BlueSci Issue 43 - Michaelmas 2018 by BlueSci

Michaelmas 2018 Issue 43 www.bluesci.co.uk

Cambridge University science magazine

FOCUS Coral Reefs

Human Cell Atlas . Carbon Capture Food Security . Slum Rehabilitation

Your Power for Liquid Handling

Sapphire Pipettes from Greiner Bio-One

for further information or to request a brochure: tel: 01453 825255 email: sales.uk@gbo.com

ARS

Y RANT R A W 3 YEAR

Sapphire the ultimate instruments for liquid handling

www.gbo.com

Join the pioneers Oxford BioMedica is a world leader in gene and cell therapy. With over 20 years’ experience, we were the first organisation to treat humans with in-vivo lentiviral vectors. We aim to change things, to find new ways and weapons to fight debilitating and life-threatening diseases. It’s no small challenge - and every one of us has a part to play.

 A culture with people at its heart

 Highly skilled, focused and friendly people

 Cutting edge

technology in gene and cell therapy

 Amongst the newest

and best laboratories

View opportunities online at: www.oxfordbiomedica.co.uk/careers

Easter 2018 Issue 42

Contents

Cambridge University science magazine

Regulars

Features 6

Can We Predict Volcanic Eruptions?

On The Cover News Reviews

Matthew Gleeson discusses the ways in which we can monitor volcanic activity 8

The Ultimate Tool for Medical Navigation: the Human Cell Atlas

Slum Rehabilitation: Putting the ‘Home’ into ‘Homeostasis’

Striving Towards a Polio-Free World: a Team Effort

Ramit Debnath’s discusses his PhD project on architectural engineering to improve life quality in slums in Mumbai

Alexandra Klein speaks to World Health Organisation’s Darcy Levison about eradicating the polio virus

Electrified Carbon Capture for Singapore: Closing the Carbon Loop Louise Renwick speaks to researchers

FOCUS PROTECTING AND RESTORING OUR CORAL REEFS BlueSci investigates how scientists are regenerating our corals in the International Year of the Reef, with insights from Dr Mark Spalding of Mapping Ocean Wealth

Autonomous Vehicles: Looking at the Road Ahead James Macdonald interviews Professor

The Map of Health: Odra Noel

Weird and Wonderful Quantum Technologies for Precision From codebreaking blunders to magnetoreception, we Measurements Adam Barker discusses the applications

Brexit: a Cause for ConCERN?

Bruno Barton-Singer discusses the future of CERN with Professor Ben Allanach

RIPEning Crops for Global Food Security

Rebecca Rebis discusses the ambitions of RIPE to optimise the photosynthetic capabilities of our crops 26

Dr Chloe Moss speaks to Dr Kerstin Meyer about mapping our cells

behind a new project aiming to convert CO2 into useful chemicals 22

3 4 5

of up-and-coming high-precision quantum technologies

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.org, 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

John Miles and start-up Wayve about the future of autonomous vehicles

Honor Pollard explores science-artist Odra Noel’s Map of Health, which portrays the main causes of death worldwide

bring you the strangest stories from recent literature

President: Alexander Bates ��president@bluesci.co.uk Managing Editor: Laura Nunez-Mulder..................managing-editor@bluesci.co.uk Secretary: Mrittunjoy Majumdar.......................................... enquiries@bluesci.co.uk Treasurer: Atreyi Chakrabarty �� membership@bluesci.co.uk Film Editor: Tanja Fuchsberger �� film@bluesci.co.uk Radio: Emma Werner.....................................................................radio@bluesci.co.uk News Editor: Elsa Loissel ��news@bluesci.co.uk Web Editor: Elsa Loissel....................................................web-editor@bluesci.co.uk Webmaster: Adina Wineman.............................................webmaster@blueci.co.uk Art Editor: Laura Nunez-Mulder, Serene Dhawan.........art-editor@bluesci.co.uk

Contents

Issue 43: Michaelmas 2018 Issue Editor: Hayley Hardstaff Managing Editors: Alex Bates, Laura Nunez-Mulder Second Editors: Alex Bates, Atreyi Chakrabarty, Emma Davies, Isobel Hambleton, Matthew Harris, Hayley Hardstaff , Seán Thór Herron,Victoria Honour, Kashif Katib, Alexandra Klein, Anna Klucnika, Elsa Loissel, Laura Nunez-Mulder, Amelia Sadat, Hannah Thorne, Jenni Westoby, Cara Woods, Bryony Yates Art Editor: Serene Dhawan, Laura NunezMulder News Team: Emma Davies, Eva Pillai, Bryony Yates Reviews: Rachel Fox, Elsa Loissel, Bryony Yates Feature Writers: Adam Barker, Bruno BartonSinger, Ramit Debnath, Matthew Gleeson, Alexandra Klein, James Macdonald, Dr. Chloe Moss, Honor Pollard, Rebecca Rebis, Louise Renwick Focus Team: Hayley Hardstaff Weird and Wonderful: Dr. Joanna-Marie Dear, Victoria Honour Production Team: Alex Bates, Laura NunezMulder, Seán Thór Herron Caption Writer: Alex Bates Copy Editors: Laia Serratosa, Max Wilkinson Advertiser: Christina Turner Illustrators: Alex Bates, Alex Hahn, Hayley Hardstaff, Imogen Harper, Joseph Jones, Richard Johnson, Guosté Kukcinavičiute, Odra Noel, Eva Pillai,Tamsin Saunders, Irene Taptas Cover Image: Carys Boughton 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.

Global Science Globalisation has benefitted science hugely, as it has most other fields and industries, via increased interaction between people. The adjoining of scientific minds around the globe has given rise to a vast array of scientific achievements, advances and projects. In this issue we explore some of these international collaborations—both the small and the large. Ramit Debnath talks about his PhD research into slum rehabilitation housing in Mumbai, whilst Dr. Chloe Moss’s article explores the enormous Human Cell Atlas project, which involves researchers all across the globe striving to ‘map’ human cells. Amazing projects are now working on the most imminent issues facing our ever-expanding global population: Alexandra Klein talks about the continuing efforts of the World Health Organisation to eradicate the global disease of polio and Rebecca Rebis discusses how the RIPE project is trying to improve the photosynthetic efficiency of our food crops to find solutions to food shortages. In addition, Matt Gleeson explores the ways in which we can monitor and predict volcanic activity worldwide. He explains how international collaborations have enabled new research, such as in the case of the previously unmonitored volcano that spans the border between China and the Democratic People’s Republic of Korea. Now that these gateways for global scientific progress are open, it is important to consider what the consequences will be if they are closed again, perhaps via politics or war. Bruno Barton-Singer addresses this issue in his interview with Professor Ben Allanach on the effects Brexit could have on the scientific community of CERN. In this issue’s FOCUS piece, we embrace this year as being the ‘Third International Year of the Reef’, with a huge proportion of corals having been damaged over the last 4 years due to climatic events. We explore some of the multiple independent efforts around the globe attempting to protect and restore coral reefs. These range from more traditional planting methods in Florida to novel reef-patrol robots being built in Australia. We also speak to Dr. Mark Spalding about the Mapping Ocean Wealth project, which is working to place a value on marine ecosystems to provide a comprehensive map for policy and decision-makers around the world. By sharing methodologies and successes through publication and media, these efforts ‘subconsciously’ work together to give a globe striving to increase coral reef coverage. Science itself is largely responsible for the incredible rate of globalisation, by invention of transport and communication technologies and is hence responsible for its own productivity through international collaborations. However, the scientific community must now face the consequences of its own success. Advancements in transport technology have had detrimental effects on our atmosphere and on marine and terrestrial habitats. Louise Renwick writes about the eCO2EP project, which is looking into using excess electricity and carbon dioxide produced in the petrochemical industry for conversion into useful products for other chemical industries. James Macdonald interviews experts in the field of autonomous vehicles, who hope that the technology will help reduce emissions and other negative side effects associated with transport. This is also an example of how globalisation may continue in the future through more efficient technologies. This concept is emphasised in Adam Barker’s article on how future quantum technologies may allow us to measure time, distance, acceleration and even gravity to whole new levels of precision. In our special pavilion feature, Honor Pollard explores Odra Noel’s mesmerising piece of art “The Map of Health” that explores the main diseases that have caused death in different regions of the globe. Odra’s art invites the observer to consider the future of global health as medical advancements continue worldwide. While scientific ideas and knowledge circulate the globe, it is important to consider that not all countries have sufficient resources to practise scientific research, or are limited in the fields of science that they can engage in. This leaves the voices and knowledge of scientists residing in such countries, unheard and unnoticed. This is an issue that must be addressed in order for us to achieve a fully globalised scientific community

