BlueSci Issue 32 - Lent 2015

Lent 2015 Issue 32 www.bluesci.org

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Endosymbiosis: life inside life

Japanese temple geometry . Breathing liquids Psychology of torture . Bananas

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Lent 2015 Issue 32

Contents Features 6

Regulars

Fat-Fighting Fat Vivian Peirce explores fats that can make us fitter

8

Thinking Big

History

Robin Lamboll looks at how size and setting affect how organisms move 10

Do Animals Get Lost?

Ornela De Gasperin explains how animals orient themselves

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The Thermodynamics of Evolution

Sebastian Mizera searches for a physical understanding of life 14

A Real Prisoner’s Dilemma Shiran Ashraf explores the links between human behaviour and mathematics

16

On The Cover News Reviews

FOCUS

3 4 5 22

Thomas Hitchcock goes bananas about bananas

Science and Art

24 24

Tariq Desai explores the history of geometrical offerings in Japan

Science and Policy Sarah Binney explores the different approaches to science education around the world

Initiatives Daisy Hessenberger asks for evidence, and challenges you to do the same

Perspective

26 26

28

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Bill Baloonarm investigates the psychology of torture and interrogation

Life Inside Life BlueSci investigates how multicellular life depends on layers of smaller lifeforms living inside each other.

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.

Weird and Wonderful

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Contents

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Issue 32: Lent 2015 Editor: Aneesh Aggarwal Managing Editor: Zaria Gorvett Second Editors: Robin Lamboll, Nathan Smith, Aneesh Aggarwal, Zaria Gorvett Copy Editors: Nathan Smith, Robin Lamboll, Aneesh Aggarwal, Zaria Gorvett News Editor: Joanna-Marie Howes News Team: Verena Brucklacher-Waldert, Amelia Thompson, Caroline Steel.

Reviews: Zaria Gorvett, Jackie Carozza, Jason Kwong Focus Team: Zaria Gorvett, Robin Lamboll, Nathan Smith, Aneesh Aggarwal, Ornela De Gasperin Quintero Weird and Wonderful: Aneesh Aggarwal, Nathan Smith, Jenni Westoby Production Team: Robin Lamboll, Nathan Smith, Aneesh Aggarwal, Zaria Gorvett Illustrators: Sue Smith, Aneesh Aggarwal, Rowena Hill, Sarah Binney Cover Image: Sarah Luke

ISSN 1748-6920

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.

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Editorial

Better Together have you ever questioned your complexity? The tasks of bridging the gaps from eukaryotic to prokaryotic and microscopic to macroscopic are some of nature’s greatest challenges. In our Focus article, we explore some of the key evolutionary steps which have enabled such progression. The viruses and unicellular parasites which we regularly stigmatise have, in a succession of hijackings deep in our evolutionary history, invaded our bodies to the point of indispensability. They have been crucial to the development of multicellular life as we know it. Learning about how they transformed our cells and genomes was fascinating for us, and we hope that we have captured this excitement for our readers.

With a strong “international trend” in many articles, global ideas and thought processes are summed to convey the direction in which specific fields may be heading. Education in science is core to the progression and sustainability of the field; in our science and policy article, the importance of grouping opinions from countries with a variety of tried and tested approaches is shown. The study of game theory can provide a preliminary basis on which ethical and logical decisions can be made in real life scenarios, with analyses situations based on traditions and concepts in a range of countries providing original research and data.

With an abundance of talented writers pursuing a range of disciplines, this issue BlueSci has seen the diversity in the articles flourish. From bananas, to breathable liquids, to Japanese temple geometry, this issue we provide insight into the exciting – and sometimes quirky – depths of science. 2014 has seen the Rosetta spacecraft’s probe complete the first ever touch-down on a comet, the chaos of Ebola, and the discovery of Dreadnoughtous, the largest land dinosaur known. It has certainly been an eventful year and we hope that the discoveries in 2015 will follow suit.

It has been a real pleasure working on BlueSci alongside a fantastic team of editors and writers. We warmly welcome and actively encourage students interested in any aspect of writing, editing or publishing to get involved.

Aneesh Aggarwal Issue 32 Editor

Lent 2015

On the Cover Max Gray discusses the implications of our global lust for palm oil

Lent 2015

Malaysia has been researching how biodiversity might be improved within oil palm plantations, by keeping forest fragments intact within the agricultural landscapes, or by maintaining the borders between forests and the edges of rivers.

Not only do these measures increase biodiversity, they also improve water quality, and maintain the services provided by a healthier, more diverse ecological community. These ecosystem services can then limit the need to use of potentially expensive and environmentally damaging fertilisers and pesticides. As a result not only can we feel better as environmentalists – but the plantations also benefit by reducing their costs.

Sustainable palm oil is not yet the norm, and greater market pressures will be necessary to strengthen these practices. This is where you, sat there reading this, come in. When you next go to buy biscuits or shampoo (or anything else come to think of it) take a couple of seconds to read the label. Unspecified ‘vegetable oil’ is almost always palm oil, and if you don’t see the word ‘sustainable’, it’s probably not. Take the time to find an alternative that is – and then go about the day feeling good about yourself for doing a little bit to make the world a better place.

marco schmidt

There are six million hectares of oil palm plantations in Indonesia

an ironwood tree lies felled amongst the crop that has been planted to replace it, and the rainforest it once stood in. The fact that this one lies unused and wasted only adds to the tragedy of the deforestation story it tells. The image (the cover photo of this issue, taken by PhD student Sarah Luke) is a poignant reminder of the problems associated with palm oil.

For readers unfamiliar with palm oils, these are vegetable oils derived from the kernel of the oil palm tree. They are present in over 50% of everything we consume – from nearly every type of foodstuff to cosmetics, household products and fuel.

The deforestation of tropical rainforests to convert that land into oil palm plantations is an all too common story. In Southeast Asia, oil-palm plantations are ever expanding. Unsurprisingly, this has engendered environmental havoc. Deforestation has a crippling effect on biodiversity and leads to vastly elevated carbon emissions, as whatever remains after trees have been logged is typically burnt. To add insult to injury, the bare soil is quickly degraded. For the environment, palm oil is unequivocally bad news. Sarah’s photograph captures this sad story beautifully.

But is this an avoidable problem? There are significant humanitarian benefits to oil palm development. As an industry it is a major contributor to the development of Southeast Asian nations. The livelihoods of millions of families rely on this crop. It would be callous in the extreme to shut down oil palm plantations without taking into account these people’s lives.

So is there a solution, one that limits the negative environmental impacts of oil palm, while allowing the developing nations that rely on these plantation to continue to develop? As it turns out, the answer may be ‘yes’. That is according to the Round Table on Sustainable Palm Oil (RSPO), who promote the use of sustainable palm oil products with their mark of sustainability and ethical approval. They hope to encourage responsible growing through responsible shopping, using their stamp to inform consumers of the environmental and social practices of the supplier.

Alongside international efforts like the RSPO, researchers like Sarah are investigating how oil palm plantations might better limit their impact on the biodiversity losses associated with converting land into monocultures of oil palm. The Stability of Altered Forest Ecosystems (SAFE) project in

Max Gary is a PhD student in the Department of Zoology.

The image by Sarah Luke was submitted for the 2014 Graduate School of Life Sciences’ Poster and Image competition.The competition was sponsored by Linguamatics and Science Magazine.

On the Cover

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patrick nouhallier

News

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

Holes in the Brain

Looking for Water on the Red Planet?

what happens when a large part of the brain is missing? The surprising answer can be, ‘Not that much’.

In August 2014, neurologists Feng Yu and colleagues published a case study in the journal Brain. Their 24-year-old patient had been admitted to hospital in Shandong Province for severe nausea. She also had life-long problems walking. A battery of scans revealed that she had cerebellar agenesis – an entire brain region, the cerebellum, had failed to form during brain development and was missing.

Cerebellar agenesis is an extremely rare condition. Few cases have been reported, and fewer are diagnosed while the patients were still living; most are found at postmortem. This is unsurprising given that the cerebellum – despite its small volume – contains nearly half the nerve cells in the brain.

The symptoms of Feng Yu’s patient were comparatively mild. Her speech and walking difficulties were in keeping with the cerebellum’s known functions in controlling voluntary movement. Otherwise, though, daily life was normal: she was able to live independently and was married with a daughter.

However, the picture is vastly different for those who damage their cerebellums in adult life, who suffer from motor and cognitive impairment and epilepsy. The case provides further evidence of the developing brain’s resilience – and suggests that the ‘normal’ population does not use its 85 billion cerebellar neurons effectively enough! at

Try Washington First katie wall, a 21-year old undergraduate student, has been looking for evidence of water on Mars – in Washington. Her work has roots in the influence of water on crystal formation in basalt. The dark volcanic rock, which is visible to the rover Curiosity, is also found widely in Washington and Oregon, and Wall has been comparing the two.

Firstly, Wall and colleagues at the University of Washington came up with a method to quantify the texture of volcanic rock using an index called ‘groundmass crystallinity’. According to Wall, the texture of volcanic rock is like the texture of a chocolate chip cookie- with the rock the dough and crystals the chips – it varies according to method of cooking and cooling. “We were interested in the cookie dough part of the cookie,” she said.

When liquid volcanic rock hits water it rapidly cools and flash freezes to form glass. In the absence of water it takes longer to cool and crystals form. Wall analysed basalt samples from across the globe using X-ray diffraction imaging and compared them to the volcanic rock analysed by the Curiosity rover on mars.

The rocks analysed by Curiosity were similar in structure the volcanic rocks on earth that had not formed in the presence of water. This indicated that there was no water on Mars at the time of formation of any of the analysed rocks. However, only two sites were sampled and Wall intends to use the same method to look for water elsewhere. cs

Flu: how Viral Infection Causes Intestinal Disease often suffer from vomiting and diarrhoea during a bout of the flu? Is a question which is unlikely to be keeping you awake at night, but has been puzzling scientists for decades. The influenza virus infects the respiratory tract, yet vomiting and diarrhoea are symptoms of gastrointestinal disease.

Now researchers at the University of Science and Technology of China have found a mechanism by which they are connected.

Using a mouse model of influenza infection, Dr Jian Wang and colleagues found that lymphocyte immune cells, which usually reside in the lining (mucosa) of the respiratory tract, migrate specifically to the intestinal mucosa during influenza infection.

There they secrete inflammatory molecules which

marc van norden

why do people

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News

alter the composition of the microbial community and damage the intestine, eventually resulting in the gastrointestinal symptoms.

But why do lymphocytes migrate from the lungs to the gut during at all? According to the authors, this process could be a mechanism for dealing with an overwhelming immune response. It is a trade-off: diverting the cells from the lung into the intestine is possibly less dangerous than allowing lung tissue to be damaged by a strong immune response.

These findings support the concept of a ‘common mucosal immune system’; immune cells and structures contained in mucosal tissues are universally connected within the body and should therefore be considered as one large but distributed ‘organ’. jh Lent 2015

Reviews Guns, Germs, and Steel - Jared Diamond

Microbe world

forget self-help, spiritualism, or philosophy – if you are looking for a book that will

W. W. Norton & Company, 1997

change the way you view the world – this is for you. In the 425 pages of this ambitious work, Diamond charts the entire history of the human species. His mission? To answer a question posed by Yali, a Papua New Guinean politician: “Why is it that you white people developed so much cargo and brought it to New Guinea, but we black people had little cargo of our own?”

