and research budget. There are 56 research establishments across the UK and Africa. The MRC supports research in all areas of medicine. Last year alone, the MRC funded 1,100 grants totalling over £309.9 million. In Cambridge, the MRC is currently committed to awards totalling over £130 million. It provides around 700 jobs in Cambridge at the MRC Laboratory of Molecular Biology and its other units and many more through the grants held in the University of Cambridge, and other local research institutes.

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The MRC has a long history in Cambridge. In 1944, the MRC set up the Applied Psychology Research unit with Cambridge University’s Department of Psychology. The unit made advances in the field of service personnel research, such as the selection of aircrews, pilot fatigue and the design of aircraft controls and instruments. After the war it made a number of major contributions to our understanding of such psychological processes as attention and memory and continued to tackle practical problems. For example, the unit was responsible for the heptagonal shape of our 20p and 50p coins. Research into the lives of the blind or partially sighted revealed that a range of entirely circular coins were incredibly difficult to tell apart by touch, leading to much frustration for the partially sighted. The introduction of the heptagonal coins removed much of the difficulty, as each British coin is now distinctively different to both sight and touch.

In due course, it was renamed the MRC Cognition and Brain Sciences Unit. This more modern counterpart is engaged in active collaborations with many other research institutes, and uses a range of brain imaging techniques.

Other major contributions in Cambridge by MRC units over the years span such fields as nutrition, protein engineering and cancer, covering topics

Marjorie McCarty

2013 marks the 100th anniversary of the Medical

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David-P-Howard

as diverse as the biology of mitochondria, and the contribution of genes and lifestyle to the incidence of diabetes across Europe. One of the most exciting breakthroughs was the discovery of the helical structure of DNA by Watson and Crick in 1953 in what is now called the MRC Laboratory of Molecular Biology (LMB). With the invention of DNA sequencing techniques by Fred Sanger, also at the LMB, the stage was set for the human genome project, with the Cambridge contribution led by John Sulston who moved from the LMB to found the Wellcome Trust supported Sanger Institute, where much of the UK effort was undertaken.

To coincide with the centenary, change is happening for the MRC. In Cambridge, the new building for the LMB is complete, and research groups have been moving in since February 2013.

The previous building was opened by the MRC in 1962, and was home to 9 Nobel Prizes, shared between 13 scientists at the LMB. As a result, the institute was nicknamed ‘The Nobel Prize Factory’.

The new building is the flagship building for the extension of the Cambridge Biomedical Campus and the MRC hopes that it will continue to provide first class facilities to some of the world’s leading scientists.

The laboratory will have cost £212 million, and will provide space for more than 400 researchers. The overall structure of the new building is evocative of paired chromosomes, with two long laboratory areas joined by a large entrance hall, containing seminar rooms and a lecture theatre. In keeping with the concept of partnership, the University have contributed towards the cost of the building, which will also house several University research groups.

Some may argue that not much has changed since the Royal Commission; the aim of the MRC remains first and foremost the furthering of medical knowledge and understanding through scientific research. The biggest change in the last 100 years has been an increase in collaborations between research bodies. The MRC was founded as the first research body of its kind, but today, there is a wealth of research funding institutions, including sister research councils to the MRC. In Cambridge, the MRC works very closely with Cancer Research UK, the British Heart Foundation and the Wellcome Trust. Adrian Penrose, Regional Communications Manager for Cambridge and the Midlands has described it as a “catalytic coming together of scientific expertise”.

With the complexity of the research questions to be addressed, and the need to bring together scientists from across the biological, physical and social sciences, collaborations have become invaluable. Expertise and experience are now found in a wide range of locations, and it is only by pooling knowledge and financial resources that research can be done effectively.

The MRC’s centenary year will be a way of emphasising these collaborations. As it moves into its next 100 years, the MRC is embarked in a new form of collaboration, the ‘university units’, to strengthen the ties between the MRC and their academic research colleagues. As well as collaborations with universities, the MRC is also developing more collaborations with industry. The latter has had less money to spend on research, which has spurred on partnerships between industry and research bodies. This is particularly the case in the field of pharmacology, not least as a number of the expensive drugs are starting to come off patent.

Late in 2012, the MRC announced a deal with AstraZeneca, a large UK pharmaceutical company.

The company agreed to allow scientists access to certain compounds that did not go all of the way to becoming patented drugs. These compounds might nevertheless be useful for a different research area.

Access to data from the pharmaceutical industry can, if shared, save valuable time and money, and allow scientists to make new discoveries.

The centenary year will be used by the MRC to extend their reach to a wider community. The MRC units regularly take part in the Cambridge Science Festival, and in June they will open their doors in the first MRC open week. More than 40 units and centres will be open to the public, some for the first time, so that members of the public can see for themselves the work carried out by the MRC.

The new building for the MRC Laboratory of Molecular Biology was completed in 2013

Felicity Davies is an MPhil student at the Faculty of Philosophy Commemorating a Commission 13

Emily picroft

Cracking Codes

Daniel Kuperman

Philipp Kleppmann deciphers the advance of cryptography throughout the centuries

Enigma, the machine used by the Germans during World War II to encipher messages

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recently, a dead carrier pigeon with a secret message from World War II was found during renovation of the chimney of a house in Surrey. It is believed that the message was sent from Nazioccupied Normandy in June 1944. The encrypted message has been sent to the UK Government Communications Headquarters to be deciphered, so far without success. The amount of press surrounding this incident is uncommon for a subject that usually stays out of the limelight: cryptography. The purpose of cryptography is to alter a message in such a way that it makes no sense to anyone except for the intended recipient. In the past, it was only used by governments and the military, but nowadays everyone who surfs the internet uses it, whether they know it or not.

Cryptography started with simple methods: Caesar is known to have used an encryption in which each letter of the alphabet is shifted by a fixed distance (for example, ‘message’ turns into ‘nfttbhf ’ by replacing each letter by its successor). The distance by which the letters are shifted is called the key. If the recipient knows the key, then he can easily decipher the message. The idea is, that anyone who doesn’t have access to the key has no chance of understanding the coded text. However, Caesar’s code could be easily broken if his enemy knew the method of encryption.

For this reason it was necessary to invent more complex codes to ensure the security of the message.

This was the beginning of the battle between friends and enemies, governments and criminals, code makers and code breakers.

By World War II, the encryption techniques had developed significantly. The Germans enciphered their messages with a mechanical coding machine called Enigma, which they thought was unbreakable. But some machines and encryption keys fell into the hands of the British forces, and so British military intelligence, first and foremost Alan Turing, were able to decipher the code and thus change the course of the war. Their effort drove the

development of the first programmable electronic computer, the Colossus.

There is a method of encoding messages that is provably unbreakable: it uses a random sequence of numbers (the key) to turn the message into a string of letters which looks entirely random. Decoding the message is easy for the recipient who has access to the key, but it is impossible for anyone who doesn’t know it. Each key can only be used once—hence the name: one-time pad.

However, the one-time pad isn’t widely used.

The problem that this method shares with all other encryption techniques developed before the 1970s is the distribution of keys. It was thought that encryption and decryption is a symmetric process: that the same key is needed to encrypt a message and to reverse the encryption. For this to work, both the sender and the recipient of the message have to be in possession of the same key. But as the Germans experienced in World War II, this is a risky business; keys can be lost by accident, corruption, or blackmail.

A breakthrough came with the inception of public key cryptography. Before its invention, enciphering a text was essentially a mechanical procedure, designed to muddle up the letters. However, using mathematical techniques, it is possible to design codes that are asymmetric. Every person has a pair of keys, a private key and a public key. The private key is kept secret and the public key is made available to everyone. If two people, Alice and Bill, want to have a secure conversation, they don’t have to meet in order to agree on a key. Alice just sends a message to Bill by encrypting it with Bill’s public key, and Bill uses his private key to decrypt it. The asymmetry of the mathematics working in the background ensures that the message cannot be decoded except with Bill’s secret private key.