Laura Nunez-Mulder 2

Editorial

Michaelmas 2018

Art in the Issue Issue editor and Focus author Hayley Hardstaff turns BlueSci’s lens outwards from Cambridge to the global efforts in science - in particular, the collaboration between international research teams. Carys Boughton’s thoughtful front cover shows a gloved hand placing a glass continent into a rack that has room for different test tubes, and conveys how scientific research has space for multinational cooperation. Carys wanted to “celebrate the variety of contributions that different regions can bring to the table, or the test tube rack”. The Focus showcases an inspiring example; parallel lines of research around the world are sharing information, methodologies, and resources to protect and restore coral reefs. Hayley Hardstaff provides a striking visualisation of coral bleaching, while Richard Johnson illustrates the patrolling robot that protects coral from predators. Elsewhere, illustrators highlight how scientific research strives to benefit humankind, with people at the heart of many works. Tamsin Saunders’ driver relaxes in an automated car while Eva Pillai’s ghostlike crowd wait in goal for the eradication of polio. Near-silhouettes in profile from Guosté Kukcinavičiūtė and Joseph Jones accompany projects that delve deeper into what it means to be human, representing an atlas of cells and a sense of home, respectively. Finally, Irene Taptas’ paper cutting and collage piece shows scientists working hard to hold together a leaf of cogs and chlorophyll; a beautiful illustration of teamwork and innovation Laura Nunez-Mulder Art Editor

You can follow some of our illustrators on instagram at: carysmapix, yeonnah joejonesillustrations, blop_a_gram, irenetaptas_illustration, iscience&iart

News Check out www.bluesci.co.uk, our Facebook page or @BlueSci on Twitter for regular science news and updates

A Bright Future for ‘Three-Person Babies’

Shining New Light on Submarine Quakes

Three years ago, the UK Parliament was the first in the world to approve controversial Mitochondrial Genome Replacement Therapy (MGRT), or “Three-person baby”, techniques. Soon, Singapore and Australia may follow. In Australia, a Senate Committee has recently endorsed its legalisation, whilst Singapore is currently undergoing a review process. MGRT can prevent severe genetic diseases that would otherwise arise due to abnormal mitochondria. Mitochondria are energy-generating sub-cellular structures that contain less than 1% of a human cell’s genes. Mutations in these genes can cause debilitating, even life-threatening, conditions that typically affect energy-intensive tissues such as brain and muscle. Mitochondria are inherited exclusively from the mother. Therefore, by replacing the faulty mitochondria in the mother’s eggs with ones from a non-paternal donor, healthy babies with DNA from three individuals can be produced. The UK gave MGRT the go-ahead in 2015 and the first MGRT babies to be born here are expected later this year. It is the only jurisdiction that explicitly permits MGRT, although it is legal in some countries with more relaxed genetic modification laws. MGRT is distinguished from genetic engineering on the basis that the mitochondrial DNA from the donor is transferred unmodified; the technique has been likened to an organ transplant. For some women, MGRT currently offers the only opportunity to have healthy genetically-related children. However, there are concerns regarding the unknown long-term effects and fears that it paves the way for ‘designer babies’. When the UK legalised MGRT, proponents of the technology hoped that other countries would follow its example. Indeed, these hopes may soon manifest in Singapore and Australia, provided progress is not hindered by the complex social and scientific issues that surround MGRT by

Submarine cables are the unsung heroes of global communication. Around 99% of transoceanic data is trafficked via these underwater fibre optic cables, which currently connect all the world’s continents (excluding Antarctica). In June 2018, Marra and colleagues reported that these cables could also be used to ‘spy’ on planet-wide seismic activity. Most seismic activity is monitored from land-based stations and from a smattering of permanent ocean-bottom stations. However, since over 70% of the Earth is covered by water, many oceanic quakes go undetected. Unfortunately, building and linking up more permanent ocean-floor stations would be highly expensive. So, what if we harnessed the pre-existing network of communication cables criss-crossing the ocean floor, and used them as earthquake sensors? Light from a laser can be shone into one end of the fibre optic cable and the light leaving the other end can be monitored. The optic fibre forms a loop within the cable, such that the light makes a round trip during which any vibrations from the surroundings would warp the path of the laser. Hence, by comparing the wave properties (e.g. phase shift) of the entering and exiting light, local and distant seismic activity can be detected. Additionally, by comparing measurements from two cables following different paths, we can locate the epicentre of these quakes. Sensing the vibrations of seafloor quakes would increase our capacity both to detect and better estimate the origin and magnitude of quakes that have been difficult to pin-point thus far. This will help us further understand the dynamics of the Earth’s interior and improve existing tsunami warning systems. Furthermore, beyond seismic monitoring, these sensors also have the potential to track marine life migration and monitor the underwater noise pollution levels that disrupt it. There may yet be light at the end of the tunnel ep

To Clean the Ocean, Think Like the Ocean: Success for the Big Ocean Clean-Up

To find out more about the impact of plastic pollution in our oceans, see this guide by SLO active: sloactive. com/plastic-pollution

News

At just sixteen years old, Boyan Slat became aware of the increasing amount of plastic waste polluting our oceans and the threat this poses to marine life. He wondered why others thought it impossible to clean. He developed a theory that to catch the plastic, a clean-up system would need to act like plastic. Within two years he had founded The Ocean Clean-Up. This non-profit organisation develops artificial coastlines that use ocean currents, waves and wind as motors to locate, catch and remove ocean plastic. The system consists of a 2km floating pipe of polyethylene, with impermeable screens that drop down into the ocean. Sea life can pass freely underneath the screens but plastic floating on or near the surface accumulates behind them. Each pipe is weighted by an anchor that slows the drift of the artificial coastline, allowing plastic, which is faster-moving, to concentrate within the screens.

In July of this year, five years on from its inception, The Ocean Clean-Up announced the success of their first tow-test. They stated that the system withstood severe storms and ocean currents, as well as various towing manoeuvres. With only minor adjustments needed, the team are proceeding with plans for the deployment of their first fully operational system set to target the Great Pacific Garbage Patch (GPGP). At around three times the size of France and estimated to contain 80,000 tonnes of plastic, the GPGP is the biggest wasteland of our seas. With the goal of deploying 50 pipe systems to the GPGP, the organisation aims to remove half of the Patch’s plastic in just five years. Additionally, they hope that by recycling the collected plastic into branded products, the project will become self-sustaining ed

Michaelmas 2018

Reviews MICROBE WORLD

Sound Experiment - Úna Monaghan and Ita Monaghan

Newnham College, Cambridge 2018

In this sound-art installation produced as part of the international conference Sensing the Sonic, musicians and artists Úna and Ita Monaghan aim to break down the conflict between scientific and creative research through their transformation of a disused fume cupboard in the “Old Labs”, Newnham College, Cambridge (formerly laboratories, now a performance space) into a thought-provoking artwork – and a recording of the work is now available online. Where, until recently, spiders dangled from webs, test tubes now hang suspended. Their emptiness reflects how many disciplines experiment, not with physical samples, but with less tangible ones: thoughts and concepts. The test tubes “float” away from the confined space of the cupboard, for, unlike chemical fumes, responses to art cannot be controlled and, likewise, the consequences of scientific experimentation are often unexpected. The visuals are accompanied by three layers of sound. The first comprises sounds as they are received by two microphones: a “reactant” microphone positioned inside one test tube (which “hears” only the chinking of colliding tubes) and an “observer” outside receiving additional noise from the environment. These are electronically processed to generate the second layer of sound; the third comes from recordings of the set-up. The result is ethereal: the bright, clear ringing of glass intermixed with artificial, alien-like sounds, irregular and echoing. Sound Experiment also features voice extracts from interviews with academics. The context of the research is removed to leave only connecting phrases, highlighting that, despite their disparate subjects, there are many recurring themes in how the interviewees approach experimentation. This unique installation demonstrates how, whether an artist or scientist, we all go about research in the same way: we sample, isolate, investigate, consider, test, expect, combine, define, compare and classify by