The reader is invited to peer through the lens of an anthropologist and view the development of civilisation as we know it, from prehistoric times to the modern industrial age. But this is human history without the human. In Diamond’s version of events, conquest, colonialism and European hegemony have been shaped by geography, not ingenuity; climate, resources, and rivers have determined the fates of human societies.

Diamond leads a voyage across every continent, systematically tracing key developments in human civilisation- from the invention of farming, to writing, to guns – and the environmental features which enabled them. Here is a masterwork in scientific inquiry, with the power to violently shift your perspective on the world as we know it. zg

How I Killed Pluto and Why It Had It Coming - Mike Brown the international astronomical Union’s 2005 decision to oust Pluto and the newly

Spiegel & Grau, 2010

discovered Eris from the ranks of planethood was met with controversy from scientists and the public alike. In How I Killed Pluto and Why It Had It Coming, astronomer and discoverer of Eris Mike Brown narrates his side of the story, starting from the crux of the confusion – what does it mean to be a planet? Keeping in mind the term’s nebulous definition, Brown dives into the story of his work leading up to the discovery of multiple Pluto-like objects in the far-flung Kuiper belt, cheerfully recounting sleepless nights at the telescope, the oddities of astronomical naming, and confessing to plotting his newborn daughter Lilah’s feeding schedule to look for patterns. A well-spoken perspective of a dedicated husband, father, and self-proclaimed Pluto-killer in the niche between scientific research and public perception, How I Killed Pluto is a healthy reminder that human definitions are not infallible, and we’re not finished learning about our own patch of the universe. Brown captivates with his commitment to unearthing scientific truth, and his readers can’t help but agree that Pluto was doomed from the start. jc

The Simpsons and Their Mathematical Secrets - Simon Singh many scientists would agree mathematics is fundamental to uncovering the secrets

Bloomsbury Publishing, 2013

Lent 2015

of nature. What might be surprising is that it also forms the beating intellectual heart of popular TV show The Simpsons. In his most recent work, Simon Singh, a particle physicistcum-science populariser, reveals the mathematical backgrounds of many of its writers.

These include Al Jean and Ken Keeler, who have mathematics degrees from Harvard. A former writer, Ken Keeler, has a doctorate in applied mathematics from Harvard. He reveals how episodes contain mathematics in the form of subtle allusions, freeze-frame gags and occasionally plotlines. These tidbits allow Singh to launch into a number of of mathematical discussions. For instance, during a 1998 episode in which Homer becomes an inventor, a blackboard of equations is displayed. The first line is an early prediction of the mass of the Higgs-Boson, t. The second is an apparent counter-example to Fermat’s Last Theorem.

Singh explains topics from topology to Hilbert’s hotel problem in accessible terms that still convey the elegance of the mathematics. However, the most interesting parts of the book are Singh’s attempts to explain why this combination of mathematical minds managed to write one of the defining television shows of the 90s and 00s. In addition to this fascinating story, the book would have benefited from a deeper investigation into the link between mathematical aptitude and comic ability. jk Reviews

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Fat-Fighting Fat Sarah Binney

Vivian Peirce answers the question: are all types of fat bad for us? adipose tissue, more commonly known as fat,

may be the least aesthetically desirable of all our body parts. Nevertheless, it plays many key roles, from simple insulation to complex communication with other parts of the body, via the release of chemical messengers to regulate metabolism and appetite.

Adipose tissue’s best-known function is to store extra calories that we eat but don’t immediately use, so that they can be used in future situations of food shortage. The cells that make up adipose tissue, called adipocytes, store these extra calories as fat.

This role in modern western society is essentially redundant. Given the abundance of calorie-rich food that most of us enjoy, the fact that adipose tissue stores surplus calories has turned from a survival advantage to a potential health risk. In situations of chronic calorie overconsumption, adipose tissue first expands to accommodate those extra calories. Existing adipocytes grow larger as they accumulate more fat, and additional adipocytes are made. Unfortunately, at a certain point adipose tissue becomes “full,” and fat accumulates elsewhere in the body. The consequences can accelerate the development of other diseases. For example, fat accumulation in arteries can contribute to heart disease. Additionally, the adipose tissue of obese

public

Western diets tend to have large amounts of calorie rich food

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Fat-Fighting Fat

individuals secretes chemical messengers that promote inflammation and insulin resistance, which can result in type 2 diabetes.

Unlike conventional epidemics, obesity cannot be fought with quarantine, antibiotics, or vaccinations. A simple rule of thermodynamics controls body weight: energy is neither created nor destroyed. You gain weight when you eat more calories than you need; you lose weight when you use more calories than you eat, so your body must use calories stored in adipose tissue. Therefore an obese individual can only lose weight by reducing their food intake or increasing their energy usage. Diet and exercise: it really is that simple. However, to accelerate weight loss, scientists and doctors are creatively enhancing the effectiveness of these tried and true approaches, whilst still obeying the laws of nature.

Exercising to lose weight takes time and will-power.

Though resisting the increase in appetite associated with increased energy usage is a major challenge, for some obese patients their weight is a physical impediment to meaningful exercise. Unfortunately, it is impossible to burn extra calories without doing more exercise – right? Maybe not. In 2009 a potential weight-loss cheat was discovered. In the same issue of the New England Journal of Medicine, three research groups published evidence of brown adipose tissue in healthy adult humans1–3. In contrast to the previously discussed white adipose tissue (WAT), brown adipose tissue (BAT) accumulates fat not for storage, but instead for heat production, known as thermogenesis. Brown adipocytes uniquely express a protein called uncoupling protein 1 (UCP1), which turns their mitochondria from cellular energy converters to heat generators. Therefore BAT is “fat-fighting” fat – a type of adipose tissue with an innate ability to burn off calories.

Why would an organism need such a tissue? Well, a mammal’s core body temperature is almost always higher than the environmental temperature, so heat Lent 2015

Long-term cold exposure increases BAT mass in rodents and humans

vincent van zeijst

loss from the body to the environment is inevitable.

To maintain the correct core body temperature, the body needs to insulate itself to slow heat loss, and to create more heat to replace that which is lost. Rodents depend on BAT thermogenesis to create this heat, and they are useful experimental models to investigate BAT physiology. In rodents, the brain controls BAT thermogenesis via the sympathetic nervous system.

To switch on BAT thermogenesis, sympathetic nerve endings in BAT release norepinephrine, which binds to receptors on brown adipocytes. This initiates a domino effect of intracellular signals that activates heat production. Sustained activation of BAT by the sympathetic nervous system also increases the mass of the tissue, increasing its capacity for heat production.

Indeed, compared to mice living at warmer temperatures (30oC), mice living at colder temperatures (20oC) have to eat up to 60% more calories to maintain their body weight. This is because their enlarged BAT is working furiously to create heat, using up huge amounts of energy. At most BAT represents 1% of a rodent’s body weight, so its energy burning potential per gram is huge---higher than any other organ or tissue. Norepinephrine-mimicking drugs can be used experimentally to increase BAT thermogenesis, and interestingly such treatments trigger weight-loss in obese rodents.

Like rodents, human infants also depend BAT thermogenesis to defend their core body temperature.

However, until recently it was believed that in the progression from childhood to adulthood, infant human BAT loses its thermogenic character, becoming more similar to WAT. The recent proof that BAT persists in adult humans may be a game-changer in obesity research. If BAT can be exploited to cause weight-loss in obese rodents, could we apply this approach to human obesity? At room temperature, evidence shows that adult human BAT is usually inactive, and therefore not burning off energy.

Promisingly, though, BAT can be “switched on” in most healthy adults by decreasing the room temperature to 16-18oC, indicating that it is coldresponsive like in rodents. However, opinion is currently divided as to whether activated BAT could increase whole-body energy usage enough to tip the

scales towards weight-loss. Estimates of BAT mass in healthy humans fall range from 50g to 80g, a mere 0.1% or less of the body weight of a 75 kg adult. This may not be enough to make an impact. Worse, largescale analyses of BAT mass and activity in the general population suggest that BAT mass decreases with increasing BMI, and that the BAT of obese patients may be less responsive to cold activation.

Nevertheless, researchers are not discouraged by these trends. Long-term cold exposure increases BAT mass in rodents, and the same may be true for humans.

A study in 2013 demonstrated that 10 days of cold exposure (15-16oC for 6 hours daily) increased BAT mass in healthy volunteers by 37%4. Applying this approach to obese patients could increase the amount of BAT they have, theoretically increasing the amount of energy the tissue would use upon activation.

Alternatively, some of an obese patient’s existing excess WAT could be turned into fat-burning BAT. In mice that live for long periods in cold temperatures, adipocytes that express UCP1 appear in WAT, referred to as “browning” of WAT. Encouragingly, a recent study documented increased levels of UCP1 in WAT of healthy adults after cold exposure, suggesting that WAT “browning” occurs in humans too5. Like BAT, “browned” WAT may also be able to use energy to generate heat. Therefore strategies to “brown” the WAT of obese patients may increase their capacity to burn off calories as heat. Importantly, the impact of approaches to increase the amount of BAT or “brown” WAT that a person has depends on the ability to activate the tissue, so that it produces heat and therefore uses energy. So far, we lack a reliable pharmacological agent that can do this; cold-exposure is the only reliable method known to increase human BAT activity.

Though there is still much progress to be made before we can use BAT to help obese patients lose weight, BAT’s future as a tool to curb the obesity epidemic looks promising. As the saying goes, “fight fire with fire”; in this case, we may be able to fight fat with fat.

BAT is, at most, 1% of a rodent’s body weight

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Vivian Peirce is a PhD student in the Institute of Metabolic Science

Lent 2015

Fat-Fighting Fat

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Sarah Binney

Thinking Big Robin Lamboll looks at how size and setting affects how organisms move “physicists have unbreakable laws;

engineers have guidelines; biologists do what they want.” Two particularly disparate fields are physiology and human mechanics. But are there laws of motion which apply to both? Clearly these laws can’t be absolute – animals and machines have varying priorities and amounts of energy they can spend. But behind the individual variation, we can find general relationships which hold for creatures and creations over a remarkable range of sizes.

For instance, we tend to assume that larger creatures tend to move more slowly, yet the opposite trend is actually true. Smaller animals may be able to accelerate faster, but larger creatures tend to sustain higher speeds in the long run. The reasoning behind this involves noticing a subtlety of how animals move: the bounce in our step. When running or walking, there’s a point in our gait where we can feel our body falling, a point almost impossible to freeze at. Then the foot comes down, and pushes us up again slightly. This rise and fall pushes the body up so that the legs can move. It is not only found in creatures with two legs, but also in those with four or even more.

Energy is needed to lift the body up, but converted into kinetic energy when the body comes down.