The asymmetry behind public key cryptography is obtained by mathematical operations whose computation is easy in one direction, but very time-consuming in the other. For instance, the RSA Easter 2013

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easy for communications to be monitored on a large scale. Using modern software it is possible to check all emails passing through a server for certain key words. If a message contains several of these key words, it can be investigated more closely. This can be exploited by illegal businesses by sending targeted scam emails. What is worse, it allows totalitarian regimes to monitor emails of political dissidents or journalists, which could lead to personal danger to the individuals and their families. Cryptography can be used to prevent such unwanted access.

At the moment, code makers seem to be the winners in the battle against code breakers. However, the advent of quantum computers will have a profound effect on the science of cryptography. So far, no practical quantum computer has been built. But when they become a reality, it will be easy for them to break the conventional codes, giving the code breakers a strong advantage. Anticipating this development, code makers have started conducting research in the direction of quantum cryptography, which aims to exploit physical properties of light, instead of general mathematical principles, in order to make secure communication possible. And so, the battle between code makers and code breakers continues.

len adlmen

algorithm, named after its inventers Ron Rivest, Adi Shamir and Leonard Adleman, is a method of encryption that relies on the (very likely but as yet unproven) assumption that it is easy for computers to multiply two numbers, but it is a hard task to find the prime factors of a given integer.

Since personal computers became popular, public key cryptography has become ubiquitous. It is used in many areas of every-day life: bank cards, emails, industry, and electronic commerce. It is so effective that a message encrypted in a second could take millions of years to break using the entire computing power of all computers on Earth.

In fact, the algorithm is so powerful that many governments around the world restricted its use.

The US government classified encryption software as a weapon, thus making its export illegal without a licence. These restrictions have been loosened since, but in China the use of cryptographic software is still strictly regulated.

The use of cryptography has recently become important not only for governments and business, but also for individuals who want to protect their own privacy. Checking communications between people used to be a laborious activity, because opening letters and tapping phone lines cannot be done by machines. For this reason, the police only monitored people who were suspected criminals.

But since the rise of the internet it has become very

Leonard Adleman (upper left), Ron Rivest (upper right), and Adi Shamir (lower) invented the RSA algorithm

Philipp Kleppmann is a 1st year PhD student at the Department of Pure Mathematics and Mathematical Statistics

A new generation of engineering leaders for the water sector Funded Research Engineer opportunities exist within stream, the Industrial Doctorate Centre for the water sector. Enhanced stipend of ÂŁ19,000 rising to ÂŁ20,000 for the final two years.

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Could you be an engineering leader of the future, delivering usable science to drive a step-change in the sustainability of water services for people, agriculture, industry and the environment? If so, the stream programme offers an opportunity to pursue your ambition.

For a full list of available projects and details of how to apply for a Research Engineer position on the programme please visit www.stream-idc.net or call +44 (0)1234 750111 ext 5570.

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A World of Music

lambdachialpha

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

listen. silence? Or the strange cacophony of ordered sound that is the latest Rhianna track or a Bach partita? If you are not currently plugged into your iPod or humming a tune, chances are you have been at some stage today. Music is the soundtrack to our lives; we use it to bring pleasure, cure boredom, connect with others, and even to approach the divine.

For some it is a reason to live. What’s more, music, in one form or another, is ubiquitous across all cultures; it is part of what makes us human.

And yet, coming up with an explanation of why we make music is not easy. What is it that makes us sing, go to concerts or dance at a disco? To find possible reasons, we shall look at what music really is and the effects it has on us. But starting at the beginning, we should probably ask ourselves, where did musicality come from and why did it arise in the first place?

Darwin, in The Descent of Man, described man’s musical ability as “amongst the most mysterious with which he is endowed”. Since then, the great ‘Why?’ about music has often been avoided by scientists.

Evolutionary theories are difficult to test: present-day advantages of musicality are likely to be different to those of our ancestors. The psychologist Steven Pinker famously dismissed music as “auditory cheesecake”: a pleasant enough concoction designed to tickle the senses, but not of any special evolutionary importance. His claim, widely followed by scientists since, was that our capacity for producing and appreciating music is nothing more than a byproduct of the brain mechanisms required for other functions, such as language. Indeed, language centres in the brain have been implicated to be involved in the ‘grammar of music’. However, we shall see that this does not necessarily mean that music is a “useless” by-product, as Pinker would have us believe, but that it might serve important functions in its own right. Music may, for example, allow communication between mother and child before true words and

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Musical ability is developed very early in infancy

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Doug Janson

Humpback whales (left) and Palm Cockatoo (right) use their musical skills to attract mates

National ocean service

language are acquired. In fact, young infants already display a prodigious ability to discriminate between musical stimuli. They prefer pleasant sounds to dissonant ones, recognise tunes even when they are transposed, and express surprise when unexpected chords flout the normal rules of ‘musical grammar’.

An alternative theory to why it is we make music was proposed by Darwin and has been maintained by many musicologists since. In this theory, the purpose of music is seen as originally lying in courtship, giving musicality a selective advantage as better musicians obtain better mates. For Darwin, this explained why seemingly arbitrary combinations of pitches and beats have an all-powerful influence over the emotions: music evolved because it evoked feelings of love and attraction. However, in humans musical ability develops very early in infancy and neither sex is more musical than the other, both contrary to expectations for a sexually selected trait.

Therefore, Darwin’s hypothesis is unlikely to hold true when it comes to mankind.

For animals, however, a sexually selected role for music is much more probable. Deep in the ocean, it is the humpback whale responsible for many of the haunting melodies that we refer to as ‘whale songs’.

These songs tend to come from the male during the mating season so it is likely that they are used to attract a female. They are perhaps the equivalent of the showy plumage of a peacock’s tail. The same is true for the majority of bird species. Darwin noted that it is mostly male birds who sing and that they

do so mainly during the mating season. He thus saw sexual selection as a critical factor in the evolution of bird song. Today, we know that the music of birds can have other purposes, for example the marking of territory. Surprisingly, not all such bird sounds are sung; some birds have been reported to use percussion instruments. For example the Palm Cockatoo breaks off a twig and shapes it into a drumstick. It then finds a hollow log, which produces the desired resonant frequency, and beats on the log by holding the stick in its foot as part of its courtship ritual. Some birds also use feathered structures to produce sounds, the most well-known example being the Common Snipe, which spreads specialised tail feathers to produce increasingly loud humming sounds as it dives from the sky.

So far it seems that sexual selection may indeed have played a role in the evolution of musicality. To some extent it is true for animals. What is more, it is believed that we find the sounds of some animals pleasing because their musical compositions hold a degree of similarity to our own. Whale songs, for example, tend to use rhythms and length of phrase similar to human music. They can last anything from between 5 to 30 minutes, suggesting that they also have a similar attention span to humans. Like us, they often create themes out of several phrases and reiterate them. Similarly, the music of birds can have parallels to human music. Birds follow the same scales as found in our music. The North American Canyon Wren sings in the chromatic scale (the 12 semitones, which make up an octave) and its trill cascades down a musical scale like the opening of Chopin’s Revolutionary Etude. The Hermit Thrush on the other hand uses the pentatonic scale (five different tones within the octave), which is characteristic of Asian music.

But is our music really so similar? Are animal songs actually music? Looking closer, birds are unable to recognise melodies that have been shifted up or down in pitch, which implies that this trait evolved after the divergence of birds and mammals.

The picture becomes even clearer if we look at our closest relatives. The ability to learn complex novel vocalisations is absent in non-human primates. The

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it when heard. There are many theories as to why some people have more of an innate ability to do this than others, such as a particular genetic trait, or their cultural or geographical upbringing. In any case, it is yet another example of the complex relationship between our brains and music.