“... unlike chemical fumes, responses to art cannot be controlled and, likewise, the consequences of scientific experimentation are often unexpected“

The Immortal Life of Henrietta Lacks - Rebecca Skloot Henrietta Lacks died from cervical cancer in 1951, aged 31. However, a sample of cells from Lacks’ particularly aggressive tumour has continued to divide into the present day. These ‘HeLa’ cells have revolutionised the study of human cells due to the fact they can survive outside the body within cell culture. An estimated 60,000 scientific articles use HeLa cells, which have contributed to development of the polio vaccine, mapping of the human genome and understanding AIDS. In her book, Rebecca Skloot charts the work of scientists who pioneered cell culture alongside the story of Henrietta and the Lacks family. Reading more like a novel than a typical popular science book, The Immortal Life of Henrietta Lacks is gripping. Skloot emphasises how exploitation based on race and class enabled these scientific advances to occur. Lacks was a black woman in the American south, raised in former slave accommodation and treated at a hospital with separate coloured entrances, wards and operating theatres. The cancer cells were taken without Lacks’ knowledge and her family were unaware of their mother’s scientific immortality for decades. Skloot invites you to admire the remarkable achievements of the scientists involved, but forces you to consider the profound impact that the use of HeLa cells has had on the Lacks family rf

Pan 2010

“Skloot emphasises how exploitation based on race and class enabled these scientific advances to occur”

How to Survive a Plague: The Inside Story of How Citizens and Science Tamed AIDS - David France “Both a documentary and a book, How to men being diagnosed with Kaposi’s sarcoma. ‘4H disease’ – for Homosexuals, Hemophiliac, Heroin users and Haitians; gay cancer; Gay-Related Immune Deficiency; the Plague: the disease we know today as AIDS had made its Survive a Plague tells arrival in the United States. For us, the generations that followed, it may be hard to recall a time when HIV was not this story, his story; shaping our sexual lives, or to measure the impact it had on the gay community, and our society as a whole. “Some their stories” The year was 1982, and the Morbidity and Mortality Weekly Report had just reported on 26 homosexual

Deckle Edge 2016

day, there will be people alive on this Earth, that will hear the story that once, there was a terrible disease, and that a brave group of people stood up and fought, and sometimes died, so that other can live, and be free,” once hoped Peter Staley, one of the main players of ACT UP. Both a documentary and a book, How to Survive a Plague tells this story, his story; their stories. From how two activists coined and popularised the concept of ‘safe sex’, to the way non-scientists became biology experts to shape the course of drug development, this book and movie retrace the lives of those who stood up against the disease and the social forces that allowed it to spread el

Michaelmas 2018

Reviews

Can We Predict Volcanic Eruptions? Matthew Gleeson examines why following seismic unrest is important, and how we do it from space THE CASE OF MT. AGUNG

Having begun in 2017, the Mt. Agung's latest eruption has been ongoing up to the time of writing

With an estimated 500 million people at risk from volcanic hazards, improving our ability to forecast volcanic events remains a major scientific objective. For those living near to active or potentially dangerous volcanoes, the ability of local authorities to monitor changes in volcanic behaviour and predict future changes in activity is vitally important. However, despite recent advances in our understanding of volcanic systems and the development of new monitoring techniques, many volcanoes around the world remain unpredictable. In September 2017, the onset of volcanic unrest at Mount Agung Gunung in Bali attracted interest of volcano scientists from around the world. Mt Agung last erupted in 1964 killing over 1000 people. Since this time, the population of Bali has more than doubled, and tourism in the country has greatly expanded. As expected, when the seismicity associated with the volcano started to increase above background levels, the local authorities ordered the evacuation of those living closest to the volcano. As the weeks progressed and earthquake activity remained high, more and more people were forced to leave their homes. By the 13th of October, roughly 138,000 people had left their homes to be temporarily housed in one of 350 locations.

By November, it had been over two months since the volcano’s rumbling began. People might have been forgiven for asking what the hold up was. In the end, Agung erupted at roughly 5:30pm local time on the 25th of November 2017. Since then a series of eruptions have occurred, and are still ongoing at the present day. It is important not to understate the humanitarian crisis that the volcanic unrest has caused. Although there have been no recorded deaths directly as a consequence of the eruption, over 71,000 people remain homeless, and may not be able to return home for months or even years. A similar scenario is currently playing out around Sinabung volcano (Indonesia). Here an ongoing eruption since September 2013 has decimated surrounding farmland and after 5 years there are still over 7000 people without a permanent home. Events such as these highlight the humanitarian crises that may result due to volcanic unrest. However, what if the seismic unrest at the volcano hadn’t led to an eruption? Often shallow intrusions of magma into the Earth’s crust below a volcano (identified by increased number of volcanic earthquakes) may lead to an eruption, but this is not always the case (e.g. the ‘failed eruption’ of Mt Iwate, Japan, in 1998). In addition to the humanitarian crisis already caused by the evacuation of so many people, it is possible that a false alarm may have led to distrust of the authorities, resulting in a far greater number of people remaining within the evacuation zone when the volcano next undergoes a period of unrest and potential eruption. For several weeks it seemed possible that this might have been the case at Agung. Towards the end of October, no activity at the surface had been observed, and the number of seismic events each day started to drop. Was that it? Was this simply a shallow intrusion of magma that may contribute to an eruption not in the next days or weeks, but in several years? For the local authorities in charge these questions would have been nearly impossible to answer with any certainty, especially without detailed information of the seismic activity before previous eruptions. This is a serious issue that everyone involved in hazard risk assessment has to deal with regularly, and reveals the need for better understanding of volcanic systems and pre-eruption warning signs. Michaelmas 2018

NASA EARTH OBSERVATORY

VOLCANIC MONITORING TO THE RESCUE? Over the past few decades our ability to monitor volcanic activity has developed almost beyond recognition. Many of the world’s most active volcanoes are now equipped with a collection of devices designed to detect the slightest change in the volcanoes behaviour. Seismometers, GPS stations and tilt meters track the movement of magma beneath the surface, whilst gas sensors and thermal cameras pick up on any changes in surface activity. All of these instruments are now able to send data back to observatories almost instantly using internet or mobile networks providing a supply of real-time monitoring data. On top of this, the development of satellite-based monitoring means that we are now able to track the movement and emission of even the most remote volcanoes on earth. The Moderate-Resolution Imaging Spectroradiometer aboard NASA’s Earth Observing System (EOS) Terra and Aqua satellites tracks thermal fluctuations, whilst changes in gas flux of sulfur dioxide are monitored by the Ozone Monitoring Instrument aboard the EOS Aura. Additionally, satellite-based Synthetic Aperture Radar Interferometry (InSAR) is increasingly used to track ground displacement due to injection and/or degassing of magma bodies at shallow levels below the Earth’s surface. As a result, we are now able to monitor nearly all volcanic regions worldwide on an almost daily basis, even in regions where previous monitoring efforts were expensive and logistically challenging. Additionally, international collaborations are enabling scientific equipment and techniques to be deployed in regions that have previously been considered too remote or isolated. For example, collaborations between British scientists including Professor Clive Oppenhemier from the University of Cambridge, and local scientists from the Democratic People’s Republic of Korea (DPRK) and China have enabled an unprecedented Michaelmas 2018