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When running or walking the human gait reaches a “tumble” point

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Thinking Big

Nature has evolved a variety of ways of recycling that energy, including storing some of it in springy tendons or raising and lowering a tail, but inevitably much is lost. This is part of the reason why it is easy to keep up with runners when on a bike. The wheels keep your centre of gravity level so that most of the legwork goes into making you go forwards. With running, you also have to move your legs over much larger distances to apply the same force to the ground.

But why do you need energy to keep going forwards, even on a bike? Simple – to get air out of your way.

The energy wasted by air resistance is proportional to the area of a creature multipled by its velocity squared, whereas we need a much more complicated expression for the energy lost to maintaining up-and-down motion which favours faster forwards movement. Minimising the total energy lost per distance travelled gives a relationship between the velocity and the mass of the animal – quite a modest one overall, with velocity proportional to the sixth root of the total mass. This means that a creature twice your size will typically move 12% faster than you, though this is when they are trying to move efficiently, not when they’re chasing food!

The beauty of this argument is that it does not just apply to creatures running; flying creatures also fight air resistance and gravitational losses. It’s more difficult for them to recover the energy they lose as they fall, but otherwise the equations are exceedingly similar. You can see on the graph, from the research of Professor Bejan, in Duke University, that flying creatures (red symbols) tend to lie just above the theoretical prediction, whereas land animals tend to lie just below.

What’s even more astonishing is that with just a slight modification it also applies to swimming animals. The drag force on them is larger because they move through a denser fluid but still has the same general dependence on the swimmer’s speed and size unless the swimmer is very small and slow. But why is there a gravity force? While there are a few swimmers, Lent 2015

This graph shows the trends for organism velocities underwater and on land

JEB: Bejan, a and marden, j

vincent van zeijst public

like sharks, that require motion to stay afloat, most fish are about neutrally buoyant. This means that they don’t expend energy to stay level in the water, however it doesn’t mean they can move through water without fighting gravity.

Unlike air, water is pretty incompressible, so it needs room to maneuver around a swimmer. Near the surface this shuffling can be seen as a wave of raised water travelling above the swimmer. This wave is used in some advanced ways of looking for submarines, as it is pretty hard to prevent it when the submarine wants to stay near the surface. The waves continually dissipate, wasting energy. Swimming deeper reduces the height of the surface wave, but as sea water has different densities at different heights there are still drag forces from ‘internal waves’, where dense water rises and falls periodically. This results in gravitydependent drag even at depth, with a similar scaling factor. This means that swimmers also have the same general trend between mass and speed.

These relationships are referred to as ‘power laws’ because they state that speed is proportional to mass to a particular power, that speed = constant xnmass1/6. In this case, the constant multiple is assumed to absorb any other factors – how creatures actually go about moving, if they’re not really spherical as assumed in the fitted line and so on. Because we haven’t included these facts, we don’t get exactly the right answer, but we get the general trend.

The graph shows ‘logarithmic axes’, where moving one step along multiplies the value by a factor of 10.

This means that a small graph can clearly show a massive difference in size, from creatures weighing less

than a thousandth of a gram all the way up to things above a tonne. We can see this rule holds over about 11 factors of 10. This is about the ratio of the weight of one person to that of the entire human race.

Remarkably this law can be extended to cover nonanimals too. Airplanes must fight gravity and drag in exactly the same way as a bird, only many times heavier. Plotting them on a similar graph shows a line can be extended, still with power law 1/6, all the way from gnats to jets. However this line has been extending longer over time, as the largest possible airplane has been growing in size with every passing decade. Why? Another power law.

Larger machines can house larger engines, but an engine of twice the mass can provide more than double the thrust. This means that engines grow more slowly than the whole vehicle – over the history of the airplane, the trend has been proportional to mass x 0.8.

There’s also a second gain from a reduction in weight needed for fuel due to increasing efficiency - air resistance increases as the square of the size, not the cube. This means larger planes can carry more cargo more efficiently, and also further distances.

So why don’t birds become huge? Fortunately for humans, birds fly using muscles instead of jetpacks or turbines. These only exert a force proportional to their cross-section, scaling up as the square of the chosen length. If the creature stays in proportion (aerodynamically the best choice), the weight of its engine-equivalent increases with the cube of the chosen length. Having a higher optimal speed is no help if you can’t actually move that fast. The higher thrust to body weight ratio is another reason why small animals can often outrun larger ones over short distances.

These sorts of efficiency power laws lie at the heart of modern life; they are why transport has kept getting cheaper as we make larger ships and planes. They are also why we haven’t been eaten by flying dragons. Let’s all take a moment to appreciate that.

Water is much denser than air, so creatures move through it more slowly

Robin Lamboll is a PhD student studying the physics of solar cells.

Lent 2015

Thinking Big

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Sarah Binney

Do Animals Get Lost?

Ornela de Gasperin explains how organisms orientate themselves on a vast planet

Robins can ‘see’ magnetic fields, but only out of one eye

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Animal Navigation

home is no easy task. Humans started building maps over 10,000 years ago, and today’s technology has made it easier to find our way around, but how do other organisms manage without? Anyone who has found themselves in a foreign city without a map will understand the challenge. The remarkable abilities of animals to orient themselves have fascinated scientists and naturalists for centuries, from the tiny hummingbird which journeys 1500 miles from South to North America, to the monarch butterfly which covers 2000 miles as it flies from Canada to Mexico - without getting lost. How do animals navigate, how do they know where they are, and where they should go?

For centuries scientists have tried to find the answers to these questions. Perhaps unsurprisingly, different animals have different skills to navigate across the world. Some use environmental cues like smells, or landmarks like rivers and trees, others use the sun, the sky and the stars to find their ways, other communicate among groups to find their ways, and others use the Earth’s electromagnetic field to orient themselves.

Karl Ritter Von Frisch was an Austrian ethologist, or animal behaviour scientist, who was fascinated by how bees’ societies communicate and make collective decisions. Among other things, Karl Von Frisch showed how bees find their way in the world. He revealed that they have three orientating mechanism: the sun, the earth’s magnetic field, and the polarization pattern of the blue sky, with the sun being its preferred mechanisms, but using the other two under clouded days or inside their dark beehive. Furthermore, not only can bees find their way around, they can also tell their mates about what they have found. Bees forage for food like pollen and propolis, and when they find a good source of food they go back to their colony and tell their mates.

They do so by dances, a dance called the ‘waggle dance’. The dance consists on movements with their whole bodies which seems like the number eight, and that’s why it’s also called a figure-eight dance.

The dancing bee starts by moving forward on the vertically hanging honeycomb in the hive, and while they do this they ‘waggle’ their abdomen. She then returns to her starting point by doing a semi-circle, and starts again. The other bees gather information by being in close contact to their dancing friend.

The distance to the food is encoded by the speed of the dance, and the direction of her dance provides information of the location to the food. The angle between the straight line in her dance and the angle of the vertical honeycomb show the angle where the

Spinks

where is north, where is South? Finding our way

Lent 2015

in 1963 by Salvatore Bellini. While looking at some bacteria under the microscope, he realised a group of them oriented themselves in a peculiar way. He then grasped that they were aligned towards the north pole of the Earth, and therefore called them ‘magnetosensitive bacteria’. Further studies have shown that within their cells these bacteria have special structures with a high density of magnetite, the most magnetic of all minerals known on Earth. Thanks to this structures bacteria can orient themselves according to Earth’s magnetic field. Just as bacteria, some algae have also been shown to parallel to the magnetic field.

Perhaps more surprisingly is the fact that plants and fungi can also perceive and use the Earth’s magnetic field. Several studies have shown that many plant species use the magnetic field to orient their roots and to germinate according to the Earth’s magnetic field. Besides, plants that are grown deprived of a magnetic field generate abnormalities. Likewise, the magnetic field can stimulate or inhibit growth and reproduction in fungi. How does the Earth’s magnetic field affects these organisms is still a topic of debate, but it is likely that it affects them in an indirect way, for example, by altering the properties of solutes.

Magnetic fields can inhibit seedling germination

Flickr

direction of the flight towards the food is in position to the sun. This way, other bees in the nest can go and look for the food without getting lost.

Some nocturnal birds use the night sky to orient themselves. The Swedish scientist Ronald Lockley showed that some small birds oriented themselves with the night sky. In order to do this, he placed Warblers inside a planetarium, and saw that the birds used the sky to orient themselves towards the south. He slowly rotated the sky, and the birds kept their direction. Lockley’s findings have been groundbreaking. He not only showed that birds can read and remember patterns in the sky, but that they also have a ‘clock’ that allows them to use these patterns according to the time of the day.

One of the most astonishing ways in which animals orient themselves is by using the Earth’s magnetic field. The Earth’s magnetic field is thought to originate thanks to a process known as ‘dynamo’ in geophysics. The Earth’s core is divided in two: the inner solid core, and the outer liquid core. The outer liquid core is in motion as a result of Earth’s rotation movement, and by the heat flow generated by the inner solid core. The heat of the solid inner core of the earth puts the magma of the fluid core into motion, which creates circulating electrical currents.

The magnetic field is then produced as result of these moving electrical charges. At any given point, a magnetic field can be described by two factors: its direction and magnitude, or strength. The magnetic compass, the oldest instrument built for orientation during navigation, exploits these features of the Earth’s magnetic field. The Earth’s magnetic field causes any magnetised needle to align itself with the north-south axis of the magnetic field.

Just like compasses, many organisms use Earth’s magnetic field to orient themselves. Animals including birds, molluscs, sharks, turtles, fruit flies, and mammals have this ability. Surprisingly, a large number of bacteria orient themselves using Earth’s magnetic field too. These bacteria were first described

Whatever natures’ purposes of having compasses, we have also been able to take advantage of this talent for our benefit. Horses and camels have long been known take their riders back home, or in search of water in the desert. Homing pigeons have been used to deliver messages since the 1100s. During both world-wars, hundreds of pigeons carried messages around, and they were so efficient at doing this that the messages did not even need to be encoded. There was one little fellow, ‘Cher Ami’, who in the first world war was awarded the French Croix de guerre for delivering 12 messages despite being injured.

Although pigeons have been used by humans for centuries thanks to their ability to navigate using the Earth’s magnetic field, it still remains unclear how they actually detect it and use it.

Some bacteria contain magnetic particles, (large dots), or the genes to make them (small dots)

Pradel

Ornela De Gasperin is a PhD student in the Department of Zoology

Lent 2015

Animal Navigation

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The Thermodynamics of Evolution “what is life?” has been perplexing philosophers and biologists alike for centuries. In 1944, physicists got involved. Erwin Schrödinger’s influential treatise ”What is Life?” attempted to put the process of evolutionary adaptation on a firm mathematical footing. Fastforward to 2014 and a theory by Jeremy England, a biophysicist from the Massachusetts Institute of Technology, seems to pave a path on our way to understanding of the origins of life.

From the standpoint of fundamental physics, the definition of life proves to be somewhat troublesome: first of all, there’s no obvious way of defining processes like metabolism or reproduction, since all we can quantify are properties of particles and their interactions. Instead, we will treat a living organism as a thermodynamic system: a lump of matter that can exchange heat or work with its environment.

What constitutes a living organism is up to some human-defined taxonomy; England here quotes the 20th century philosopher, Ludwig Wittgenstein: “The borders of my language determine the borders of my world.” It may be more helpful then to look for more universal rules, which describe many systems with similar behaviour to life too.