The increased complexity of the human brain is likely to have played a major role in the development of musicality, giving us the ability to structure sound and organise it into music. This development has probably been facilitated by the ability to invent musical instruments, which we can ultimately use to produce any sound we want. But how is it possible to control the pitch of a sound? To understand that, we have to go back to the very basics and understand how sound is created in the first place.

Essentially, sound is a wave. A wave is basically a local disturbance that travels through a medium, and in doing so, transports energy from one location to another. As an example, think about the water waves produced when a stone falls into an otherwise calm lake. The energy of the falling stone is first transferred to the point of impact in the water, and then propagates away from this point through the water, producing circular waves, seen as ripples.

Looking at the physics of sound, we can break it down into three main processes: generation, transmission and reception. Sound is generated by a source, which creates some disturbance in the medium. Different sources create different sounds. In the context of music, the source can be an instrument or a voice. As an example, we’ll pick our sound generator to be one string from an acoustic guitar.

Plucking the string and then letting it oscillate causes roger mclassus

tamarin monkey, while able to discriminate pleasant from dissonant or harsh sounds, shows no preference for one over the other. Rhesus monkeys fail to recognise two melodies that have been transposed by half octaves but can do so when they are transposed by full octaves. However, the monkeys lose this skill when confronted with atonal chromatic melodies.

It therefore appears that tonality, the organised relationship of tones, has a special status.

Ultimately, it is the ability to produce any kind of note and to order them into chords and melodies that distinguishes humans from animals and that allows us to actually create music. But where does this ability come from? An obvious possibility would be that it is a result of the increased sophistication of our brains.

And yet, looking at music processing in the brain, we fail to find one music centre that could be the root of musicality in humans. Music processing rather seems to take place in different areas of the brain, some of which are primarily occupied with other functions, such as the cerebellum.

When we compare musicians to non-musicians in order to pin down the neurological differences, there seems to be a strong correlation between musical ability and the volume of grey matter in a person’s motor, auditory and visual-spatial regions of the brain.

However, it seems that these differences, occurring in several different parts of the brain, most likely arise from changes in use of the subject’s brain and are not from any differences in innate musical ability.

Interestingly, this is confirmed when looking at a musician’s brain while they are actually playing music.

The overall level of brain activity of pianists playing piano is lower than that of control groups asked to perform complicated finger movements. This seems to be caused by the pianists having developed more complicated neural pathways for playing the piano from repeated practice of the task. Taken together, it appears that much of the brain processing required to perceive and play music is acquired rather than innate.

A striking neurological musical phenomenon is that of absolute or perfect pitch, where a person can recognise the exact pitch of a musical note without any reference. While research has shown that there are no differences in the auditory system and in the ability to hear particular notes between those with perfect pitch and those without, there are nonetheless signs of neurological differences. Perfect pitch seems to represent a particular ability to analyse frequency information and probably involves high-level cortical processing. Perfect pitch is mainly an act of cognition: a person must be able to correctly remember a tone, assign it a label, such as B flat, and then have a wide enough experience of hearing that pitch as to recall

Garpenholm

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Music processing seems to take place in different areas of the brain

Sound waves transport energy from one location to another, just like water waves, produced by a stone falling into a calm lake

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The pitch of a guitar is determined by the location at which the string is pressed down

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Doubling the frequency produces a note that is one octave higher

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the air molecules to vibrate. Air is a compressible gas, and so the density and pressure of the air can vary from one place to another. This allows a sound wave to propagate through the air, via the alternate compressions (squeezing together) and rarefactions (pulling apart) of the air molecules, a bit like how a ripple is transported along a slinky. Our eardrum acts as a receiver, responding to the variations in the air pressure that is transmitted to it from the source.

As we have seen, it is the ability to organise sound that allows us to actually create music. In order to create a melody, we have to be able to control the pitch of a note. To do that, a guitarist presses the string down onto the fretboard and the location at which the string is pressed down determines the pitch of the note. We can produce a simple picture of the pitch of the sound in terms of the frequency of the string. Let’s start with the lowest note the string can produce. This is when the full string is free to vibrate and is known as the fundamental harmonic, shown at the top of the string picture (left). We can produce a note that sounds one octave higher by pressing the string down exactly halfway along the string. This note has exactly twice the frequency of the fundamental note. If we split the string into three equal sections, each oscillating with three times the frequency of the original, we produce a note that is two octaves higher than the original note.

Finally, in music we play with consonance and dissonance of different tones. In general, we perceive an interval, that is a combination of any two notes, as consonant if it sounds pleasant to our ears. This is defined by the relationship of the frequencies of the two notes. Think about the song ‘Kumbaya’ for instance. The first two notes in that song form an interval known as a major third. The frequencies of these two notes have a ratio of 5:4. The first and the third note (the ‘Kum’ and the ‘ya’) form what is known as the perfect fifth. The frequencies of these notes have a ratio of 3:2, meaning that the upper note makes three vibrations in the same amount of time

that the lower note makes two. The perfect fifth is more consonant than any other interval, except for the octave, and is often perceived as solid and pure.

Played together, these first three notes of ‘Kumbaya’ make a nice and pleasant C major chord. Dissonant intervals on the other hand usually sound harsh and unpleasant. This happens for example if you press two adjacent keys on a piano at the same time. Such an interval has a much more complicated frequency ratio, for example 18:17. This makes it appear unstable and it seems to have an acoustic need to resolve to a stable consonant chord. The reason why we perceive such combinations as unstable lies within the inner ear. Here, two frequencies that are less than a critical bandwidth apart cause interfering vibration patterns in the cochlea. This makes it difficult to discriminate between the two notes. For higher notes, this critical bandwidth can lie between two and three semitones.

We now understand how we can manipulate sound and structure it into intervals, which can then be used to compose music. We also know that this ability distinguishes us from other animals. But still the question remains: why do it? Perhaps the answer lies in the effect that music can have on our minds.

Understanding that we perceive certain sounds as pleasant allows us to investigate further and look at the physiological basis of such sensations.

Using brain scans, researchers discovered that listening to music triggers the release of dopamine in regions of the brain known to respond to pleasurable stimuli. This effect was seen across virtually every genre and type of music, showing that it reflects a universal reaction to music, rather than some intrinsic pleasurable quality of a particular song or tune. Nonetheless, we can all agree from our own experience that particular tunes or songs that are well known to us certainly arouse individual reactions, which can be particularly strong. This might at first seem contradictory: wouldn’t a well-known song, which by definition has become somewhat predictable, lead to less dopamine release and therefore lose its pleasurable quality? The opposite is in fact the case. Researchers have observed that increased dopamine activity in the brain begins before the subjects even hear their favourite part of the music—we begin to feel good just in anticipating what is to come. In their words, this anticipatory phase can “create a sense of wanting and reward prediction”. It leads us to expect a resolution to these feelings that are building up in us as we reach the music’s climax. Good composers and musicians can play with these expectations, changing their music in unexpected ways that keep our brains wishing for the ending that we thought we would hear. This in turn Easter 2013

heightens the physiological response in the brain and can lead to even greater feelings of pleasure when the resolution finally comes.

Often, such pleasure when listening to music can be accompanied by dramatic physical responses, such as changes in heart rate, breathing rate, skin conductance, piloerection (hairs standing on end), and facial expressions. These physical and emotional responses, although usually transient, can occasionally be life-changing, in some cases lifting what were thought to be intractable depressive states. It would seem that music is indeed a drug, and much research goes into how it might best be used therapeutically. However, whilst the emotions we perceive in music remain fairly consistent across time, these are not always elicited in us to the same extent. Unlike caffeine or Prozac, the effect of music is highly context-specific. It seems to require an act of will to allow music to touch us and actively change our mood.