deployment of seismic stations around Mt Paektu, a previously understudied large caldera system that borders the DPRK and China. So, with this wealth of information now available it might appear as though we should be able to predict changes in volcanic activity. Unfortunately of course, it isn’t quite that simple. Each volcanic system is inherently different. Some volcanoes repeatedly build lava domes then periodically collapse resulting in highly dangerous fast flowing currents of hot ash and rock fragments, such as Volcan Colima, Mexico. Other volcanoes erupt with great outpourings of low viscosity, and therefore fast flowing, basaltic lava, such as Kilauea volcano in Hawaii. Some volcanoes sit dormant for hundreds to thousands of years before erupting explosively in extremely violent eruption columns that may extend high into the Earth’s stratosphere, resulting in significant consequences for Earth’s climate (e.g. Mt Pinatubo 1991, Philippines). What type of activity is observed at the surface, and transitions between them, depend on the chemical and physical properties of the magmatic system below the surface. In many systems, these remain poorly constrained. Each different volcano has its own unique character and without observations of complete volcanic cycles, it is extremely challenging to determine whether a volcanic system may give several months of warning - like we saw at Mount Agung - or whether eruption may occur with only a couple of hours of warning (e.g. Calbuco 2015 eruption, Chile). Some answers may lie with studies of past volcanic eruptions. Using detailed micro-analysis of individual crystals and trapped pockets of melt within them (melt inclusions - molten magma that has quenched to form a glass on eruption), scientists can provide hugely valuable insights into the inner workings of volcanic systems, especially those without historical eruptions. Studies such as these, combined with satellite observations of recent eruptions, may provide a greater understanding of preeruptive processes in volcanic systems and how these can be identified at the surface in order to provide better forecasting of volcanic hazards. However, despite modern developments in our understanding of volcanic systems and technological advances in monitoring, volcanic systems remain inherently unpredictable. Without detailed historical records of unrest prior to past eruptions - which would allow us to determine a characteristic pattern for a given volcano - it remains incredibly difficult to identify whether changes in a volcanoe's behaviour represents an impending eruption or not

Papua New Guinea’s Manam Volcano, imaged by EOS

Matthew Gleeson is a 3rd year PhD student in Earth Sciences at Jesus College, @MattGleesonGeo. Artwork by Imogen Harper

Can We Predict Volcanic Eruptions?

The Ultimate Medical Exploration: The Human Cell Atlas Dr. Chloe Moss speaks to Dr. Kerstin Meyer about mapping all the cells in our body

How many different cell types are there in the human body? It is a tricky question to answer, because 'cell type' is hard to define, and scientists get different answers if they try to do so anatomically, developmentally or genetically. HCA will use single cell geonomics to cluster like with like, but one difficulty will be dissociating cell type identity from changes in gene expression the same cell type experiences in dfferent states and contexts

We all start life as a single fertilised egg. Then from that single cell, we grow − becoming a unique human composed of trillions of different cells performing a plethora of diverse tasks. So, how did we get from one cell, or zygote, to a walking, talking and thinking human? Each of our cells contain DNA, the genetic code made up of bases (A, G, C and T), which holds the instructions on how to make a human. DNA was first discovered in white blood cells in 1869, by a Swiss chemist called Johannes Friedrich Miescher. Almost a century later, in 1953, Watson and Crick famously discovered the three-dimensional structure of DNA, using crystallographic data collected by Rosalind Franklin and Maurice Wilkins. Another 65 years later and we are now able to precisely sequence the DNA within cells. In the past 20 years, DNA sequencing technologies have advanced exponentially, becoming simultaneously more efficient, precise and inexpensive. DNA sequencing is now arguably one of the most influential techniques of modern day research, having driven countless discoveries, enabling us to learn more about the human body than ever before. A great example of this is the discovery of the BRCA1 and BRCA2 genes. These are tumour suppressor genes infamously associated with hereditary ovarian and breast cancer. Fortunately, thanks to the advances in DNA sequencing, patients can now easily be screened for mutations in these genes, enabling them to take preventative measures to minimise their risk of cancer. Perhaps an even more impressive example of the power of DNA sequencing to date is the Human Genome Project. Completed in 2003, the Human Genome Project was a massive global endeavour to sequence the DNA of the entire human genome − that’s 3 billion bases! Following on from the huge success of the Human Genome Project, the Human Cell Atlas (HCA) project is an equally ambitious global initiative involving scientists across different disciplines from around the world. The HCA project’s goal is to create a complete map of all the cells in the human body; detailing their genetic, proteomic and physical properties. This means deciphering not only the DNA sequence in each individual cell, but the various proteins expressed, the

The Human Cell Atlas

location of cells in the body, how they interact with each other and how they are localised within the body from the developing embryo. By creating a comprehensive atlas of human cells from people of different ages, different ethnic backgrounds and with various diseases, the goal is to develop a powerful tool for understanding and treating human health and disease across the globe. The HCA project launched 18 months ago when Dr Sarah Teichmann (Cambridge, UK) joined forces with Professor Aviv Regev (MIT and Harvard, USA) with the idea to create a map of the various different cell types found in the human body. The project involves scientists from across the globe, with many based in the UK playing a pivotal role in the research. So why are scientists only just doing this now? Dr Kerstin Meyer, scientific lead of the HCA project at the Wellcome Sanger Institute near Cambridge, says that the timing of this project is largely attributed to the advances in single-cell technology. Single-cell sequencing is a technology that allows us to read the DNA sequence from individual cells, rather than averaging over hundreds of thousands of cells, which is how DNA has traditionally been sequenced. “We are now able to, in principle, sequence up to one million individual cells in parallel…[thanks to the] huge development in technologies over the past 5 to 10 years…making this project both practically feasible and affordable.” In short, the rapid advances in technology mean that we are now able to create a much more detailed picture of cells than has ever been possible before. Cost is an important consideration with such a big endeavour. The scale of this project is massive and therefore expensive. “By utilising expertise from many different institutes around the world we can harness multiple funding streams...and avoid redundancy of research by coordinating the scientific research strategy across the board” says Meyer. “The international collaboration is critical to the success of the project.” Most remarkable of all is that all the data collected by the HCA consortium will be publicly available. Contrary to traditional academic practice whereby results and data remain confidential until they are published, the HCA consortium believes that the key to success is in sharing their progress worldwide. “We want to avoid the Michaelmas 2018

scenario where groups hide away their data in a little drawer until they publish…by sharing the data you can accelerate the discovery process,” says Meyer. It is the vision of the scientists involved that the data that comes from this project will be available to everybody and anybody who wants to access it. Of course, data is the bread and butter of the HCA project. With hundreds of different cell types in the human body, trying to collect and analyse data about the different features of all our cells is a huge and complex challenge. More than ever before, large-scale biological projects such as this require the expertise of bioinformaticians, statisticians, computer scientists and mathematicians to turn complex data into meaningful results. It is for this reason that the project involves Michaelmas 2018

experts from all fields, from across the world including countries such as the US, Germany, Israel, Australia and India. It is this multidisciplinary, multi-national collaboration that is key to the success of the HCA. The HCA is an innovative project that is sure to have a huge impact on our knowledge and understanding of the human body. The exciting thing about this project, as Meyer puts it, is that “we do not yet know what we are going to find.” In the short-term, it is predicted that the study will provide key insights into many common diseases, as well as helping to map complex networks such as the immune system. However, in the long term, the possibilities are endless. It is not hard to see that the HCA project could be able take us into deeper into the realms of personalised medicine. “If you can map the cells of the human body, you can tailor therapy much more directly,” claims Meyer. Imagine going to the pharmacist with a prescription specifically tailored to you based on your genetics and cellular ‘type’, rather than relying on a one-fits-all approach. This is certainly something worth getting excited about and has the potential to revolutionise modern healthcare. The HCA is a brilliant example of the power of international collaboration and let’s hope that this collaborative and open access approach will pave the way for the future of science in the UK and abroad

HCA will have to receive terabytes of data on billions of cells that might comprise thousands of cell types, generated by hundreds of laboratories world wide, standardise that data and organise and share it with the scientific community

Dr. Chloe Moss is a postdoctoral research associate of the Balasubramanian group within the Department of Chemistry @chloe_moss3, more with @humancellatlas. Artwork by Guosté Kukcinavičiūtė

The Human Cell Atlas

Slum Rehabilitation: Putting the ‘Home’ into ‘Homeostasis’ Ramit Debnath disucsses his research on the shortcomings of slum rehabilitation projects in Mumbai

An image captured through our infrared temperature sensors is shown below indicating the indoor temperature in the kitchen in one of Rabit's surveyed houses