Eggs smash if dropped but never spontaneously reform; hot things cool down but never the other way around. This is the essence of the second law of thermodynamics. Any system tends to its equilibrium state, that is a configuration where the energy is the most dispersed, simply because there are more ways to do so.

This is analogous to shuffling a deck of cards. Starting from a sorted set there’s a huge chance we’ll end up with a disordered configuration and hardly ever get any sort of pattern. The measure of this disorder is called the entropy, which by the second law, can never decrease.

It is useful to think about entropy as quantifying irreversibility. A biological example of this might be the question

A bacterium reproducing is much more likely than two bacteria combining.

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The Thermodynamics of Evolution

found in bacterial cell division. How likely is selfreplication to occur, compared to the likelihood of the reverse process happening, i.e. a spontaneous breaking of all of the peptide bonds forming the proteins in one of the newly-born cells? For a typical bacterium the breaking is estimated to be at least 10−10 times less likely than division. Speaking more generally, the high statistical irreversibility implies high entropy production.

The theory of thermodynamics has been hugely successful in describing statistical phenomena and used in a variety of applications, from steam engines to renewable energy to even black hole evaporation!

Nevertheless chemists, physicists and engineers usually work with thermodynamic equilibria, which don’t allow for complex life-like organisation.

Due to the lack of appropriate mathematical tools, we didn’t know how to treat far- from-equilibrium systems until quite recently. Here comes England who in 2013, building up on the previous work of Chris Jarzynski, Gavin Crooks, and others, managed to derive a succinct formula for the entropy increase. This governs the behaviour of non-equilibrium phenomena, possibly even living organisms. His prescription reveals three key ingredients in an equation, which can be applied to the physics of evolution.

NAIAD

Rowena Hill

Sebastian Mizera takes a look at life and how it develops... through the eyes of a physicist

Lent 2015

Lent 2015

Thermal image of a steamengine. In order to move faster, it must dissipate more heat

Does life have to involve DNA?

Victor Svensson

Jagokogo

First of all there’s the order or internal entropy term; evolutionary transitions will in general result in lower-entropy systems, just like any other change. The second, non-intuitive contribution is durability, which is related to how likely any activity is to spontaneously reverse. We find that self-replication is more likely to happen when the reverse transition also happens relatively frequently, as this implies that it is easy to go through the intermediate stages in self-replication. This therefore means the forwards process happens even more frequently.

The last and most intriguing ingredient comes from dissipation of energy into the surroundings. In a nutshell, the more entropy the organism releases, the more fit it becomes from an evolutionary perspective.

Thus, constantly high dissipation rates seem to be enough for an organism to proliferate more rapidly.

This interpretation has an immediate impact on our understanding of evolutionary adaptation in physical terms. “Winning Darwin’s game happens to be about dissipating more than your competitor, and doing so more reliably”, England says. The theory is meant to detail Darwinian evolution on a lower level of abstraction, rather than replace it completely.

Although mathematically sound, to what extent it actually describes biological phenomena remains a controversy. Most importantly, the theory implies that the distinction between living and inanimate matter is not as sharp as we thought before: after all, the equations don’t give any preference to either.

Some credibility to this idea is given by a recent discovery by Philip Marcus from UC Berkeley and his collaborators. They have observed behaviour mimicking spontaneous replication of vortices in a certain class of turbulent flows. In previous years, Philipp Holliger and his colleagues from the MRC Laboratory of Molecular Biology in Cambridge managed to build a synthetic RNA enzyme functioning as a self-replicator.

England’s idea has to face a series of scrutinising checks, both at a lab bench and in computer simulations. The former, although so far elusive due to technical challenges, is uncomplicated in principle; studying a spectrum of mutations can reveal correlations between dissipation and replication success rates. The latter is currently being investigated by an MIT biophysics group, which has devised a chemical

experiment where a system is fed by an oscillatory drive meant to exhibit the same dynamics as real-life systems. In such an arrangement, one could expect a form of self-organisation to spontaneously arise in the process of maximising entropy production rates. Indeed, a similar emergent behaviour has been observed in silver nanorods, which self-assemble into structures with an excited state that adapts to the wavelength of light shining on them.

Besides experimental verification, there are many possible directions for the extensions of the thermodynamic formalism of adaptation. England speculates that since it is favourable for organisms to adjust to their fluctuating habitats, there will be a thermodynamic drive towards organised states that behave in ways appearing to anticipate future outcomes of their environments. “It suggests a possibility that we could see emergent computation in systems that don’t even have brains”, he says.

Remarkably, all of this is a consequence of simple laws of statistical physics that intrinsically have nothing to do with the notion of life. Schrödinger wrote “We must not be discouraged by the difficulty of interpreting life by the ordinary laws of physics. [...]

We must be prepared to find a new type of physical law prevailing in it.” It is possible, with further evidence, that our core understanding of evolution could soon change.

Sebastian Mizera is a mathematician studying quantum gravity.

The Thermodynamics of Evolution

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Public

A Real Prisoner’s Dilemma

Shirin Ashraf cross-links human behaviour and mathematics to explore real world situations human behaviour is one of nature’s biggest

enigmas. Our understanding of the working of the human mind is not yet complete. However, people have developed ways to study patterns in human behaviour so as to derive some general inferences about our actions in simple scenarios. By sampling from different populations in these constrained scenarios, scientists have been able to formulate hypotheses about how humans behave, and can compare this to the best, most ‘rational’ behaviour.

One such exercise investigates the instinct of cooperation between individuals, called the Prisoner’s Dilemma (PD). It is a hypothetical situation wherein two partners in crime are arrested and questioned separately. There is not enough primary evidence to convict them, unless they testify against each other.

Here, each convict has the option to either cooperate with his partner or defect. The combination of their choices results in four possible outcomes. Payoffs are set in terms of jail sentences of varying lengths. In this case, the best overall payoff for the pair is to cooperate (e.g. 1 year sentence for each). Betrayal on both parts leads to lesser overall payoff (e.g. 2 years sentence for each). However, in cases of one betraying the other, only the convicted serves the maximum sentence (e.g. 3 years) while the other is set free. This canonical example of game theory was introduced by Merrill Flood and Melvin Dresher in 1950.

Of course setting out a perfect scene like that involves some assumptions: there being no chance of future reciprocation on the convicts’ part and

A table of how long the prison sentences might be for partners in crime

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no pre-conviction indication of intent on either convicts’ part. If individuals are self-interested and wholly rational, they will act to maximise their own benefit. We know that they do not do this in reality, so behavioural psychologists have invented a variety of human that does, called homo economicus, to investigate what happens if they do. The best strategy for these individuals is betrayal on both parts, which is not in fact the best overall payoff. It is, however the most stable solution, and is referred to as the Nash equilibrium. This is the tactic which, if everyone else is following, you can’t do any better by picking another option. For instance, in rock, paper, scissors, if one player always picks rock, you can do better than them by picking paper, however if any player picks at random then there is no tactic that can beat them: everyone picking at random is therefore the Nash equilibrium. In this case, whatever player 1 picks, player 2 should defect - so both players defecting is the Nash equilibrium.

When this model is put to test using subjects drawn from the general population, it appears that defection is not the norm. Studies show a significant rate of cooperation, indicating there are other forces at play, and human behaviour is not entirely dominated by immediate self-interest. Upon mobilizing some the variables involved in the system, factors that raised the level of cooperation included larger payoffs from mutual cooperation, identity of the partner player, pretest communication, equal or unequal payoff for either participant, and exit options. The game has also been played using two versions of the scene. Players can either be questioned at the same time (simultaneously), or one after another (sequentially), after they have seen the other player’s actions. Which version of the game they are playing affects the rate of cooperation, although in both versions the best option for a selfish player is always to defect.

Lent 2015

Lent 2015

alone. PD and similar games have been applied to a range of situations ranging from an individual to whole nations.

Advertising is an example of this. Two competing companies need to strategically decide their level of advertising. Less expenditure on advertising accrues higher profit. However, lesser advertising than competitor would dramatically reduce income.

Climate change, for instance, is really a case of a multiplayer PD involving multiple nations. Each country has immediate benefit in carrying on with current harmful behaviour, while all countries would eventually benefit if each member cooperates. This is an example of the “tragedy of the commons”, where everyone’s individual interests conflict with that of the whole group. Commons were originally land that any cattle could graze, that were said to get overgrazed as no one wanted to leave food for other people’s cattle, however this reduced the rate of grass growth. How to limit the exploitation of common goods is a point of ongoing debate for policymakers and scientists.

Competitors deciding how much to advertise is a real-life example of Prisoner’s Dilemma Public

Until now this game has been played with subjects from the general population. But what if someone took it off the stage and to the field for some real testing in a real prison with real prisoners. Do we expect the outcome to be the same?

That is exactly the question Menusch Khadjavi and Andreas Lange have asked in their paper “Prisoners and their Dilemma”. They recruited 90 female inmates at the penitentiary for women in Vechta, Germany.

Of course, prisoners could not have their sentences altered or repealed for the sake of a psychological study, therefore the reward for participation involved coffee or tobacco; and variable phone credit based on their responses (payoffs). Around the same time they recruited 92 female students at the University of Hamburg to study in parallel and compare responses.

Students received an equivalent monetary remittance (€5). Assuming strictly rational human behaviour, with no underplay of personality, the outcome from students and prisoners should be the same.

The model was tested in a simultaneous as well as sequential mode of play. In the simultaneous setting, researchers found that prisoners displayed a significantly higher tendency to cooperate, at 56%, in comparison to a cooperation rate of 37% among students. When the game was played sequentially, 63% of students as first movers tended to cooperate compared to only 46% among inmates. In sequential dilemmas, the choices of the first mover are largely dependent on their beliefs about the second player.

If the first mover believes the other participants to be socially inclined, they are more likely to cooperate than if they believe them to be self-interested. Of course, as far as the second mover goes, students and prisoners reciprocate cooperation equally well. From above, they conclude that students tend to cooperate more often in sequential game play, while inmates are fairly consistent in their choice, irrespective of the mode of play.

From this example, Khadjavi and Lange infer a difference between the behaviour of the two study groups and the relevance of choice of subject group in game theory. It also appears that being jailed does not necessarily indicate an individual to be more selfinterested and criminal behaviour is not a self-selected process. Although this study is a step close to analysing human behaviour, it is still not the last word in PD. It demonstrates how individual differences in personality affects the outcome. In fact, a prisoner, faced with a real choice between cooperation and defection where the pay-offs entail life-changing decisions will make very different choices. However, it is a good attempt to highlight the complexity of human behaviour.

The prisoner’s dilemma, albeit the name, is really just an understanding of cooperative behaviour between parties. And this obviously, is not limited to prisoners

A similar game is called ‘Chicken’, where two cars are heading towards each other on a collision course.

If neither stear away, both will die, but the first to steer away is seen as weak. How long do you wait to steer away? This was considered a good model of the nuclear arms race, where one side must lower tensions to avoid mutually assured destruction. It has been argued that the winner is whichever side ‘disables their steering wheel’ first - if one side cannot steer away, the other side then has no option but to steer aside.