Finally, the idea that the evoked emotions are relatively fixed is perhaps the key to understanding music’s ultimate function. Dr Ian Cross, working in Cambridge, certainly believes so. He describes music as conveying “floating intentionality”. It may be communicated between people in a reliable but imprecise manner: it is nearly always obvious what sentiment a piece of music is conveying, yet almost impossible to put this into words. This could provide a means of communication that transcends language in many ways. In particular, music-mediated interaction has a lower risk of conflict than language; it is difficult to accidentally offend someone with a tune. The ultimate function of music might therefore lie in its social aspect. Musicality could have evolved under the selection pressures of increasing social organisation, with all its requirements for clever

thiophene_guy

FOCUS

communication. This view becomes clear when we look at musical traditions across the world: song and dance are often integrated parts of daily life, used to bind groups of people to a common purpose, for example work, celebration or grief. One especially prevalent example can be found in lullabies. Nearly every culture has a type of music intended to placate infants, and there is considerable consistency in how they sound. This brings us back to the very beginning: music is universally used as a form of prelanguage communication between mother and child.

But what is more, it is equally important for adult communication and for emotional well-being.

In the end, it seems that there is no one way to explain why we make music. There are evolutionary reasons as well as physiological and social ones. But by understanding what music actually is, where it has evolved from, how we use it, and what effects it has on our minds and hearts, we can appreciate that among the many things that make us human, our musicality is indeed “most mysterious”. After all, music can be a soundtrack, a song, a chord, a wave, and a drug we cannot seem to live without.

Matthew Dunstan is a 2nd year PhD student at the Department of Chemistry

Taiko drums are an essential component of folk and classical music in Japan

“Play me, I’m yours”—over 700 pianos have been installed in 34 cities across the globe for the public to play and enjoy music

Nicola Hodson is a 3rd year PhD student at the Cambridge Institute for Medical Research

ed yourdon

Zac Kenton is a 4th year undergraduate at the Department of Applied Mathematics & Theoretical Physics

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Elly Smith is a 2nd year undergraduate studying Biological Natural Sciences at Trinity Hall

Focus 21

Waste of Research

Recycling is becoming more important in biomedical research facilities

A CO2 incubator, often filled with single-use plasticware, consumes high amounts of energy

22 Science and Policy

the uk is very proud of its large biomedical research sector, but there is a darker side to this innovative part of the economy: the amount of waste. Whether we look at the physical rubbish produced or the amount of energy used, a laboratory’s carbon footprint far exceeds that of a normal office space, shopping centre or school.

The high level of safety measures required by a lab makes it unpopular with the energy-efficiency community, but it doesn’t mean that nothing can or should be done.

The majority of the rubbish may not be contaminated with anything dangerous, but it is still most likely to end up in a landfill, not recycling.

Most of a lab’s bin contents have been classified as bio-hazardous and therefore as posing a threat to human health or the environment—not an enticing starting point for recycling.

Anyone involved in biomedical research will tell you how keeping things sterile is extremely important. This requirement, together with evergrowing health and safety measures, dramatically increases the amount of waste produced by a lab, although laziness has its part to play as well. It is simply much less effort to open a fresh bag of sterile, single-use plastic lab implements than to go through the complicated process of sterilising their more sturdy equivalents. A few decades ago, bacteria were grown on glass petri dishes, which had to be washed and sterilised by baking at a very high temperature. Alternatively, you can sterilise your instruments by immersing them in highly concentrated ethanol and burning it off with a flame but that is not only time-consuming, it is also a fire hazard. In fact, well-meaning scientists, who are horrified with the amount of plastic waste that they produce, have very few options to improve the situation without jeopardising their experiments by potential contamination. As a result, instead of reusing anything, biologists nowadays simply reach for another plastic pre-made unit.

Like in the fruit and veg section of a supermarket, everything is packaged and wrapped in plastic.

Precious and delicate reagents are delivered with ice packs, dry ice, polystyrene chips and in general so much packaging that it is often difficult to spot your item in the enormous box. However, this excess is being curbed, if not by environmentally friendly policies then by the financial crisis. New England

BioLabs now ask for their polystyrene boxes and ice packs to be sent back to them so that they can be re-used for other orders. Boxes are getting smaller as profit margins fall.

The Improving Engineering Education Project of the Cambridge-MIT Institute has published a report on recycling that highlights some major problems.

It’s time-consuming and therefore expensive to collect and separate different types of rubbish. The end product, for example pellets made from plastic bottles, is of lower quality than ‘virgin’ plastic made from petroleum and so has fewer applications and lower market value.

A lot has been done to make recycling easier and more popular in Cambridge. Gone are the days of 27 different material-specific bins that were far away or always full. Cambridge City Council has introduced one blue bin for recycling almost all household waste, which makes life a lot easier.

Businesses are encouraged to recycle by financial incentives and the public opinion is slowly moving towards stigmatising wastefulness and applauding anything labelled ‘green’. Even the University of Cambridge has recognised the importance of doing

Shinryuu

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Maja Choma discusses the environmental impact of biomedical research

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The University of cambridge environmental office

Lawrence Berkeley National Laboratory

something to help the environment. The University website proudly displays a graph, which shows small but steady growth of recycling of its waste (http:// www.admin.cam.ac.uk/offices/em/sustainability/ environment/guidance/waste.html). It does not comment on the rise in the amount of rubbish going to landfill in most recent years. University Policy on Environmental Issues states that: “The University will (…) make continued efforts to reduce its environmental impact through the implementation of an Environmental Plan, which sets out a range of objectives and targets related to its significant environmental impacts, including (...) to minimise waste and pollution, and to operate effective waste management procedures.”

One of the goals set out by the Environmental Plan is to “enhance the reputation of the University”, as well as reduce the costs of waste disposal. To this effect, the blue recycling bins have been introduced to the Cambridge Institute of Medical Research. A bold move for the University, but it also caused a bit of confusion. Most people at the Institute agree recycling is good and desirable, but what to recycle in a lab? The helpful brochure suggests telephone books and cans, but doesn’t mention gloves and tubes. Even when they are not biohazardous waste they sure look that way and in the end were banned from the recycling bins. So much for recycling in the lab.

However, physical waste is only the tip of the iceberg. The amount of energy a typical lab uses is staggering, mainly because of the many pieces of equipment, which use a lot of electricity and are always on. It’s not just the constantly running computers or office lights, but the huge energetic cost of running CO2 incubators at a specific temperature, fridges and freezers, pumps, ovens, water baths and heat blocks, some of which are left on mostly for convenience. But as the energy costs are rising and being environmentally friendly becomes not only fashionable but a legal obligation, new policies might be cracking down on this excessive usage. According to the Vice-Chancellor,

Sir Leszek Borysiewicz, the University’s target is to reduce its energy-related carbon emission by 34 per cent by 2020 as compared to 2005. A new initiative called ‘Switch-Off week’ ran in February across the University’s departments and colleges in an attempt to raise awareness amongst both the staff and the students of how much energy is being wasted.

Using a dedicated website (http://www.admin.cam. ac.uk/carbon/getting_involved/sow.html) one could check the daily reports showing how much energy had been saved in total and by each department. It was also translated into how many miles a cyclist could travel on that amount of energy. An example of a more long-term solution would be introducing volunteer ‘switch-off marshals’, who make rounds in the evening trying to limit the amount of electricity wasted.

Ironically, the biggest help in the crusade for more ‘green’ lab space is the financial crisis and the funding cuts associated with it. When a smaller budget has to last longer, every moneysaving measure counts. This can start with more energy-efficient equipment, more re-usable or recyclable consumables and can go all the way to improving whole building designs. A good example is the Lawrence Berkeley National Laboratory in California, which set out to find more efficient solutions in the building design in order to achieve a U.S. Green Buildings Council LEED Silver rating.