Have you ever wondered how it feels to live in a 15 square meter room with six other family members, in dilapidated conditions, potentially for the rest of your life? This is the everyday reality for over half of the 19 million residents of Mumbai, India, who live in slums and government-assigned ‘slum rehabilitation housing’. Such housing offers at most a single room - which functions as the kitchen, bedroom, living room and the playroom - with an attached bathroom. The government employs these rehabilitation housing schemes to eradicate slums in rapidly urbanising cities like Mumbai. However, the schemes cause as many problems as they purport to solve. Without proper ventilation and access to daylight, the ‘shoe-box’ housing design leads to chronic illness and affects general well-being of the occupants. A 2018 investigation by the Indian Institute of Technology, Bombay showed that people living in the lower floors of low-income tenement houses in Mumbai have higher healthcare-seeking activity due to lack of fresh air. A lack of governmental guidelines permits faulty urban design, such as narrow gaps between buildings that restrict active air exchanges, leading to increased indoor air pollution. The phenomenon of poor design harming public health is common in the developing world, especially in areas where a significant portion of the population depends heavily on government welfare schemes. However, the poor urban design of the housing is not the only issue: the schemes are planned without regard for the socio-economic and cultural contexts of the people living in the slums. Rehabilitated occupants often choose to move back to their original slums, making the entire slum rehabilitation process highly inefficient. Why? So far, my research team and I at the Centre for Sustainable Development - part of the University of Cambridge’s Department of Engineering

Slum Rehabilitation

- have found multiple reasons to explain why people return to the slums. For example, high upfront costs of household appliances cause economic distress. Moving to governmentsponsored housing is a climb up the social ladder, and occupants buy expensive appliances like television sets, laptop computers, refrigerators and washing machines, to meet social expectations. Additionally, the poor quality of houses themselves causes distress. Poor design contributes to uncomfortable temperatures and social isolation in addition to poor indoor air quality. A lack of communal spaces causes occupants to feel lonelier and more anxious and drives them to find community back in their original slums. The problems of rehabilitation housing need solutions that meet the socio-cultural and architectural needs of the occupants. The Global Energy Nexus for Urban Settlements (GENUS), for example, adopts an interdisciplinary approach - mixing engineering principles with social sciences and urban planning. Researchers across four primary departments - geography, engineering, architecture and business studies - bring ideas and methods from their different disciplines to investigate household energy usage across different social classes and its impact on shaping the process of urbanisation and the well-being of citizens in developing countries. The team of researchers include prominent figures from the Indian Institute of Technology Bombay in Mumbai, the Indian Institute for Human Settlement in Bangalore, and the University of Cape Town, South Africa. GENUS provides an active collaborative environment to exchange expertise and derive innovative solutions to real-life problems including slum rehabilitation and even poverty eradication in developing countries. In collaboration with the Indian Institute of Technology, Bombay, and with the scholarship from the Gates-Cambridge Trust, I am investigating why slum rehabilitation projects in Mumbai are ineffective, focusing on factors that cause discomfort or distress. This discomfort and distress, which include the examples of financial strain, poor health, and social isolation, need to be understood through an interdisciplinary approach of architecture, urban planning, economics, psychology and engineering. The concept of ‘homeostasis’ from biological sciences helps to identify causes of discomfort Michaelmas 2018

or distress. In the context of housing, homeostasis refers to the neutral state of occupantâ&#x20AC;&#x2122;s comfort in their environment. My team and I hypothesised that achieving homeostasis will improve quality of life and foster sustainable development for the occupants living in slum rehabilitation housing. However, the factors that contribute to this state of comfort in real-life situations for slum housing are still unknown. We have the slum rehabilitation housing complexes in Mumbai as our living laboratory. We started carrying out surveys and talking to the local people of the slum rehabilitation housing in Mumbai. We asked them why they feel discomfort or distress in their current living arrangements and if they think that is a cause for the ineffectiveness of the slum rehabilitation process. We are also installing environmental sensors in those households in order to understand the status of indoor air quality, temperature and humidity levels. It is important to measure these parameters to understand the root-cause of the conditions inside the slum rehabilitation housing. Data from these sensors has helped us in deriving accurate computer models of the conditions inside the slum rehabilitation houses, which has given us the flexibility to simulate an entire neighbourhood of these areas. Such modelling requires significant interdisciplinary knowledge of urban design, scientific computing, engineering and human comfort, and we are collaborating through interdisciplinary groups like GENUS to progress in our research. I feel that talking to local people and understanding their attitude and emotions associated with their built environment in the slums is the most exciting part of the research. We adopted a working-backward methodology called â&#x20AC;&#x2DC;backcastingâ&#x20AC;&#x2122; for conducting our surveys. Such backcasting methodology is widely used in energy and water policy research to derive countermeasures of possible undesirable events of future. It aids in improving the resilience of a system. In our research, we work backwards through interviews and informal discussions on deriving solutions for a better quality of life in the slum rehabilitation housing. For example, we asked the occupants regarding their preferred solutions for improving the indoor air quality in their houses. Most of them responded that installing an exhaust fan would improve quality, however, they were more concerned about the associated rise in their monthly electricity bills and the maintenance of the fan. Therefore, working with the local people showed that a simple solution, such as an exhaust fan, could solve one of their problems, but it would add to their economic distress via higher electricity bills. Such findings defined the next steps of our research to investigate the cause of economic distress through the lens of people and their practices in their households. Until now, researchers have studied discomfort or distress in occupants' surroundings based on the fundamental theories of human thermal comfort. Our interdisciplinary approach expands on this theory by integrating principles from urban design, social practise theory, and public health. I hope that our efforts will redefine sustainable urban planning for lowincome settlements - and, ultimately, provide better homes Michaelmas 2018

for people who have been subjected to poorly-designed housing. Solutions to such real-life problems cannot be simulated in the lab - rather, solutions will come from fieldwork and collaboration. This is the real power of such an interdisciplinary approach Ramit Debnath is an MPhil in Engineering for Sustainable Development and is currently working on his PhD as a Gates Scholar @RamitDebnath. Artwork by Joseph Jones, photographs courtesy of Ramit Debnath

Narrow gaps between the buildings restrict active air exchanges, leading to increased indoor air pollution

Slum Rehabilitation

Towards a Polio-Free World: a Team Effort

Alexandra Klein speaks to World Health Organisation’s Darcy Levison about eradicating the polio virus

Polio can cause muslce weakness and eventually an inability to move. From the muscle weakness stage, 2-5% of children, and 1530% of adults, di. 70% of infected individuals do not manifest symptoms

The end is in sight. One hundred years ago, poliomyelitis epidemics reigned freely, spreading through cities every summer and leaving behind thousands of paralysed children. It was parents’ greatest fear, and with no cure or prevention, every child was at risk. Now, finally, complete eradication of polio worldwide is closer than ever. The infection is caused by one of three different types of poliovirus, which can be transmitted through human contact and by contact with contaminated faeces or secretions. The polio virus only causes mild symptoms or is asymptotic in most children. However, in around 1 in 200 children it infects, the virus enters the bloodstream and invades nerve cells, permanently damaging muscle and causing permanent paralysis. The tendency of the disease to weaken muscles,

Towards a Polio-Free World

left behind thousands of children with this characteristic paralysis; a painful reminder of the power of the virus. The 1916 epidemic in New York is just one example of the total panic and fear that polio provoked. Children were encouraged to stay at home and warned against drinking public water. Thousands abandoned the city to stay in nearby mountain resorts. Sheriffs of nearby towns patrolled the roads with shotguns, sending back all cars that tried to enter with young children. Myths and paranoia abounded–upon suspecting that cats were spreading the disease, more than 70,000 were caught and killed. By the end of the summer, over 27,000 people across America were reported to have been paralysed, with 6,000 deaths. The race was on for scientists to develop a vaccine or treatment. Michaelmas 2018