The ‘prisoner’s dilemma’ as we see is not just a prisoner’s dilemma, it is everyone’s dilemma when it comes to making choices that affect another person’s life. Everyday we decide to lie or not, to buy or not, to save or not. These choices sometimes shape our lives and because we are all different, these choices are what make the human community diverse.

Shirin Ashraf is a PhD student working in the Department of Pathology

A Real Prisoner’s Dilemma

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Macroscopic Solutions

Endosymbiosis: Life Inside Life

FOCUS

BlueSci looks at what happens when organisms make their homes inside other lifeforms

approximately one and a half billion years ago, on a small, hostile planet known as Earth, two single cells met in a vast ancient ocean. What happened next was possibly the most important step in the evolution of our species, and that of most multicellular life on the planet; one organism slowly engulfed the other, and swallowed it whole.

The result was the mitochondrion - a stripy, slug-like feature found inside complex (eukaryotic) cells such as our own. Mitochondria “burn” glucose to release energy which is used to complete cellular tasks; they are the power stations of cells. Just like burning coal the process requires oxygen, but it happens in four highly controlled steps and instead of electricity, mitochondria produce the energy-rich molecule adenosine triphosphate (ATP).

In 1922, a young American biologist was working on a way to visualise bacteria when he noticed something surprising. The staining technique Ivan Wallin had been honing was also particularly good at highlighting mitochondria.

Furthermore, they looked identical. Could this ubiquitous and essential machinery once have been an independent organism?

It was a heretical idea, but further evidence emerged in the 1960s with the discovery that mitochondria have their own DNA. The victim of the gulping incident wasn’t just any bacteria; our distant, single-celled ancestor struck lucky with its prey. The closest genetic match for mitochondria are the Rickettsia, a group of small, rod-shaped bacteria. They have an unusual knack for producing ATP, and use the same biochemical pathway as mitochondria. The precursors to modern eukaryotes were quick to exploit this capability and the relationship blossomed into one of mutual benefit, an “endosymbiosis”. Now nearly every plant, animal, and fungi on the planet has them.

This cellular heritage has left an inconvenient hangover- some modern antibiotics do not discriminate between harmful bacterial and mitochondria. Scientists at Boston University applied clinical amounts of the common antibiotics ciprofloxacin, ampicillin, and kanamycin to human cells under laboratory conditions. The drugs disrupted mitochondrial function and led to the generation reactive oxygen species (ROS), damaging DNA, proteins, and fats inside the cells.

Mitochondria have close relatives in oceans and fresh water to this day. In fact, Pelagibacter ubique is probably the most numerous bacteria in the world, making up approximately half of all cells at the ocean’s surface. P. ubique is immobile, drifting

Many squid house fluorescent bacteria

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Louisa Howard

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Mitochondria provide high-energy ATP for their host cells

around at the mercy of currents, and popular opinion is that the mitochondrial ancestor was much the same. However, this may not be the case.

Nathan Lo and his team at the University of Sydney were studying an obscure cousin of mitochondria called Midichloria mitochondrii when they found a set of unusual genetic instructions. The bacterium has kept the genes needed to make flagella, whiplike accessories used for propulsion and a common feature among parasites.

It’s not possible to know for sure if mitochondria originally had flagella too, but it opens up an intriguing possibility; mitochondria may have imposed themselves on eukaryotic precursors as parasites, instead of passive prey.

And there are other, more personal, secrets hidden in mitochondrial DNA. The organelles are passed down the generations to offspring from their mothers only, and by analysing mitochondrial DNA it is possible to trace human evolution. Scientists have done this, all the way back to a woman from Southern Africa who lived between 100,000 and 200,000 years ago. “Mitochondrial Eve” is the common ancestor of every present-day human being. She was not the first human but the only female lineage to survive, eventually giving rise to all the diverse ethnic groups in existence today.

Some scientists think mitochondria are not the only endosymbionts in our cells. The nucleus, where genetic information is stored, may have bacterial origins too. The theory was pioneered

by Lynn Margulis, who provided key evidence for the idea in mitochondria, and suggests that two radically different organisms - the archaea and nascent eukaryotes - teamed up, with the former evolving into the nucleus. The archaea are a group of single-called organisms best known

NEON

False-colour electron microscope image of a chloroplast

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Focus

for inhabiting extreme environments such as hot volcanic springs or salty lakes, and feeding on strange chemical energy sources. They can also be found in a wide range of normal environments, including the human gut, where they produce methane. Eubacteria include most types of bacteria that we are familiar with, including all those that infect us, and the ancestors of mitochondria.

Plants and algae have taken cooperation with other organisms to another level. Plant cells are packed with chloroplasts which store the green pigment chlorophyll and use the sun’s energy to make sugars.

Several prokaryotic cells can perform this reaction (photosynthesis) too. Of these, cyanobacteria are the most common, inhabiting nearly every terrestrial and aquatic environment. They do not have chloroplasts, and store the pigments they need for photosynthesis in the folds of their external membrane. We have a lot to thank them for - it is cyanobacteria which transformed the atmosphere of the Earth billions of years ago by producing oxygen. Their activity kickstarted the evolution of oxygen-dependent life, and led to the near-extinction of the oxygen-intolerant species that used to dominate.

One billion years ago, just after eukaryotic cells acquired nuclei and mitochondria, history repeated itself and one cell engulfed another - this time an early eukaryote engulfing a cyanobacterium. Like mitochondria, the cyanobacteria survived inside its predator, helping out by harnessing the sun’s energy to produce sugars. As time passed, most of the cyanobacteria’s genes were transferred into the nucleus of its host cell, so proteins required by the guest could be made directly by its captor.

Furthermore, there’s tantalising evidence that the mutually beneficial relationship was actually a threesome. While the origin of chloroplasts is clear, a number of important plant genes needed to transport sugars out of the chloroplast may have originated from a Chlamydia-like bacterium.

Like mitochondria, chloroplasts have their own DNA and the instructions for making them are not encoded in the cell nucleus. Instead, they reproduce like bacteria, duplicating themselves to yield two genetically identical daughter chloroplasts. The catch is that cells which don’t have any can’t make new ones. There are, however, ways to steal them.

Careful examination of some algae shows that their chloroplasts are encased in multiple sets of cell walls; when chloroplast-containing algae are engulfed by another eukaryote, a Russian-doll style algae results; the chloroplast is encased in its own membranes inside the prey algae’s membrane, and finally sheathed in the predator algae’s membranes.

Lent 2015

Middlebrooks

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In sea slugs, there are even stranger happenings.

The creatures aren’t born with their own chloroplasts, however, when young Elysia chlorotica eat algae they digest the outer layers and keep the chloroplasts alive. Without the host cell’s genes, the chloroplasts can’t reproduce, but they continue to photosynthesise. It’s not entirely clear how much benefit the slug gets from this – it can’t properly mature into its adult form without taking in these chloroplasts, which certainly provide it with camouflage as it grazes on more algae. But experiments show the risk of starving to death is much the same in the light as in the dark, suggesting

the sugars provided by the chloroplasts aren’t particularly useful as a source of food.

Vertebrates have been known to poach chloroplasts, too. The spotted salamander contains algae as an embryo, which provide oxygen and sugars and soak up waste products (nitrogen and carbon dioxide). In oxygen-poor water, surrounded by other eggs, this gas exchange can be more valuable than the extra food. The algae live inside the salamander cells, surrounded by mitochondria which make use of the oxygen and sugars.

The anglerfish does the opposite, using bacteria to produce light. They live in the pitch-dark in one of the most inhospitable habitats on the planet the deep sea. To capture their scarce prey, the fish use a luminescent lure on the end of a “fishing rod” structure above their toothy jaws. The lure is illuminated by resident bioluminescent bacteria which are recruited from the environment. In some species there is evidence the bacteria may be evolving towards a more permanent endosymbiosis; the bacteria are unable to produce light outside of their hosts.

Some sea slugs, like those in the Elysia family, take chloroplasts from the food they eat

Schuessler lab

Arbuscular mycorrhization allows fungi to function as extra roots for a plant, and occasionally bacteria

NOAA

Coral hosts a type of algae which contains several layers of its own endosymbionts

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Majiscup - the papercup & sleeve

Retroviruses produce DNA in the host cell, which is integrated into the genome

In the plant world, endosymbiosis is surprisingly common. The most significant of these is arbuscular mycorrhization, where a fungus provides plant roots with phosphate and nitrogen and protects them from pathogens. In return, the fungus receives sugars from the plant. The partnership is widespread, with up to 90% of plants capable of adopting fungi, and is believed to have played a critical role in the colonisation of land by plants.

A similar relationship lets panic grass grow at temperatures of up to 65o C. For comparison, humans can only survive similar ambient temperatures for a matter of minutes. The grass is found growing in partnership with Curvularia protuberata in Yellowstone National Park, but only when the fungus itself is ‘infected’ with a virus which conveys thermal tolerance. Scientists have demonstrated the protection provided by the virus under laboratory conditions, by allowing the infected fungus to colonise the roots of tomato plants and testing their ability to withstand heat.

The involvement of viruses in endosymbiosis is surprisingly widespread. The human genome is peppered with alien DNA sequences, a legacy of infections which may have occurred millions of years ago. The viruses in question are retroviruses,

a group which includes HIV and specialises in embedding their own DNA into the genomes of their hosts. However the viruses in the human genome have infected germline cells (sperm or egg), a way to ensure their DNA is passed on through the generations. They are “endogenous retroviruses”, and there are about 98,000 in the human genome, comprising nearly 8% of our DNA. Most have been inactivated through mutations, deletions or rearrangements - just one family has persisted since the divergence of humans and chimpanzees.

Once thought to be “junk”, scientists have identified numerous important functions carried out by endogenous retroviruses, primarily in regulating when genes are turned on or off, and encoding proteins required for reproduction and development; we couldn’t live without them.

One example is syncytin, which encodes a protein involved in the development of the placenta. When syncytin was discovered in 2000, the team of Boston scientists noticed something unusual. Syncytin is only produced in the layer of the placenta in contact with the uterus, and causes neighbouring cells to fuse together. The interface between the placenta and the mother is crucial for nutrient transfer to the developing foetus, but there is a problem.

Some nematodes rely on bacterial endosymbionts to reproduce.

Public domain

Erika Mancini

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White blood cells from the mother are able to squeeze through normal tissues, and could trigger a potentially lethal immune response if they were found on the wrong side. The new layer acts as an essential barrier: fused cells are dense enough to prevent white blood cells from getting through.

Viruses typically insert three key DNA components, gag, pol and env - gag (group-specific antigen) code for the core virus proteins, pol (polymerase) is responsible for making the viral DNA or RNA and env (envelope) is for the outer proteins. Syncytin is a type of env protein. Env proteins are involved in cell recognition and this feature has been exploited by our cells. The gag and pol genes that go with the syncytin in our genome are inactivated by mutations, but the env gene is used with the characteristics of a retroviral envelope protein. Its job is to co-ordinate the fusion between the placenta and the uterus, not something that cells are normally equipped to do.