Thanks to a very efficient ventilation system and an energy-efficient boiler and chiller plant, they managed to surpass expectations and were awarded the LEED Gold rating. As one of the engineers involved in the project implied, reducing the carbon footprint of a lab is challenging and sometimes quite difficult, but with the right attitude and new technologies it is entirely possible.

The Molecular Foundry facility of the Lawrence Berkeley National Laboratory received an LEED gold rating

During ‘Switch-Off Week’, scientists at the University of Cambridge were encouraged to save energy

Maja Choma is a 4th year PhD student at the Cambridge Institute for Medical Research Easter 2013

Science and Policy 23

Making New Scientists Elizabeth Mooney reflects on the opening of the new Cambridge Science Centre cambridge has a reputation as a world-class centre

Cmglee

The Cambridge Science Centre on Jesus Lane opened in February 2013

for excellence in scientific research and some of the most significant discoveries in modern times have been made here. It therefore seems obvious that as a city we should seek to inspire younger generations to explore science and make their own discoveries about how things work in the world around them.

However, unlike many other cities we have never had a dedicated hands-on science museum providing these opportunities. The opening of the new Cambridge Science Centre has changed all that. Open six days a week, the Science Centre is filled with a fascinating array of hands-on exhibits ranging from infrared cameras to giant anatomical models, and also features a large magnetic wall on which complex cog and gear contraptions can be constructed.

The Cambridge Science Centre first burst on to the scene in October 2011, staging a oneday ‘Science Xchange’ event at the Cambridge Guildhall. The event featured scientific artwork, guest demonstrations by student society CHaOS and the main attraction, a ‘Rube Goldberg’ machine made up of interconnecting modules, manufactured by science centre staff and groups of local schoolchildren. Each module was made up of moving parts, which tipped,

24 Initiatives

dropped or sprang to trigger movement in the next section, creating a chain reaction that travelled around the room and culminated in the firing of a high-speed air rocket the length of the hall to release squealing balloons. The event was such a hit that the ‘Science Xchange’ returned to the Guildhall in October 2012, with members of the public adding to the mayhem by building contraptions on the day.

This time, the chain included dominoes, hydraulic systems, catapults and a fantastic musical organ constructed from mouse traps and party poppers.

Between these two events, the Cambridge Science Centre team were hard at work taking their unique hands-on exhibits further afield across Cambridgeshire. The ‘Library Science Lab’ tour in summer 2012 saw interactive stations, featuring equipment from microscopes to electromagnetic generators, installed in public libraries across the county. The tour proved to be a great success, receiving excellent feedback, and soon after completion the first full-time home for the Cambridge Science Centre was confirmed: the old Marshall’s Garage workshop on Jesus Lane. The opening of the Science Centre in early February was the culmination of many months of hard work by a small but dedicated team of science communication enthusiasts. This hard work proved worthwhile; the venue was packed with excited visitors throughout lent half-term. School groups will be able to book to visit the centre on weekday mornings, while during afternoons, weekends and school holidays the centre will be open for the public to drop in or attend a variety of scheduled workshops. Special events, including those aimed at adults, will also run in the evenings.

Despite the small size of the centre, it is crammed with a range of exciting exhibits, which will change on a regular basis, making repeat visits worthwhile.

The centre is well worth exploring whatever your age or background, and in addition will provide excellent opportunities for both volunteering and employment in the field of science communication.

Visit www.cambridgesciencecentre.org to find out more, or follow @camsciencecntr on Twitter for regular updates on the progress of new exhibits in the workshop!

Elizabeth Mooney is a 2nd year PhD student at the Department of Pharmacology Easter 2013

Altitude Science

Carsten.nebel

Two weeks before he treks out, Elly Smith talks to Dr Andrew Murray about science on Everest

Mount Everest is the Earth’s highest mountain, with a peak at 8,848 metres above sea level

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at the foot of the highest mountain in the world, surrounded by rocks and ice, lies one of the most hostile environments on the planet. Here, the air is too thin for helicopters to approach; one wreckage lies sprawled against the craggy ground. Breathing is the perpetually oppressive imperative, and hypoxia drains the body’s capacity to carry out trivial physical tasks. Performance on basic mental functions, like remembering a list of 15 words or joining numbered dots, is embarrassingly impaired. Even sleeping can become arduous.

Most trekkers to Everest base camp are thrillseekers, but Dr Andrew Murray and the Caudwell Xtreme Everest team have other purposes in mind.

They are driven by the pressing need to improve care for the critically ill. In the UK, one in five of us will end up in intensive care, where the mortality rate is 40 per cent. Despite this being one of the most sophisticated areas of modern medicine, “we really don’t understand why it is that some people die and some people survive”, Dr Murray explains. “But the one thing that almost all of these patients have got in common is low oxygen levels. Equally, we don’t know why some people perform well at altitude and others get awful crippling mountain sickness.”

So, for a period of three and a half months in 2007, the team set up a lab at 5364 metres, performing tests on 208 volunteers in the hope that studying the genetic and physiological factors behind the human body’s response to hypoxia will allow the development of better treatments. I asked Dr Murray about some of the difficulties faced when trying to do science in such an environment: “Absolutely everything has to

be trekked in on a yak or with a porter...” What would otherwise be minor details become major logistical problems; all lab equipment is subject to testing in an environmental chamber first as even laptop hard drives won’t work (solid state equivalents are used instead).

That’s not to mention the challenges faced by members of the team. “We’re testing in an environment where we hope we’re going to have really profound changes on physiology, but then we’ve got to operate as researchers and try to ignore the fact that we’re very, very short on oxygen.” A long day in the lab is even longer at altitude: “...it doesn’t really help when you’re trying to think straight at the end [of the day], so you’ve just got to try and acclimatise as best you can”. Several researchers went one step further, ascending to the summit to experiment on themselves. Blood oxygen was measured at the highest ever altitude (found to be the lowest ever value for a ‘healthy’ subject), and muscle biopsies were endured.

Dr Murray says: “it wasn’t just a scientific opportunity, although I did obviously still believe in that, it was an opportunity to go to a part of the world I’d read about since I was a child and always wanted to visit”. He tells of evenings and weekends during his postdoc spent working on the project, focussed not on how this would get him papers, grants and jobs, but driven purely by a desire to get out there and do something exciting. “People asked me ‘why are you wasting your time getting involved in this project?’ but the simple reason was: I wanted to do it.”

So, what does Xtreme Everest 2 hold in store?

“What’s going to be really rewarding is that, unlike our previous expedition where we were just looking at lowlanders, this time we’re also looking at Sherpas.”

This native people of the Nepali Himalayas are “the supreme altitude performers”; their genetic distinctions are well studied but nobody knows what functional differences make them such successful highlanders. “There is something clearly remarkable about their physiology; you’ll be carrying a very light day pack, walking up a moderate slope, and you’ll be out of breath, and the natives, you’ll see them stroll past you, carrying huge weights, wearing a pair of flip flops.” To discover what they find, follow the progress of the expedition (starting 1st March) at http://www.xtreme-everest.co.uk.

Elly Smith is a 2nd year undergraduate studying Biological Natural Sciences at Trinity Hall Away from the Bench 25

The War Against Infection

Pu bl ic

Nathan Smith explains how the pre-antibiotic era could come back to help us

John Tyndall noted the antibiotic effects of penicillin in 1875

DR gRAHAM bEARDS

Electron micrograph of bacteriophages on a bacterial cell

26 History

we stand on the brink of the post-antibiotic era, with bacteria becoming increasingly resistant to existing drugs and with few new ones in the pipeline. In light of this fact, scientists are revisiting early antibiotic agents in the search for a new wonder drug with which to tackle the escalating bacterial threat. One of the most common groups of antibiotics, penicillin, only became widely available during World War II, with one of its first high profile uses taking place in the aftermath of the D-Day landings. However, researchers had first highlighted bacteria as a cause of disease about 70 years beforehand. Indeed, the history of antibiotics prior to the popularised use of penicillin is incredibly rich with attempts to find the ‘magic bullet’ against infection. Reconsideration of this early research may offer the solution to this looming medical dilemma.