The turning point came in 1955, with Jonas Salk’s development of an inactivated poliovirus vaccine. This vaccine was then used in the largest medical experiment in history to test its efficacy and was found to be safe and effective to protect children against the virus. As soon as Salk’s vaccine was licensed, mass vaccination campaigns began and polio was near-eradicated in industrialised countries. However, by the 1970s, Rotary International (an international service organisation) had recognised polio as a significant health concern in developing countries. Routine immunisation began to be introduced worldwide, using the newly developed oral polio vaccine by Albert Sabin. In many countries today, the thought of polio conjures up images of an insignificant disease, known only from the pages of a history textbook. To some extent this is true: polio cases have decreased by over 99.9% since 1988, with only three countries in the world that have never stopped polio transmission–Pakistan, Afghanistan and Nigeria. Yet many people do not realise the grave consequences of even a single poliovirus remaining. If eradication activities were to stop, it is predicted that within ten years, there could be upwards of 200,000 cases of paralysis every year worldwide, with thousands of deaths. The huge decrease in cases is due to the commitment made by the World Health Organisation in 1988 to achieve worldwide eradication of polio by the year 2000. This launched the Global Polio Eradication Initiative (GPEI), a campaign involving national governments and four major partners. Darcy Levison works at the heart of the GPEI, as a Communications Consultant at the World Health Organization in Geneva, Switzerland. On a daily basis she is involved in communicating the programme to the public and ensuring the co-ordination of the major partners. So what motivates her? “Disease eradication is one of the most sustainable and equitable interventions that we can make in public health. Everyone benefits from it, no matter where they live, and all future generations benefit from it. But that doesn’t mean that it is easy to do,” Darcy tells me. Initially it seemed that with the effective and cheap vaccine, poliovirus eradication would be achievable within a few years of setting the goal. The GPEI has been central to setting these targets by helping to co-ordinate worldwide, organised vaccination drives. However, there have been many obstacles; conflict, inaccessible communities, political instability and poor infrastructure all combine to make mass vaccination a challenging prospect. The virus also does not often present itself in a visible way, unlike smallpox, which showed symptoms in every person infected. All of this has combined to make the goal of eradication by the year 2000 unachievable. The initiative has instead focused on identifying polio as quickly as possible. So how does the programme work to detect the virus? “We have the largest environmental surveillance network ever seen in public health. We have established community-based reporting systems for suspected cases of polio paralysis, using local relationships and sometimes mobile phone applications,” says Darcy. “Hospitals worldwide are also engaged in our effort and alert Michaelmas 2018

us if any child with suspected polio is brought in. When we hear of a potential case, we work to ensure that every child is seen by health workers within 48 hours, wherever they live, from mountain passes to tower blocks, to desert.” The challenge of reaching children with suspected polio, as well as providing adequate vaccination in countries with difficult terrain or conflict zones, has been a major obstacle. The programme has developed expertise and is now well prepared to tackle conflict zones. Vaccination teams are able to enter areas as soon as they are stable enough and vaccinate all children who might have missed out on vaccine doses. A remarkable instance of this was in January, when the polio programme was one of the first to enter and vaccinate children in Raqqa, Syria, since the city was released from opposition control. Children there hadn’t been reached with vaccination services since 2016. The success of the programme has been mostly due to the global co-ordination of governments, GPEI partners, Rotarians, local leaders and volunteers. Darcy tells me more about the vast networks set up to facilitate mass vaccination. “To get to this point has taken an incredible effort from millions of people worldwide–from Sabin and Salk, the developers of the two types of polio vaccine, who refused to patent their discoveries, thus opening up low cost vaccination to all, to the Rotarians who first proposed eradication, to the thousands of community health workers who knock on doors month after month, year after year, to ensure that every child is vaccinated. The programme works with diverse sets of people–from nomads, to internally displaced people fleeing violence, to traders, farmers, people living in remote locations, and people living in cities. Every year, we vaccinate over 450 million children worldwide. My colleagues in endemic and outbreak affected countries coordinate an eradication strategy that weaves together the numerous different cultural practices, languages, perceptions and day to day routines that people have, in order to reach all children with two drops of vaccine.” Darcy finishes by telling me, “Polio eradication is hard, and the virus is tenacious, but we are closer than ever to succeeding in our mission to eradicate wild poliovirus. In 2017, there were only 22 cases detected anywhere worldwide, out of over 100,000 suspected polio cases investigated.” I come away from our conversation feeling inspired. The eradication of any disease requires international co-operation, yet polio in particular, presents many unique and demanding challenges. The Global Polio Eradication Initiative has tackled the challenge head on and has achieved promising results, giving hope that two decades later than predicted, the world will finally see successful polio eradication. It’s easy to feel disillusioned with all of the disappointing situations in current global politics, but at least there is hope provided by a concrete project working to make children equal in one fundamental respect

“Hospitals worldwide are also engaged in our effort and alert us if any child with suspected polio is brought in. When we hear of a potential case, we work to ensure that every child is seen by health workers within 48 hours, wherever they live, from mountain passes to tower blocks, to desert”

Alexandra Klein is a Master's student in Biochemistry at St John's College, more with @EndPolioNow, @UNICEFPolio, @MichelZaffran, @gateshealth, @CDCGloba. Artwork by Eva Pillai Towards a Polio-Free World

Electrified Carbon Capture: Closing the Carbon Loop in Singapore Louise Renwick speaks to researchers behind a new project aiming to convert CO2 into useful chemicals

Carbon dioxide could be converted into ethylene, used to make polyethylene based plastics, and 1-propanol, which is widley used as a solvent in the pharmaceutical industry

There is no doubt that the overabundance of carbon dioxide in the atmosphere is causing us problems. Every day we hear new stories about extreme weather, ecosystem collapse and rising mortality rates, all of which have been clearly linked to increasing levels of atmospheric carbon. As the world begins to grapple with the scale of the transformation needed to reverse climate change, two things become very clear – we need new technology and we need it quickly. Collaboration between universities and across national boundaries plays a vital role in this developmental process. The University of Cambridge is at the forefront of addressing these environmental challenges through collaborative research with their first international outpost, the Cambridge Centre for Advanced Research and Education in Singapore (CARES). CARES has been created to improve the efficiency of Singapore’s thriving chemical industry and is one of several research entities set up under the Singapore Prime Minister’s Office Campus for Research Excellence and Technological Enterprise (CREATE) programme. This programme includes other internationally renowned universities such as the Massachusetts Institute of Technology and University of California, Berkeley. All of these entities within CREATE are partnerships with the two leading universities in Singapore (National University of Singapore and Nanyang Technological University, ranked first and fifth respectively in the Times Higher Education Asia University Rankings 2018). CREATE’s unique setup provides a platform for world-leading researchers to combine their expertise and develop solutions to pressing issues, environmental and otherwise. Projects within CARES aim to decarbonise the chemical industry using a range of technologies such as catalysts, electrochemical reactors, carbon capture and waste heat utilisation. CARES has now joined forces with the University of California, Berkeley and the two Singapore-based universities to tackle the issue of carbon dioxide waste from petroleum refineries and chemical plants, in an international project titled eCO2EP. In Singapore, many of the chemical plants slightly oversupply electricity to ensure that everything functions smoothly. When electricity requirements suddenly drop, some of this electrical energy is no longer required and is usually converted to waste heat. The aim is to produce a compact electrochemical device that uses this excess to convert carbon dioxide into other molecules widely used in the chemical industry. This device will act as a testing station, for studying the viability of large-scale carbon dioxide reduction processes.