Scientists at Lund University in Sweden have provided evidence that retroviral DNA may have functions in the human brain, too. ERVs are normally suppressed by the protein TRIM28, which prevents their DNA from being read to make the proteins they encode. In the recent study, the TRIM28 gene was “knocked out” so scientists could observe how the viruses influenced the expression of neighbouring genes. The researchers found that the viruses were activated specifically in brain cells, where they regulate gene expression in neural stem cells.

Very occasionally, assimilated viral DNA is used to make the virus itself. At least two species of parasitic wasp have struck up a partnership with viruses, which help them to overcome the caterpillar prey. The wasps lay their eggs in the insects, which provide a source of fresh food for when the larvae

hatch. The larvae slowly consume the host from the inside out, without killing it, until they are ready to fly away. The only catch is the caterpillar’s immune system, which makes things difficult for the larvae.

But the mother has a secret weapon - an injection of virus particles along with her eggs. These viruses, called polydnaviruses, dramatically alter the physiology of the host. They target hemocytes - the insect equivalent of white blood cells - and prevent them from working properly. They also disrupt the hormone system of the host, preventing the transformation from caterpillar to moth, so that there’s more food for the larvae.

Understanding how animals depend on their microscopic accomplices can save lives. Nematode worms are a diverse group of animals of which more than half are pathogens. They infect billions of people worldwide and cause a panoply of unpleasant diseases, such as elephantiasis, in which the body swells to massive proportions. They can be difficult to treat, but in 2003 scientists pioneered the use of a new drug - a widely available antibiotic.

Filarial nematodes, which cause rashes, arthritis, elephantiasis, and are a leading cause of blindness, rely on bacterial endosymbionts to reproduce. An intensive course of the antibiotic doxycycline can eliminate the parasite in less than eight weeks.

In fact, almost every complex organism on the planet relies on a multiplicity of partnerships, with unlikely collaborations across the tree of life.

Captive bacteria and viruses produce ATP and encode vital proteins, while the alliance between cyanobacteria-derived chloroplasts and plants is responsible for producing the majority of the planet’s oxygen and food. As Darwin himself put it “In the long history of humankind (and animal kind, too) those who learned to collaborate and improvise most effectively have prevailed”.

Public domain

Zaria Gorvett is studying for an MPhil in the the Department of Veterinary Medicine Robin Lamboll is a 2nd year PhD student in the Department of Physics Nathan Smith is a 3rd year undergraduate student in the Department of Plant Sciences Ornela De Gasperin is a 4th year PhD student iin the Department of Zoology

Some wasps produce viral particles in their ovaries to infect the caterpillars they lay eggs in

Aneesh Aggarwal is a 2nd year undergraduate student reading Medicine

Lent 2015

Focus 21

A Bunch of Banana-Drama Thomas Hitchcock goes bananas for bananas

it is in the tropical forests of South-East Asia that our story begins, because it is here that the seventy or so species belonging to the genus Musa (the banana’s taxonomic family) have their evolutionary roots. It is also here, in the highlands of Papua New Guinea, where the story of their cultivation begins.

A combination of evidence from banana phytoliths (siliceous plant remains) and evidence of land disturbance suggest that banana farming first began around the Kuk swamps as early as 5-8000 years ago.

This was when the banana began its march across the planet, leaving its mark everywhere from the streets of Ciénaga to the aisles of Sainsbury’s.

Surprising as it may be, the banana is in fact a type of berry. Like avocados, blueberries and grapes, the banana develops from a part of the flower called the ovary (which holds the ovules) with the fleshy part of the fruit surrounding the seeds. Bananas show great diversity in appearance from the from the pink and fuzzy Musa velutina of Northern India, to the scarlet, bat-pollinated Musa coccinea in Tropical China. However, one particular banana species, Musa acuminata, and one cultivar in particular, the Cavendish, has come to dominate the globe. It’s superior shelf life and ease of transport have made it by far the most popular for export and it is unlikely that you’ve ever eaten another type. One other characteristic which makes the Cavendish and other popular cultivars stand out from their wild cousins is their lack of seeds. If you cut open a supermarket banana you will see no seeds, just some small black dots. To explain this strange seedless berry we will need to delve a little deeper into its sex life.

Sexual reproduction is simply a matter of combining the genetic information from two

steve hopson

Cavendish bananas are ubiquitous in supermarkets

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History

individuals to make a new one. However, for this to happen, sex cells must be produced by a process known as meiosis. This involves a special series of cell divisions, the result of which is that the sex cells produced will have half the number of chromosomes that were originally present in the parent cell. When two sex cells fuse to form a single fertilised cell, the cell will usually end up with the same number of chromosomes as each of it’s parents. During cell divisions that occur in meiosis, chromosomes have to recognise their partner and pair up so that when the chromosomes are separated during cell division, one chromosome from each pair ends up in each of the daughter sex cells. The problem is that if there are an odd number of chromosomes, or chromosomes fail to recognise each other, then they have trouble pairing. And if they can’t pair up then meiosis fails, and no sex cells are produced.

This sad sexless situation is exactly what happens with our seedless bananas. All of the most common cultivars we use are either products of hybridisation events, such as the plantains (a cross between Musa acuminata and balbaniasa), or have an odd number of chromosomes, such as the triploid Cavendish. If these fruit are unable to produce seeds, then how are they able to reproduce?

Whilst we commonly assume that sex is necessary for reproduction, for plants this is often not the case.

Many plants can reproduce vegetatively, and this is exactly what happens with our bananas. New shoots grow from an underground stem known as a corm and when a farmer needs a new banana plant they can simply remove a new shoot from the corm with some roots attached, replant it, and a new individual, which is genetically identical to it’s parent, is born.

With such a simple form of propagation, a year round harvest and a sweet, seedless, nutritious fruit at the end, it is no surprise that bananas soon spread beyond the coasts of Asia, finding its way into Africa, the Middle East and even sunny Cyprus. However, it was the introduction of the banana to the Americas by Portuguese sailors in the 16th century that arguably had the greatest impact upon the banana’s success.

Despite their introduction some three hundred years before, it took a fortuitous combination of an ambitious railroad project and a cash strapped Costa Rican government to bring the banana to Lent 2015

Lent 2015

Minor Keith (far right) is credited with bringing the banana to the American masses.

Fusarium oxysporium was the cause of Panama Disease

usda

public domain

the American masses. In 1882 after defaulting on their payments for the railroad between the capital San José and the port of Límon, President Próspero Fernández Oreamuno cut a deal with the manager of the railroad, Minor Keith. Keith raised the £1.2 million needed to finish the railroad in return for 800,000 acres of tax free land and a 99 year lease of the railroad. He also went on to marry the president’s niece. It was on this land that Keith first tried planting bananas grown from roots he gained from the French, an experiment that was to prove an extremely lucrative business. Before long, he had a steamboat line to New Orleans to market his bananas, along with further plantations in Panama and Colombia. By 1899 he had merged his venture with Andrew W. Preston’s Boston Fruit Company, together forming the corporate behemoth that was the United Fruit Company.

Over the next forty years, a combination of savvy marketing and low prices increased the popularity of the banana enormously, and gave United Fruit a monopoly over the industry. However, their cheap bananas came at a cost to many of the countries they grew in. Through manipulating many of these countries land use laws, they cheaply bought up huge tracts of prime agricultural land, paying low wages and little tax in return. Their economic strength gave them great political power, so much so throughout Central America United Fruit became known as ‘El Pulpo’ (the octopus), its influence pervading every aspect of society. The epitome of this are the events of December 1928, famously fictionalised in Marquez’s One Hundred Years of Solitude.

Following a strike by Colombian plantation workers, government troops, apparently coerced by United Fruit, opened fire on crowds in main square of Ciénaga, with the death toll reported to be anywhere between 47 and 2000. However, whilst means fair and foul enabled these banana monopolies to take control, their business was built on a fragile fruit.

The cultivar grown across Latin America and shipped around the world in this period was called ‘Gros Michel’. However, despite its former ubiquity,

you’ll no longer be able to buy it in Sainsbury’s, or any other supermarket for that matter. Instead, by the 1950’s this king of the banana plantations had been driven to commercial extinction, its downfall a pathogenic fungus, Fusarium oxysporum. The fungus infects through the roots of the banana, blocking its vascular system, and starving the leaves of water and nutrients. Eventually, the plant’s leaves turn yellow and wilt, and it dies. With no fungicide to stop it, the fungus swept north and south after its arrival in Panama, strangling the plantations of susceptible clones, being carried onwards each time through the soil or infected suckers. The saviour for the banana industry proved to be a different cultivar, one which was resistant to Panama disease.

That cultivar, the Cavendish, now accounts for 47% of all bananas grown worldwide, and the vast majority of international banana trade, and by any measure is an enormous agricultural success.

However, just as with the ‘Gros Michel’, the Cavendish bananas are genetically identical, and

their near sterility makes it difficult to introduce resistance to pathogens. This is even more concerning given the rise of a more virulent, aggressive strain of Fusarium oxysporum over the past twenty years – tropical race 4. Having already spread to Pakistan, Indonesia and the Philippines, it appears to be only a matter of time before it reaches Latin America, and the majority of the Cavendish plantations. Novel breeding and genetic engineering techniques are being used to try and introduce resistance before it arrives, but if these attempts are unsuccessful then the Cavendish could follow the Gros Michel out of the supermarket and into the history books.

Thomas Hitchcock is a 2nd year undergraduate studying Biological Natural Sciences at Sidney Sussex College

History

23

Japanese Temple Geometry Tariq Desai explains the history of geometrical offerings in Japan 1820 Yamaguchi Kanzan began a pilgrimage.

Friends left a farewell haiku on the start of his first day’s walk. But this was no spiritual journey – this was a pursuit of mathematics. Over two years he would visit towns north of his home in Edo (now Tokyo), eventually venturing south, as far south as Nagasaki.

In each he set about recording local theorems and techniques in his particular field of interest: intricate plane geometry painted on wooden plaques. The plaques were hung by worshippers in Shinto shrines and Buddhist temples. Some challenged visitors, others announced findings or unsolved questions, but all were acts of devotion, offerings to the kami, or spirits, and prayers.

Yamaguchi collected hundreds of examples of these wooden tablets, or sangaku, and after six tours had enough for a book, advertised but never published, called Travel Mathematics. Much of what we know about sangaku comes from his diaries.

In the Edo period, the two and a half centuries

in july

Wikipedia

Wooden tablets called Sangaku illustrated geometric theorems

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Science and Art

from 1603, Japan was governed by the Tokugawa shogunate. Compared with preceding centuries, the country was safe for travellers such as Yamaguchi. In reaction to ministering Christians, the Tokugawa drew Japan into isolation, allowing trade only with Chinese, Koreans and Dutch. No foreigner could enter the main islands, and on penalty of death no Japanese would leave. But during the Great Peace, as the period came to be known, the custom of dedicating sangaku flourished in Japanese culture.

Sangaku were dedicated as early as 1603, but the practise of leaving decorated wooden tablets at shrines pre-dates the Edo period by several centuries. It is thought to have started with worshippers leaving paintings of horses in lieu of the animals they couldn’t afford to donate.