In 1877, Louis Pasteur and Jules Joubert developed the concept of antibiosis, a process in which one microbial species attacks another. This was not the first description of antibiosis, however.

John Tyndall had previously reported the lysis, that is the destruction of a cell by rupture of the cell wall, of bacteria in the presence of a Penicillium mould.

Nevertheless, the report by Pasteur and Joubert can be considered one of the first appearances of antibiosis in literature that survives modern scrutiny, and certainly one of the most widely disseminated pieces. By 1885, Victor Babes had shown that it was chemical substances produced by microorganisms that killed bacterial species. In that same year, Arnaldo Cantani carried out one of the first recorded therapies based on antibiosis, treating a patient suffering from tuberculosis with a Bacterium termo culture, applied directly into the lungs of the patient. The tuberculosis bacteria disappeared from the patient’s mucus, replaced by B. termo, and the patient’s condition improved. Many more cases involving the replacement of pathogenic bacteria with less harmful ones were published in scientific literature in the following decades.

Other early applications of antibiotic treatment included the use of microorganism-derived lytic substances in the preparation of vaccines. However, these injected chemical agents were not truly chemotherapeutic because they did not effectively treat infection and disease—they could only prevent them. Several scientists attempted to develop

chemotherapeutic agents, and one such product, pyocyanase, became the first to be distributed to hospitals. Discovered independently by Ivan Honl and Jaroslav Burkovsky in 1898 and by Rudolph Emmerich and Oscar Löw in 1899, it was released by the latter after they observed its lytic effects against many bacteria, including those causing cholera, anthrax, typhoid and plague. Whilst they were unsure of its origin or mechanism of action, it proved bactericidal and effective in the clinic.

After several years, it had become primarily used as a local antiseptic to great effect, successfully treating a wide variety of cases ranging from diphtheria to conjunctivitis. However, by the late 1920s it had fallen out of clinical use due to inadequate quality controls in production, resulting in an inactive product and a subsequent loss in sales.

Another group of pre-penicillin chemotherapeutic agents comes from an unlikely source: a group of viruses known as bacteriophages, which solely infect bacteria and are often species-specific.

Although Frederick Twort and Félix d’Herelle independently discovered bacteriophages in 1915 and 1917, respectively, it is d’Herelle that stands out as the father of bacteriophage therapy and indeed remained one of its most vocal proponents throughout his life. Realising that commercial laboratories were producing inactive preparations due to poor quality controls, drawing much comparison with pyocyanase, he established his own laboratory to research, produce and distribute phage products in an effort to prevent their discredit. He travelled extensively to introduce phage treatment around the world, and it is largely due to his efforts that it maintained a strong presence in France until the 1990s and is still widespread in Eastern Europe today. Indeed, in the brief conflict between Russia and Georgia in 2008, Georgian soldiers were deployed with phage cocktails amongst their medical supplies. What makes phage therapy most interesting in the prepenicillin context is that no one at this time was quite sure what phages actually were, lacking the technology to visualise these viruses.

One of the last major groups of antibacterial drugs to experience a phase of strong popularity was the sulphonamides, first popularised in a prodrug form trade-named Prontosil. Prodrugs are biologically inactive compounds that are Easter 2013

against typhoid. Ultimately, the work was largely ignored, most likely due to Duchesne’s lack of scientific seniority.

It was not until 1928 that Alexander Fleming first published work on penicillin, also largely disregarded at the time, and by 1935 at the latest he had all but abandoned his work on penicillin, focusing his interest on the newly discovered sulphonamides. Others attempted work with the unstable mixture, most notably Harold Raistrick, Percival Clutterbuck and Reginald Lovell, but while they found they could biochemically purify it, they were ultimately unable to extract it from solvent. It was not until scientists such as Howard Florey, Ernst Chain and Norman Heatley at the Dunn School of Pathology, Oxford took up the task of isolating and stabilising penicillin that its large-scale production was possible, thus helping to introduce the antibiotic era.

The road to readily available and safe antibiotics was one filled with many promising compounds and many others that resulted in dead ends. Poor quality controls, temperamental products and a lack of recognition by the scientific community were all factors responsible for the lack of long-term uptake of pre-penicillin antibiotics.

Meanwhile, penicillin’s remarkably low toxicity and ease of application allowed it to dominate the antibiotic market. If and when we enter the post-antibiotic era, it will be vital to promptly establish alternative forms of treatment, and it may well be that some of these early therapies make a comeback.

Ministry of Information Photo Division Photographer

converted into their active form in the body by normal metabolic processes. Although initially patented by the German company IG Farben that first demonstrated its medical potential, the active component was later found to be a sulphonamide on which the patent had long since expired. It enjoyed a brief moment of pharmaceutical dominance in the late 1930s and was available both in a pill and powder form.

Unfortunately, it was ineffective in pus-infected wounds and therefore had limited success in treating established infections. Its derivatives are still in use today, most notably in the dual content drug Trimethoprim/sulfamethoxazole (TMP/SMX).

Another noteworthy drug is the chemotherapeutic agent Salvarsan (later replaced with Neosalvarsan), discovered by Paul Ehrlich’s laboratory in 1909. A product with a niche market, it was only effective against syphilis and remained popular in clinics until eventually superseded by penicillin.

Finally, the history of penicillin itself is not as straightforward as is often believed. As mentioned above, John Tyndall noted its antibiotic effects in 1875, while Joseph Lister, who in 1871 apparently used penicillin to treat a patient, and Louis Pasteur reported similar observations in the same decade.

The physician Ernest Duchesne also carried out key work in 1897, and his doctoral thesis on Penicillium glaucum described the mould’s use in successfully treating typhoid in guinea pigs.

However, we now know that penicillin is inactive against typhoid and so it seems likely that he misidentified the mould, perhaps confusing it with a member of the genus Acremonium, a group that produces cephalosporins—a family of chemotherapeutic agents active, among others,

Alexander Fleming in his laboratory at St Mary’s Hospital, London, during World War II

Nathan Smith is a 1st year undergraduate studying Biological Natural Sciences at Churchill College

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History 27

The Notoriety of Oliver Sacks Robin Lamboll looks at the controversial career of a neurologist who works with music

Erik Charlton

deVos

Oliver Sacks: professional neurologist and bestselling author

it is rare for a popular science author to find themselves criticised for anything much more interesting than oversimplifying their subject.

Dumbing down is not a problem many people have with Oliver Sacks, professional neurologist and bestselling author. His books are popular in the sense of being ‘accessible but enjoyed by everyone’, rather than ‘simple and containing nothing of interest for the expert’. As he opens his clinical casebook in The Man Who Mistook his Wife for a Hat, the reader explores the many curious disorders of the mind both on a personal and technical level. The reader may want to look up some of the more obscure references to the neurological principles each case brings to light, or might fall behind the scintillating analogies Sacks makes between disparate areas of medicine, literature and philosophy. However, they are likely to put the effort in—the subject is too interesting to miss out on.

Sacks originally achieved notoriety with the book Awakenings, which describes how people who suffered from sleepy sickness (encephalitic lethargica) were awoken from their decades-long sleep by the new drug L-DOPA. The book investigates how they dealt

28 Behind the Science

with restarting their lives after such a break from the world, the lingering effects of the illness and the many adverse effects of the drugs. The tale inspired both a film of the same name and the Harold Pinter play A Kind of Alaska.

However, amongst the acclamation, Sacks has faced significant criticism by several disability activists for his public depictions of the neurologically anomalous.