Electrified Carbon Capture

The technology used in the eCO2EP project works by using nature’s mechanism for converting carbon dioxide to plant biomass, but uses advanced materials and new reactor designs to scale and speed up the process. The research group has already developed an effective reactor device that makes use of nanostructured electrodes called nanocoral, a copper and silver electrocatalyst with a large surface area to maximise the reaction efficiency. Excess electricity taken from the chemical plant helps to split carbon dioxide into carbon monoxide on the silver surface. The carbon monoxide is then passed onto the copper surface of the nanocoral to create alcohol and useful hydrocarbon gases. These products can be fed back into other plant processes, reducing environmental and financial costs. The eCO2EP project is led by University of Cambridge Professor Alexei Lapkin and his counterpart from the University of California, Berkeley, Professor Joel Ager. “This is a highly exciting project. We can address the problem of excess environmental carbon dioxide starting from the fundamental theory of reactivity of carbon dioxide on copper catalysts, and take it all the way to developing a mini-plant that demonstrates the technology. This is a feature of CREATE projects – large, interdisciplinary and sufficiently flexible projects that allow us to combine great teams of researchers and make a real difference,” Professor Lapkin said. The work of eCO2EP also stands out from other research because it focuses on the subsequent separation of the desired product after the reaction has taken place. Usually in this type of reaction, the product remains dissolved in water or even mixed up with the carbon dioxide gas. The team is now working on solving the separation challenge, which would be a huge step forward and pave the way for increasingly efficient carbon reduction technologies. Singapore is the ideal place to implement these ideas. It is one of the world’s top five oil-refining centres and home to Jurong Island, a 32 km2 artificial island covered with petroleum refineries and other chemical plants. With this thriving industry comes a large carbon dioxide output, which is predicted to increase to 60% of Singapore’s total by 2020. To address these and other sustainability challenges, the Singapore government is making strong contributions to science and technology; investing $3.8 billion (£2.08 billion) into research, innovation and enterprise each year. Being a small island state, Singapore is limited in the type of carbon reduction it can undertake. Traditional carbon capture and storage relies on having available land in which to store Michaelmas 2018

captured carbon dioxide. In Singapore there is simply not enough space. By working with Singapore’s petrochemical plants, eCO2EP researchers can apply their ideas and models to real-life chemical scenarios and make use of carbon dioxide instead of storing it away. Professor Ager notes that the aim of eCO2EP is not to undermine the refineries’ production methods by reducing their harmful emissions at the cost of their product output. Rather, the technology should work with existing processes, making them more efficient and adding value by capturing and using the carbon dioxide that would otherwise be released as a waste product. “In a synergistic fashion, we’d like to use their excess electricity capacity and carbon dioxide with our process to make ethanol, ethylene, and propanol. This will make their chemical plant more efficient in a way that won’t add to the energy cost of operating it. If this works, this gives us a foothold to start accelerating the investment to really develop the technology.” This electrochemical conversion of carbon dioxide using excess electricity also has potential as a sustainable, hybrid system – one that will use this spare energy when it is available, but can switch to other sources, perhaps renewable ones, when necessary to maintain functionality. This concept is not only relevant to Singapore; the outcomes of the eCO2EP project will be readily applicable globally and will complement the move towards sustainable energy solutions. If technology like this is to be adopted worldwide, crossborder collaboration is key. According to Professor Ager, the international nature of eCO2EP has been instrumental in developing the project so quickly. “We have been able

to harness the four institutions involved and put all the researchers in a single space. With the whole research team together in the labs and CREATE working on this, we can be quite ambitious. I think that is a remarkable aspect of this type of international project. We have a multi-disciplinary team and we’ve chosen people who have complementary expertise.” The eCO2EP project kicked off in January 2018 and is making good progress. From here, their focus will be on scaling up the technology and increasing the speed and intensity of the chemical conversion. Commercial viability is important for the technology to be readily adopted by carbon dioxide-producing companies and to make a real difference to their emissions output. Other priorities are to maintain minimal environmental impact over the entire process and to ensure that the project is both financially and technically feasible. Before too long, the researchers hope to see their devices being used around the world, ideally with renewable energy sources, to reduce air pollution. There is no quick fix for our excess carbon dioxide emissions, but working together to transform this waste into something more useful is certainly a start Louise Renwick is the Communications Executive for the Cambridge Centre for Advanced Research and Education in Singapore (CARES). Artwork by Eva Pillai

“...we’d like to use their excess electricity capacity and carbon dioxide with our process to make ethanol, ethylene, and propanol. This will make their chemical plant more efficient in a way that won’t add to the energy cost of operating it”

Around the Globe: Protecting and Restoring our Coral Reefs Hayley Hardstaff investigates how scientists are regenerating our corals in the International Year of the Reef, with insights from Dr Mark Spalding of Mapping Ocean Wealth C oral reefs are one of the most diverse ecosystems on the planetâ&#x20AC;&#x201D;and they are under threat. Reefs provide great services to marine and human species alike. However, over the past three decades, coral reefs have suffered immense damage from climatic changes and from human activity on both land and sea. Nowâ&#x20AC;&#x201D;in the third International Year of the Reefâ&#x20AC;&#x201D;scientists around the world are working to protect and restore our corals. The solutions are diverse: from traditional growing and planting techniques to highly innovative robot patrollers and water

surface biofilms. Vitally, the success of coral restoration depends on collaboration across borders: sharing information, methods, and resources. The International Coral Reef Initiative declared 2018 the third International Year of the Reef, following pioneering efforts in 1997 and 2008 to increase global awareness of the importance of, and threats to, coral reefs. In previous years, this project linked up with 225 organisations across 65 countries to identify sustainable coral reef management strategies, and to implement them by uniting governments,

FOCUS Mechanism of coral bleaching |

Corals are built from hundreds of coral polyps. Polyps form from free-swimming coral larvae that anchor themselves upon a solid substrate such as rock or other corals. Polyps are soft bodied organisms that secrete hard outer skeletons of calcium carbonate or limestone for protection. These hard reef-building corals (called scleractinia) are composed of polyps that are in a continuous cycle of growing, dying and regenerating—a cycle that builds the reef skeleton upon which other corals can grow. Hard coral polyps and colonies require a large amount of energy to grow, particularly for exuding their stony skeleton. To obtain the energy for growth, corals rely heavily on colourful algae called zooxanthellae that live within their tissues. Zooxanthellae photosynthesise to produce their energy, sugars, and nutrients. Up to 95% of the nutrients produced by the zooxanthellae leak into the host coral cells. In exchange, the zooxanthellae receive shelter and protection within the coral cells, which allows the algae to exist in higher concentrations. Due to this exchange of resource (nutrients) for service (protection) that benefits both the coral and zooxanthellae, the algal-coral relationship is described as mutualistic symbiosis. Though corals also feed on zooplankton, they are so heavily dependent on their zooxanthellae as a main energy source that if kept in darkness (so that their zooxanthellae can’t photosynthesise) most corals will die within a few months. Therefore, coral bleaching is catastrophic for coral health. Coral bleaching is the process of coral polyps expelling their colourful zooxanthellae. Bleaching is induced by numerous stresses including increased water temperatures and pH associated with climate change. Other stressors that can cause bleaching include solar irradiance, sudden exposure to lower water temperatures, exposure to the air on rare Coral reefs are home to around 25% of all marine life, despite composing far less than 1% of the total sea floor area. As well as providing habitat and shelter for species, reefs are involved in reducing coastal erosion, and fixing carbon and nitrogen: roles that reduce atmospheric carbon dioxide and are essential in nutrient recycling— dispersing nutrients throughout the ecosystem.The reefs act as nurseries for many fish species, so the fishing industry is fundamentally reliant on these ecosystems. Humans also glean enormous economic benefit from reefs in the form of tourism; the Great Barrier Reef generates around 1.5 billion dollars annually for the Australian economy. It is estimated that around 800 Michaelmas 2018

extreme low tides, dilution of the surrounding seawater with fresh water (from rain or run-off), and exposure to high concentrations of pollutants. The cellular mechanism of coral bleaching has been associated with oxidative stress. High temperatures and irradiance disrupt zooxanthellae photosynthesis, leading to the production of reactive oxygen species (ROS). ROS from the zooxanthellae, alongside stress-induced elevation of ROS levels within the host coral cell, may activate the host coral’s bleaching response to expel the zooxanthellae—perhaps an innate immune response. When a symbiont is compromised, expelling it increases the chance of the host coral recruiting a new alga of a different ancestry or clade, which may perhaps be more stress-resistant, improving the coral’s chance of survival. However, this is only successful if a suitably resistant clade of zooxanthellae happens to be present in the ecosystem. million people worldwide have some level of dependency on coral reefs. In recent years, however, water temperatures have become too warm for corals, causing coral bleaching. Corals turn ghostly white when polyps, the building-blocks of coral, expel their colourful algal symbionts, called zooxanthellae. The bleaching is a response not only to temperature changes, but also to other stressors such as changes in nutrient or light conditions. Between 2014 and 2017, an El Niño event—a series of complex climatic changes that lead to unusually warm and nutrient poor waters off northern South America—sparked a Focus