Most presenters of sangaku were samurai, by this time largely a class of government administrators.

They described sangaku problems with kanbun, a formal script derived from Chinese characters, which played much the same role Latin did in universities in the West. The practise was widespread. People from all backgrounds, men, women and children, would propose problems and attempt to solve those posed by others.

And many were not easy. It took the ingenuity of the greatest samurai-mathematician of the 18th century, Ajima Naonobu, to prise open the famously obstinate “Gion Shrine” problem. He needed to reduce a 1024-degree equation to a 10-degree one and approximate a solution. Even today, no exact answer is known.

Advances in astronomy and other sciences filtered into the country during the Edo period, but nothing of calculus. Ajima himself came closest to developing a full theory of integration. Even so, sangaku often presented extraordinarily accurate solutions to classic optimisation questions while no evidence exists that the setters knew calculus, which by the 18th century had already become established in the West. In some cases they record discoveries in plane geometry ahead of their earliest statement in Western texts.

Along with striking geometric figures and calligraphic beauty, it seems the mathematics itself was considered to possess some quality of spiritual elevation. It fed from and into art and poetry.

One crotchety mathematician wrote in a preface to his 1640 textbook that children wasted their time playing tricks and writing doggerel. “If they write and read any poetry,” he claimed, “it is better that the Lent 2015

Wikipedia

The Gion Shrine contains a problem that was simplified from a 1024th to a 10th order equation

poetry concerns mathematics.” For purposes of moral rectification, he presented all his formulae in verse.

However, geometry and arithmetic were certainly valued for their utility. After the arrival of the American Commodore Matthew C. Perry, and the forced “opening” of Japan, a new regime sought rapid industrialisation in an effort to catch-up, as they saw it, with other nations. In favour of new methods, schools no longer taught Japanese mathematics and

Features

the practise of dedicating sangaku all but died out.

Of the thousands known to have been hung, about 900 can still be found, the latest dedicated in 1980. We have not yet determined how some of the problems were solved without modern techniques; solutions to others are unknown.

Tariq Desai is a PhD student studying evolutionary genomics

References:

Fat-Fighting Fat - Virtanen, K. A. et al. Functional brown adipose tissue in healthy adults. New. Eng. J. Med. 360, 1518–1525 (2009).

Thinking Big - http://jeb.biologists.org/content/209/2/238.full Do Animals Get Lost? - http://jeb.biologists.org/content/210/21/3697.full Thermodynamics of Evolution - www.englandlab.com/uploads/7/8/0/3/7803054/2013jcpsrep.pdf A Real Prisoner’s Dilemma - http://plato.stanford.edu/entries/prisoner-dilemma/

Regulars A Bunch of Banana-Drama - http://panamadisease.org/en/theproblem Japanese Temple Geometry - Hidetoshi, F., Rothman, T. (2008). Sacred Mathematics: Japanese Temple Geometry.

Science Teaching Around the World - http://www.icsu.org/publications/reports-and-reviews/ Science, Sense and Evidence - http://www.askforevidence.org Psychology of Torture - http://web.williams.edu/Psychology/Faculty/Kassin/files/kassin_kiechel_1996.pdf

Weird and Wonderful Can Conflict Cause New Diseases? - http://www.bbc.co.uk/news/health-29604204 Aquaman? AquaCan! - http://classes.kumc.edu/cahe/respcared/liquidventilation/wikeper.html How do you solve a problem like Zombie Epidemics? - http://mysite.science.uottawa.ca/rsmith43/Zombies.pdf Lent 2015

Science and Art

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Science Teaching Around the World

Students argued in unison for the employment of better science teachers

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Science and Policy

public domain

Sarah Binney explores the different educational approaches taken around the world how we learn science and how we teach it to future generations is of the utmost importance to the research of tomorrow. The UK educational system that many of us are familiar with is just one way to educate students. Here, we look at international systems of science education and ask how we can learn to teach.

Compared to literature or maths, science education is a reasonably recent invention. While mathematics has been taught in its own right since the Greek schools of antiquity, before the 19th century science was an insufficiently coherent field in its own right to justify teaching it to students.

With science’s divergence from mathematics, natural philosophy and medicine, and with the advent of science as a career rather than a gentlemanly pursuit, a need developed for courses specifically dedicated to biology, chemistry, and physics.

Now in the UK science is an essential part of the national curriculum. However the A level system requires that students to specialise at an early stage and this is frequently criticised. We spoke to four science students from other countries to hear their opinion on the matter.

The interviewees were surprised by the degree and rate of specialisation made necessary by the A level system for UK students. For a university course to have requirements based on decisions made at age 16 is rare, and all four agreed that keeping options open is important.

All four also said having a good teacher is crucial for a productive education. A good teacher can rescue a struggling student or drive an able student to unexpected heights.

Correspondingly, almost everyone complained of a lack of effective science teachers. Universally, teachers were paid too little so people with good science degrees tended to go into fields where they could earn more money, or they would emigrate.

Often maths and science teaching was seen as a high-status job which paid too little to justify the expertise required.

In Denmark we have none of this obsession with “fairness” that you do in England. Most of our written exams are open-book but that’s not the only way to be tested. We have maths oral exams, for example; you write a proof on the blackboard in front of the teacher and an external examiner. Grades are more or less subjective.

We have a good mix of learning methods, from problem solving to labs to progressive project-led learning. You can do a big project, like a lab report or a thesis, which is worth the same as the highest exam.

You keep your subject options open right up until leaving school. There are only a handful of subjects, like medicine, with explicit subject requirements. I think it’s important to keep your options open, but having done so means that I did less science at school than UK students.

Our university application system is poor. They just rank applicants by exam score and pick the top candidates from that list. There used to be less competition for places but now people are focussing more and more on grades. Many people think that because the world is becoming more globalised we should make the top grade in exams easier to get. However that means that the grade is worth less, which I think is wrong.

The UK system has flaws. There are too many private schools – it’s a powerful arrangement in Denmark that people can go to the same schools and get the same opportunities. That’s very important to me.

Denmark: JØRN (engineering) – “We have none of this obsession with “fairness””

USA: ANON (chemical engineering) – “No child left behind means no child gets ahead”

Lent 2015

Science education is a very political thing in the US. Arts subjects are seen as unemployable so pursuing science has higher status.

The main differences with the UK are the extent of specialisation and who decides what you learn. Even at college level you take subjects other than your major; you specialise way too early. Our system is mainly teacherbased, rather than subject-based or curriculum-based.

I picked my subjects mainly on who was teaching them, because few college courses have explicit subject requirements. Having the teacher set the syllabus means they can tailor it to their class and make sure everyone is keeping up, but no child left behind means no child gets ahead.

We have rolling exams throughout high school. Finals only contribute to 30% of your grade; you have frequent short exams all the time which force you to keep abreast of work – I’ve had difficulty here because everything is crammed into a much more concentrated exam period!

However continuous testing means that you cram for the papers and forget everything afterwards.

Lithuania: KAMILE (engineering) – “I’m truly terrified by how poorly they teach it” I was one of twelve people from my country who came to Cambridge, five of whom came from my school.

If you’re a really motivated student there’s not much to do. There are Olympiad competitions and part-time courses which get able students interested in the subject (and inspire them to apply to university) but not enough people know that they exist.

My teachers were really motivated, which is really important. However many of them had degrees in education rather than what they were teaching which meant after a while the students overtook the teachers.

What made me most angry at school was computer science - I’m truly terrified by how poorly they teach it.

Programming in Logo or Pascal or HTML is taught far too slowly and you have to spend half your time learning

how to use Word! This is the digital age; everyone knows how to double-click or send an email! Computers are everywhere so people need to learn how to program.

Bulgaria: MARIA (computer science) – “I feel really sorry for those people because they’re really clever but there’s no money.”

Maria describes the implications of poverty on education

I went to a specialist maths and science school in Bulgaria. That’s not representative of most of the country – most schools are general high schools which offer lots of subjects. Most schools are state run and you sit exams to get in.

Academic competitions are very important. There’s a lot of prestige associated with them and they count towards university applications.

The main problem in Bulgarian schools is money.

There isn’t enough funding for schools to offer practical physics experiments so there’s a lot of rote learning. That means the exam is too easy and that the students lack interest, so it’s a vicious circle. Schools tend to offer what is easy to teach rather than what is important, like geography rather than economics.

Teaching is also a problem; a bus driver gets the same salary as a high school teacher. We need to start making the teaching profession more desirable so that people don’t go into other fields. Make it competitive and then standards will rise.

From the interviews it seemed that most systems struggle to find a happy medium between helping struggling students to succeed and allowing able students to flourish. This highlights the benefits of streaming but also the importance of extracurricular actvities. Many of the students mentioned competitions and Olympiads which allowed them to get ahead without compromising the progress those less able.

The most striking part was the universal lack of science teachers. This is not just a problem in the UK, but proves the importance of schemes like “Teach First”, a charity program aimed at ending education inequalities. We need to prove that going into teaching is not seen as failure, for example compared to remaining in academia. Instead teaching should be seen for what it is: a crucial social force, a way of giving something back. Most importantly, it is a way of playing a part in the next generation of scientists, engineers, and doctors.

The Raspberry Pi (imaged left) is an example of a novel programming aid

FLICKR

Sarah Binney is a 3rd year undergraduate studying Natural Sciences at Clare College

Lent 2015

Science and Policy

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Science, Sense and Evidence Daisy Hessenberger questions the facts presented to her, and challenges you to do the same

in another step in the fight against misleading claims,The Ask for Evidence campaign has gone live! Lead by Sense About Science, a charity aimed at equipping people with the tools to make sense of scientific claims in the public domain, anyone can now ask for evidence via their new campaign website: http://askforevidence.org/index.

A lot of science communication aims to educate people on certain scientific topics, but Sense about Science aims to teach people how to critically approach scientific claims and how they might get answers to their questions. Rather than putting people back in school, this approach seeks to empower people to ask and answer their own questions.

Specifically the Sense About Science website offers guides on what makes good science and what questions there are to ask. However their new Ask for Evidence campaign website goes a step further:

they have a tool with which you can request evidence via the campaign. Simply state the claim in question, where you heard about it, and who made the claim and Ask for Evidence will help you get to the bottom your question. They can call on a database of over 6,000 scientists who can aid in your quest for the truth.

Every day we are bombarded by science in the form of news stories covering the latest discovery to advertisements of products claiming scientific support to old wives tales. So how can we pick out the good science from the bad? We can ask incisive questions!

How does Detox shampoo work? Does drinking green tea really help against wrinkles? Are genetically modified crops actually bad for the environment? How can super berries cure cancer?

Throughout your day these types of questions might pop into your head – but how often do

apeman

It is often claimed that green tea prevents wrinkles, but is this true?

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Initiatives

Lent 2015

Quinn Dombrowski

Adverts often present dubious scientific claims.

mojzagrebinfo

you chase down the answer? Perhaps it is too time costly or you do not know who to ask. No longer!

Now when you have a scientific question you will know where to go.

If you a buying a product, or even basing a health associated lifestyle choice on a claim, you deserve to know if that claim is based on fact or fiction. “Evidence matters. And we should ask for it”, says Dr. Chris Peters, the scientific liaison for Sense About Science. “Anyone who wants us to vote for them, believe them, or buy their products should expect us as voters, consumers, patients, and citizens to ask for evidence.”