Called “the man who mistook his patients for a literary career” by geneticist and disability activist Tom Shakespeare, he is accused of being nothing more than an intellectual freak show host, presenting each new monstrosity of the mind for our amusement. He is also accused, along with the rest of his profession, of institutionalising the ‘imperialist’ approach to diagnosis: the syndrome is described by the doctor, not the patient.

What is quite remarkable, though, is that many of those he studies barely realise that there is anything abnormal about them: for instance, people with memory problems soon forget them. The man who mistakes his wife for a hat would continue to do so if she did not complain, and our imperialist clinician often has to go to great lengths to demonstrate that he actually has a problem other than bad eyesight (his eyesight is actually fine).

Sacks notes that he only describes case studies after the patients (or, where relevant, the family) have consented, and never with original names.

More recently, he has revealed that one case is in fact his own. The Man Who Mistook his Wife for a Hat includes the tale of a man who discovered ‘the dog beneath the skin’, an extraordinarily strong sense of smell that lasted for three weeks after he took a cocktail of drugs. His addiction to amphetamines during his time in San Francisco in the 60’s is not the only source of psychological abnormality. He has suffered from migraines accompanied by visual hallucinations since the age of four and also has the relatively common condition prosopagnosia, or faceblindness. Like other sufferers, he has developed other means of identifying people and these conditions are not generally a problem for him. What he considers his ‘disease’ is his shyness—he has never married and has spent much of his life with few friends. He says he finds it difficult to start conversations: “I never initiate contact. It’s a little bit like some of my Parkinsonian patients, who can’t initiate movement but can respond to music or a thrown ball.”

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This interplay of music and psychology is a theme in many of his works but particularly in his book Musicophilia, where he investigates the restorative power of music both on typical individuals and those suffering from severe neurological problems. He is an amateur classical pianist and as a child he described his two favourite things as “smoked salmon and Bach”, so naturally has a general interest in both the clinical and the more spiritual aspects of music. As an art form involving multiple areas of the brain, he finds music more psychologically robust than simply speaking, finding that it brings to life many sufferers of Parkinson’s disease who have largely lost the ability to react to other things. Not that music is universally enjoyed; amusica sufferers are unable to distinguish between music and noise yet live an otherwise normal life, which prevents Sacks from overemphasising music’s importance. Nonetheless, for him “music communicates being alive”.

This idea of music as a form of therapy is also the basis for one of his more recent television series, Musical Minds. The idea is surprisingly controversial.

While undoubtedly a fun experience, studies suggest that music has only short-term beneficial effects and although Sacks mentions a few exceptions, people may question what makes it a ‘therapy’ rather than ‘a relaxing or stimulating hobby’. Criticism of the TV series from disabled rights activists is also harder to shake off. The use of physical images of parkinsonian patients listening to music prevents anonymity. Sack’s general style of discussing persons as a whole, of sharing odd quirks and personality traits unrelated to their syndrome, also seems to have been reduced in the television series. It can be understood why this and other television series have not met with the same roaring approval as the books.

Features

As an individual, Sacks has plenty of quirks of his own. He usually eats canned fish for lunch and supper, and as a self-confessed compulsive eater does not keep too much of it in the house. He eats standing up, sometimes reading a book while he does so—the old Oxonian’s love of literature is clear in his works. As with his approach to patients, he has a fairly holistic approach to knowledge, and is as happy exploring the philosophical implications of a woman unable to feel her body as the physical. We normally sense the body directly through proprioception, which allows us to know that our hands are where we put them. This is part of an attack on scepticism championed by G. E. Moore and Wittgenstein, yet here is a woman who doesn’t know where her hands are unless she can see them!

Yet sometimes this holistic approach is to his detriment. A compassionate, individualised response to patients is necessarily opposed to the doubleblinded try-it-and-see approach that progress in medicine arises from. While we all want a doctor who does the former, we also want doctors to base their treatments on large, formal studies rather than case studies, and there are times when his erudition spills into the realm of pseudoscience. He refers to Freud in his works more often than to actual scientists and has had twice-weekly sessions with his psychoanalyst for over four decades. However, this does not diminish what he has achieved: a lifetime of bringing to the general public an awareness of the many curious features of the mind, how it can malfunction and how people can continue to function regardless.

Hippiedude

The interplay between music and psychology is a theme in many of Sacks’ works

Robin Lamboll is a 4th year undergraduate at the Department of Physics

References:

Have You Heard the Northern Lights?

Macdonald, J. (1998). The Arctic Sky: Inuit Astronomy, Star Lore, and Legend. Toronto: Royal Ontario Museum The Myriad Genes http://blogs.nature.com/news/2012/11/us-supreme-court-to-decide-on-gene-patents-in-myriad-case.html Open to Everyone - http://en.wikibooks.org/wiki/Open_Source Commemorating a Commission - http://www.centenary.mrc.ac.uk/ Cracking Codes - Singh, S. (2000). The Science of Secrecy. London: Greener Books

Regulars

Waste of Research - http://www.admin.cam.ac.uk/offices/em/sustainability/environment/guidance/waste.html#heading1 Making New Scientists - http://www.cambridgesciencecentre.org/ Altitude Science - http://www.xtreme-everest.co.uk The War Against Infection Florey, H.W. (1945). Use of Micro-organisms for Therapeutic Purposes. British Medical Journal, vol. 2, no. 4427, pp. 635–642 The Notoriety of Oliver Sacks http://www.telegraph.co.uk/culture/9661347/Oliver-Sacks-most-mind-bending-experiment.html On a Scientific Note - http://easternblot.net/category/musicians-and-scientists/ Easter 2013

Behind the Science 29

On a Scientific Note

Albert Einstein was not only a scientific superstar but also a talented musician

In their video for “House of Cards”, Radiohead used 3D plotting techniques

30 Art and Science

at first glance, science and music seem to have little in common with one another. Scientific research is rational, detail-oriented and protocoldriven, the complete opposite of highly imaginative abstract musical creations. However, by examining these two disciplines more carefully, similarities start to emerge. There are two elementary components in music, composition and performance—the first is highly creative, while the latter requires accuracy.

For instance, a musical composer must be both imaginative and precise when writing a score. In doing research, scientists must also be creative to design novel experiments or techniques but also accurate when generating and analysing their data.

Interestingly, some of the most distinguished musicians possess strong scientific backgrounds, suggesting an overlap in the skills required to succeed in music or science. Brian May, the guitarist of Queen, completed his PhD in astrophysics on light reflecting from interplanetary dust. Meanwhile, Brian Cox is probably the only pop star to become a celebrity later on for his scientific contribution. Prior to gazing at the stars and working on theoretical physics, the University of Manchester Professor was a keyboardist for the group D:Ream and even entered the UK charts with the song “Things Can Only Get Better”. Other examples include Ladytron vocalist/geneticist Dr Mira Aroyo and Dexter Holland, who gave up his PhD studies in molecular biology to focus on The Offspring.

If you think the latter is pretty cool for a punk rock front man, you should also consider Bad Religion lead singer Dr Greg Graffin, who currently teaches life sciences and palaeontology at the University of California, Los Angeles.

Of course, artists do not need a PhD in order to embrace science. For many, technological advances have served as a source of lyrical inspiration that deals with the loss of humanity in an increasingly machine-dominated world. Others utilise scientific achievements to create original presentations. For example, in their video for “House of Cards”, Radiohead used 3D plotting techniques to visualise information about shapes and the relative distances of objects instead of traditional cameras. This artistic fascination with science should not come as a surprise. Undoubtedly, a memorable musical performance is characterised by emotional drive and passion. However, underneath the aesthetic appeal of melancholic melodies or uplifting rhythms, there is a

clearly defined structure and methodology. Classical concertos typically consist of three movements, with a fast-slow-fast scheme, while pop songs have an introduction, verses and a chorus. In all performances, pitch, duration, tempo, and dynamics are accurately encoded through musical notation symbols and when musical arrangement deviates from standard models it is referred to as ‘experimental’, drawing parallels with the robust experimental work undertaken by scientists to explore innovative ideas. Beyond the artists, the modern music industry relies heavily on the use of technology, from sound engineering to optimising concert hall acoustics and creating visual projections to accompany live performances.

But is the reverse also true, do scientists significantly indulge in music? Some of the most admired human minds in history have expressed a clear enthrallment with music, and in some cases this has been paramount for important inventions. Walther Nernst, who received the Chemistry Nobel Prize for devising the third law of thermodynamics, was the first to fashion electronically amplified instruments. John Pierce combined his engineering and musical abilities to construct the first computers capable of making music.

In addition, the study of electron harmonics by Louis de Broglie and others was the foundation for the development of magnetic resonance imaging.

However, perhaps the most illustrative example is none other than Albert Einstein, a keen violist and pianist, who argued that “imagination is more important than knowledge”. In Einstein’s view, musical engagement functions as an essential recreational process that allows scientific innovation.

He believed that all scientific breakthroughs are the

j4mie

E. O. Hoppe

Christoforos Tsantoulas explores the relationship between music and science

Easter 2013

Easter 2013

micropix

simply different manifestations of an idea and how the combination of the two allows substantial progress to be made. Similar approaches have led to arrangements describing the behaviour of the Higgs boson, as well as star data collected by NASA’s Kepler telescope (the latter being a reggae tune).

It is evident that music and science foster one another, so naturally, a number of educational initiatives have embraced this interconnection. In 2009, John Boswell launched the ambitious Symphony of Science project, designed to deliver scientific knowledge to the public in musical form, while NASA organises numerous events as part of their Music and Astronomy Under The Stars program. Teachers increasingly incorporate music into their tutoring methods and many institutions now offer specialised or conjunctional courses, such as the Physics and Musical Performance degree at the Royal College of Music.

Finally, the internet thrives with inspired scientific song collections (including “Pi”, “Elements”, “GTCA” and “The Sun is a Mass of Incandescent Gas”), which entertain but also assist learning. Hopefully, such developments will further promote the synergy between music and science, an interaction that has proved beautiful and valuable throughout history and will undoubtedly continue to do so.

Christoforos Tsantoulas is a postdoctoral researcher at the Department of Pharmacology Oosoom

result of intuition and inspiration, rather than logic or mathematics. He was so certain of the creative value of musical engagement, that he explicitly stated it was the driving force behind conceiving his theory of relativity. Another Nobel Prize winner, Max Planck, was also musically gifted, playing the piano, organ and cello and even composing operas. It was the realisation that electrons, like musical strings, have harmonic frequencies due to their perinuclear vibration, that led to Planck’s quanta theory of electromagnetic radiation.

Planck and Einstein collaborated closely on physics puzzles and indeed often played music together at Planck’s house.

Scientific research can be intense and somewhat isolating, so musically-mediated relaxation can provide a less demanding, creative outlet. Moreover, scientific innovation seems to be correlated with creative activities outside science. The physiologist Root-Bernstein has shown that scientists are more inclined than the general public to play a musical instrument and that scientists engaging in the arts are more likely to be Nobel laureates. He suggested that successful scientists are highly versatile and able to apply their talents across a range of disciplines. In this way, a plethora of musical skills can be fruitfully integrated in science. Such abilities may range from enhanced hand-eye coordination, pattern recognition, analogising, visual imagination and aesthetic sensibility to improved analytical, communication and team-working skills. Consistent with this, studies have demonstrated that students who regularly listen to Mozart or play instruments score higher on visual problem-solving tasks.

In more recent times, the combined efforts of musicians and scientists have produced some interesting and amusing results. In 2011, the British Academy of Sound Therapy and the band Marconi Union created “Weightless”, a euphoric composition of carefully arranged harmonies, low ambient tones and trance-inducing patterns that is allegedly the most relaxing song ever. It is thought to be so effective at inducing sleep that it is recommended that the song should not be listened to whilst driving. In another inspired application, biologists studying the life cycle of algae species from the English Channel used music as an alternative way of representing their large datasets.

To their amazement, when the researchers converted measurements of interest into musical notes, they were presented with what sounded suspiciously like songs.

For instance, in the resulting melody “Bloom”, low or high notes correspond to decreased or increased microbial abundances, while chord progression was derived from day length and chlorophyll concentration in the water. Importantly, this type of analysis helped researchers identify previously intangible connections between studied parameters. Such examples demonstrate how science and music are

Life cycle data, obtained from algae, were transformed into musical notes to create the song “Bloom”

Concert hall science: Symphony Hall in Birmingham contains an adjustable canopy and a special reverberation chamber to improve the acoustics

Weird and Wonderful A selection of the wackiest research in the world of science Catch That Thought mind reading has just become easier—at least where fish are concerned. In January this year, Akira Muto and colleagues published techniques for visualising neuronal impulses in the brains of zebrafish larvae, which effectively allowed them to track the fishes’ ‘thoughts’ in real time. To do this, they first developed a fluorescent probe sensitive enough to detect the activity of single neurons.

They then engineered zebrafish that produce this probe in the visual processing area of their brains.

Finally, they presented the fish with a free-swimming Paramecium, a tasty morsel by zebrafish standards, and watched the fluorescent signal dart through the fishes’ brains as they stalked their lunch. Zebrafish larvae are transparent, so the signal was easily visible; indeed, the Paramecium’s path precisely mirrored the pattern of neurons lighting up. One application of this novel technology is the high-resolution mapping of functional neuronal circuits. Since zebrafish and mammalian brains share the same basic organisation, these methods could also be used to screen new psychiatric medications: just add drugs to the fishes’ water and watch the resulting light show. Food for thought indeed. jt

Could We Get Another Report, Please? the united states Secretary of Defence recently

gave a speech outlining plans to reduce expenditure by cutting down on the number of costly reports undertaken by the Department of Defence (DOD).

In response, the DOD prepared a report to provide guidelines for estimating the costs required for reports to be prepared. Naturally, this report about DOD reports had to be evaluated by the Government Accountability Office (GAO), for which they prepared a report entitled “Defense Management: Actions Needed to Evaluate the Impact of Efforts to Estimate Costs of Reports and Studies”.

32 Weird and Wonderful

In their report, they praised the DOD for its report about reports, but recommended a few changes. In particular, the GAO reported that the DOD should evaluate and report on the effectiveness of its report about reports. In the long run, it is hoped that the GAO’s recommendation in its report about a report about reports for a report about the report about reports will cut down on the number of reports.

For their efforts, the GAO won the 2012 Ig Nobel Literature Prize (http://www.improbable.com/ig/), but sadly did not show up to receive their award. jr

Practising Alchemy Before It Was Cool

for humans, alchemy might be a lost art; but in some bacteria, making solid gold from the mundane is simply part of their survival plan. Like many heavy metals, dissolved gold is toxic to life. The bacteria Cupriavidus metallidurans have been shown to swallow up dissolved gold from the environment.

They then turn it into solid gold nanoparticles, which are non-toxic and can be stored inside the cells.

Recently, a team from McMaster University found that Delftia acidovorans, a bacterium often found alongside C. metallidurans, takes a different approach.

Instead of uptaking gold, it produces a novel protein called delftibactin to do the ‘dirty work’. Delftibactin, the alchemist’s secret weapon, turns dissolved gold into solid particles. Thus, toxic gold can no longer enter the bacterial cell and harm the alchemist itself. Last year Adam Brown, Associate Professor from Michigan State University, created the awardwinning artwork The Great Work of the Metal Lover, bringing modern microbiological gold-digging to the historical context of ancient alchemy. While we may not see bacteria-run alchemical factories in the near future, researchers suggest delftibactin may be used to accelerate industrial chemical reactions or treat waste waters from mines. tw

Illustrations by www.alexhahnillustrator.com

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