For example, when Max Templer saw headlines claiming that drinking red wine could reduce acne he decided to ask for evidence (http://www. askforevidence.org/articles/is-red-wine-treatmentfor-acne-spot-on). The articles had been based on study which tested the effect on Propionibacterium acnes of applying an antioxidant, resveratrol, directly to the skin. Resveratrol is found in red wine, but upon contacting one of the co-authors of the study, Max was told that there was no evidence that drinking red wine would reduce acne. Max emailed the publications to inform them of his findings and although The Independent amended its article, both the Drinks Business and Business Standard did not. The Ask for Evidence campaign has seen other successes such as changes to staff training at Ann Summers and Vision Express, and the removal of evidence-free advertising from of a leisure centre chain.

Anyone can get involved by going to the website and asking for evidence. The campaign aims to get both the uninformed and the informed leading the charge. Dr. Chris Peters commented, “We’ve seen lots of students already getting involved and leading the way by asking about claims they come up against. This is geeks holding to account those who make decisions on our behalf.”

The campaign has also seen distinguished scientists get involved. Dr Jon Otter, a research fellow at the Centre for Clinical Infection and Diagnostics Research at King’s College London, contributed a blog post on the validity of claims on new antimicrobial surfaces derived from tea, wine and chocolate. Whilst he found them promising candidates, he concluded that “there is a long way to go before they are ready for widespread adoption for healthcare and other applications”. Such support gives the campaign a sense of legitimacy that will only help its cause.

However if you don’t have a question you can instead get involved with other aspects of the campaign. Students in particular can get involved with the Voice of Young Scientists network, a community of early career scientists, engineers, and medics who would like to get involved with the behind the scenes process of asking for evidence.

The first step in correcting bad science is identifying and challenging it, and Sense About Science is one of many organisations aiming to highlight issues of bad science to the public.

Though there is still a long way to go, the Ask for Evidence campaign represents a change that may one day lead to a firm scientific basis in claims about a products efficacy; a change that’s surely better for everyone in the long run.

There is no direct evidence for red wine reducing acne

Daisy Hessenberger is a PhD student in the Department of Plant Sciences

Lent 2015

Initiatives

29

The Psychology of Torture Bill Baloonarm investigates psychological problems with the use of torture and interrogations if a terrorist plants a bomb somewhere, is it

moral to torture him into revealing where he placed it?

A question that’s often asked but one of no relevance.

Firstly, for all the times this question has arisen in films and TV shows, there are no known examples of it happening in real life. Secondly, the question is framed to reinforce the myth that torture is an effective means of gathering new, true information.

We should start by making a distinction between interviewing and interrogating. Interviewing is aimed at getting information out of someone, and involves asking a few non-leading questions and allowing the suspects to answer them in their own way.

Interrogating is aimed at extracting confessions from someone – the interrogator does most of the talking, convincing the interrogated that their guilt is known and they had best co-operate. All they want is a few specific details, and an admission of guilt. Torture is clearly an example of the latter. But even when not torture, this process raises a number of psychological problems: memory fabrication on the part of the person interrogated, and confirmation bias on the part of the interrogator.

Humans invent memories easily, and without intending to. In one experiment, people were asked if they had met Bugs Bunny at Disneyland. 8% remembered doing so, but if they read an advert mentioning the rabbit being in Disneyland before

being asked the question, this number rose to 30%.

Many of them were even willing to describe the meeting. However, Bugs Bunny is not a Disney character, so this clearly can’t have happened.

Another study upped the stakes a little. People were asked to type letters into a keyboard, either fast (high-stress, or high certainty) or slow (low-stress, or low-certainty). They were instructed not to press the alt key, or the computer would crash, losing all data.

This then happened automatically a minute into the experiment. An experimenter entered the room and asked what had happened. All 79 participants first denied pressing alt, as indeed they hadn’t. In half of cases, a witness in the room claimed to have seen the button being pressed, in the other half they said they didn’t. Participants were then taken into another room and twice asked to sign a confession saying they had pressed the button. In the original experiment, there was no particular penalty for signing, but the experiment has since been replicated with a financial penalty for participants who agreed to sign, with much the same results. At least a third of suspects signed the confession even when the witness had seen nothing. This doubled when they had been typing more quickly, and increased further when the experimenter in the room said they had seen them press the alt key. If a witness accused them and they were typing quickly, all participants signed. They were

Wikimedia

A range of torture tools used in Prague Castle are shown here

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Perspective

Lent 2015

Waterboarding is a method banned

by Obama in 2009 for interrogation of detainees

Flickr

asked questions by the ‘next subject’ waiting outside, who was really another experimenter wanting to see if they had convinced themselves of their guilt or just complied for social reasons. None of the people under low-stress, no-witness conditions said they had really pressed the button here, but two-thirds of the high-stress, witness-accused did. Half of those also invented details of how the accident had happened.

This is just with a normal accusatory interview, with only minor social disapproval if they failed to sign. We know that this also happens in real court cases. The Innocence Project uses new DNA data to re-evaluate old cases, and found that in around a quarter of the hundreds of convictions overturned, the defendant had pleaded guilty. Again, this is without the police needing to torture them.

There is a good reason why evidence obtained by torture is not legally valid: it gives bad data, which is worse than no data at all. Like misnamed truth serums, such as sodium pentathol, torture induces a sort of altered state of consciousness that can sometimes make people more likely to talk, but it doesn’t make them more likely to tell the truth. Torture is designed to be particularly stressful and dehumanising, and gives an incredibly strong incentive for the victim to give details. So in the many cases of mistaken identity, or innocence (and the majority of those tortured are never convicted of anything), or people just not knowing answers, they have an incredibly strong incentive to make things up. Genuine, knowledgeable victims may just as easily make things up, and may have prepared a cover story. In cases where widespread governmental torture was expected, such as at the end of the French occupation of Algeria, rebels would be told to name known enemy collaborators as being their allies. The torturer will disregard all claims of innocence, but has no way of establishing whether a suspect is telling the truth. Studies indicate that trained police interrogators are, if anything, actually worse than untrained individuals at telling when real convicted criminals are lying about their crimes, but have higher degrees of confidence in their conclusions. They also have a systematic bias to

assume people guilty when they are actually not.

Proponents of torture have a small series of situations that it has actually produced data for, however to demonstrate its utility, they also have to show that it is better than alternative. Controlled, systematic studies of the efficacy of torture in real situations is limited, for obvious ethical reasons. The only publicly available comparison of torture with non-torture is that by Albert Biderman, looking at the experience of American soldiers captured in the Korean War. Although he discovered that almost all divulged more than the permitted “name, rank, and number”, soldiers were more likely to do so when subject to non-coercive measures. Whereas hurting someone can cause a stiffening of their resistance, creating and exploiting a social bond was generally effective at getting information. This exploitation included ‘interpreting silence as a form of interaction’, that is, asking questions in such as way that not answering them appeared to convey information, as well as seeming rude. Alternatively the North Koreans used frustration, asking questions the Americans couldn’t possibly know the answers to in order to get them talking. This created the impression that the prisoner had ‘broken’, so might as well tell a little more. Violence or threats were less likely to achieve any answers, and vague threats are generally more effective than actual harm.

Torture is not an effective way to extract information from someone who doesn’t want to give it to you. It is a way to dehumanise people you assume to be guilty and to make them parrot back at you whatever you want to hear, and that’s the truth.

“In vino veritas” translates from Latin to “in wine there is truth” - alcohol is the original truth serum

Public Domain

Bill Baloonarm is a 2nd year PhD student researching in Physics

Lent 2015

Perspective

31

Weird and Wonderful A selection of the wackiest research in the world of science Can Conflict Cause New Diseases? although we may think of the main cause of death in war to be the battlefield, wars often claim far more lives due to spread of disease. Indeed, several new diseases have arisen during wars and conflicts over the last 50 years in Central Africa. The majority of these diseases originated in animals and gained the ability to infect, and be transmitted between, humans. This crossover often occurs when humans eat or butcher infected animals.

It is difficult to quantify how many new diseases arise or spread due to conflicts, but there are clearly features of conflict zones which can help a disease become well established in a population. Bush meat has been linked to several new diseases including Ebola, and sales of bush meat often rise during wartime because local control methods to limit sales are lost. Inadequate disease surveillance systems and warning responses in conflict zones can allow new diseases to spread, making them more difficult to contain. Conflict can cause the breakdown of healthcare infrastructure which not only means that some patients are unable to receive treatment, but also that lack of infection control methods in hospitals can cause healthcare workers and uninfected patients to catch the new disease. New diseases arise constantly, but conflicts increase the chances of them infecting humans and becoming endemic. jw

Aquaman? AquaCan! breathing underwater is one of the many superpowers we wished we had as children and, as superpowers go, it’s a lot more realistic than most.

However as our child-like imagination slowly fades, so the ability to breath underwater without the aid of a machine begins to sound increasingly unlikely.

Perfluorocarbons (PFC), molecules which contain only carbon and fluorine atoms, have a unique set of properties . They dissolve large quantities of gases due to weak intermolecular interactions between the molecules and can carry 33-66 ml/100ml O2 and 140-166 ml/100ml CO2, over three and four times greater than the carrying capacity of blood for these gases respectively. Furthermore, Kylstra’s famous 1962 paper “Of Mice as Fish” illustrated how, with training, mice could breathe oxygenated liquid saline at pressures equivalent to a mile beneath

32

Weird and Wonderful

the sea. Clark and Gollan later identified PFCs and silicone oils as additional potential mediums for use breathing underwater. The latter exhibited high toxicity on return to normal air whereas those submerged in PFC survived weeks; the ultimate issue being CO2 removal. A PFC, Perflubron, is currently in FDA clinical trials, being used for the treatment of premature infants. It seems breathing through liquid may no longer be limited to the comic books. aa

How do You Solve a Problem Like Zombie Epidemics? we’ve all been there. That moment when imagine

what we’d do in the event of a zombie epidemic.

We might think to head for the countryside or perhaps towards London.

We may decide to go lone wolf or gather up family and friends. But it’s unlikely we would have considered population dynamics. Luckily, a group from Ottowa did, and proceeded to model several possible scenarios in the event of the zombie apocalypse. Their results are interesting, but perhaps not reassuring.

They found that whilst the fall of humanity could indeed be stopped, it would require aggressive control methods. Quarantine was found to be ineffective unless extreme measures were implemented, a prospect which the authors judged to be unlikely. Similarly, a cure would have some effect but would ultimately result in a small population of the uninfected coexisting with a much larger population of zombies. Only the method of frequent attack with increasing force was determined to eradicate the zombies. The authors also noted that their model assumes the outbreak took place over a short timescale, meaning births and deaths could be ignored. If the outbreak took place over a larger timescale, these births and deaths would provide zombies with a limitless supply of susceptibles to infect and the war against the undead would be lost. Only a quick response would ensure the survival of the human race. So if the dead start to rise, grab your cricket bat and do your part to tilt the mathematics in our favour! ns

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