FOCUS

El Niño | The El Niño Southern Oscillation is

a climate phenomenon that fluctuates periodically between three states: the cooling phase (La Niña), the warming phase (El Niño), and neutral. The mechanisms underlying the initiation and periodicity of the phases remain under study and ambiguous. El Niño (warming) events are thought to have been happening for thousands of years and each episode lasts for between nine months and two years. El Niño is characterised by a warm pool of ocean water in the central and eastern equatorial Pacific and corresponding changes in air pressure. The events lead to droughts and changes in ocean nutrients, which most commonly affect agricultural and fishing communities living on the Pacific coast of South American countries such as Peru. No direct links between global warming and the intensity or frequency of El Niño episodes have been demonstrated thus far but research continues to investigate the possibility. However, El Niño cycles are clearly linked to mass coral bleaching events. Mass bleaching occurs in response to localized and short-term periods of increased sea temperatures. The recent El Niño conditions, which impacted an estimated 70% of the word’s coral reefs between 2013 and 2017, included areas of reef that had never bleached before. It is currently the most widespread and longest coral bleaching event on record. This mass bleaching event was thought to be so catastrophic due to the combination of El Niño conditions with global warming, which sent warm waters across the tropics, followed by an La Niña event. Experts worry that the reefs may not have long to recover before the next El Niño rears its head.

catastrophic three-year coral bleaching event impacting 70% of the world’s reefs according to the National Oceanic and Atmospheric Administration’s coral reef watch. The catastrophic bleaching episode is now believed to have ended, but many other threats remain. One of the threats is climate change, which not only increases surface water temperatures, but in addition causes ocean acidification and increased frequency of tropical storms, both of which damage the calcium carbonate reef skeleton. Pollutant and nutrient run-offs from land also severely affect reef ecosystems; polluted sediments can smother corals, and nutrients can increase the presence of organisms that prey on coral polyps—such as the crown-of-thorns starfish—and drive algal blooms on the surface, which block light for the photosynthesising zooxanthellae living in coral polyps below. Overfishing of larger fish species can lead to similar changes in the food chain. Other 18

Focus

forms of boat activity and unsustainable fishing practices, too, have drastic effects: anchors and trawling equipment rip through reefs. Coastal development also damages reefs in this way—for example, by dredging new marine traffic channels for maritime ports. Considering the diverse variety of ways and places in which corals are threatened, diverse strategies are needed to protect the future of coral reefs. One such strategy, developed by the Mote Marine Laboratory and Aquarium in Florida, is the micro-fragmentation and fusion method for restoring corals. Mote researchers rescue damaged coral fragments from over 20 species, including brain, boulder and star corals, which are renowned for slow growth in the wild. Fragments of 1-3cm² are spaced evenly over ceramic tiles in tanks where their growth rates can be monitored and optimised. Then, the team plants suitable fragments in the wild so that they grow and spread until each fragment fuses. They have so far planted over 20,000 corals onto depleted reefs across Florida Keys. While the micro-fragmentation and fusion method relies on asexual reproduction (coral cloning), other countries are basing their planting efforts on sexual reproduction. In the Philippines and on the Great Barrier Reef, scientists use larval reseeding to restore reefs. Larval reseeding traditionally involves collecting coral gametes (sperm and eggs) during large-scale spawning events and releasing the resulting larvae back into the ocean under underwater mesh tents. This has an advantage over asexual fragmentation methods as it increases the corals’ genetic diversity, creating increased potential for coral adaptation to changing environmental conditions. In the UK, the Horniman Aquarium has also been using sexual reproduction as a technique of coral restoration. However, instead of collecting gametes from spawning events in the oceans, the team has managed to simulate the environmental conditions for coral spawning within carefully controlled closed-system aquariums. By replicating temperature, lunar and migration cycles found in real coral environments, the scientists can now accurately predict and induce coral spawning in their laboratory. These captive corals then undergo in vitro fertilisation. This breakthrough means that laboratories around the globe can use the Horniman Aquarium’s protocols to rapidly increase coral reproductive rates in vitro for much more efficient restoration of coral reefs via planting. As well as working to restore reefs, some countries are acting to prevent further damage. Hawaii is pushing towards banning sunscreen that contains the two UV filtering chemicals oxybenzone and octinoxate, which are thought to stunt growth of baby corals and even kill some coral species. Studies have also suggested that oxybenzone may cause coral bleaching. In places such as Hawaii where coral tourism is booming, something as innocuous as sunscreen is a formidable threat.

Michaelmas 2017

To protect the Great Barrier Reef from further damage, researchers from Queensland University of T-echnology and the Great Barrier Reef Foundation are designing and testing an artificially intelligent underwater robot patroller. In the most recent tests, it successfully identified its target—the crown-of-thorns starfish—99.4% of the time, which it kills by lethal bile-salt injection.The robot is also able to monitor reef health indicators such as coral bleaching and water quality, as well as provide an underwater map of the reef.The “RangerBot” will be available at an affordable cost to reef-reliant communities around the world in the near future. Another innovative method for protecting the coral that has been trialled by the Great Barrier Reef Foundation is the use of one-molecule-thick biofilms on the water surface. Testing this biodegradable film in sea simulator tanks has reduced light penetration by 30% via light scattering. Partially reducing light penetration limits the heat stress and reactive oxygen species induced in corals by high solar irradiance, hence reducing coral bleaching in most species. The biofilms need further Michaelmas 2018

trialling before being applied to the ocean, but look to be a promising way of protecting corals in the most vulnerable areas of the reefs. These numerous independent efforts across the globe all summate into one large united effort to save the world’s coral reefs; an effort that is given more power by sharing of information and technologies across research groups and communities. Even small communities in developing countries, who may not possess the funding or resources to carry out such research themselves, can utilise methodologies developed elsewhere to protect the reefs local to them. According to the Ocean Agency, over half the world’s corals have died in the last thirty years. There is now hope that the global scientific community can work together to restore these essential ecosystems. In the words of the International Coral Reef Initiative, “Coral reefs are in crisis—they could disappear on our watch and potentially within in our lifetime. It’s not too late— together, we can solve this crisis.”

Focus

FOCUS

Dr Mark Spalding is the global science lead of Mapping Ocean Wealth and an honorary research fellow of the Department of Zoology, Cambridge, based at the University of Siena, Italy

Focus

The Mapping Ocean Wealth (MOW) project is a global collaboration of scientists, policy practitioners, and financial advisors that was launched in June 2014 by the Nature Conservancy. Their mission is to provide scientific information in an accessible format to policy makers on all governmental levels. The MOW project builds on existing research and knowledge to demonstrate the value of coastal ecosystem productivity. To assess the value of a certain coastal ecosystem, such as a mangrove forest or coral reef, MOW researchers review, model and map the value in question. Ecosystem service value is not always defined as economic but considers food security, risk reduction, job creation and seafood harvest. The ecosystem services are mapped to provide a comprehensive tool for understanding their value. The maps and data provided by MOW help advise on best coastal-use decisions for different regions and coastal ecosystems. Dr Mark Spalding has worked for the Nature Conservancy for fourteen years and is a senior scientist and global science lead in the MOW team. Based at the University of Siena Italy, he is also an honorary research fellow of the department of Zoology, Cambridge University. Dr Spalding explains how the MOW project came about. “It sort of evolved into being. I think I probably made my name on doing ‘bigger-picture’ synthesis of knowing what’s where in the oceans. So a lot of global mapping. Once you have got a map you can start to ask questions about the map.” Dr Spalding elaborates on how the UN-REDD movement also inspired the early stages of the MOW project. The REDD initiative (reducing emissions from deforestation and forest degradation) was first

discussed under the United Nations Framework Convention on Climate Change in 2005 as a means to reduce climate change by improving forest management in developing countries. “There was a realisation in the marine community that marine ecosystems also had a role to play in mitigating climate change: mangroves, saltmarshes and seagrasses, all three are probably amongst the most productive ecosystems on the planet, per unit area. They pack the carbon and they do something that terrestrial systems don’t do because [these marine ecosystems] also lock it away in the soil. We had just produced a map of the world’s mangrove forests, so I said, ‘I wonder if there’s any mileage in trying to model the carbon storage in the world’s mangrove forests’.” To address such challenges—modelling carbon storage for example—Dr Spalding explains that MOW researchers often find that a lot of the science has already been done. It’s a case of reviewing the available scientific material to build the models and eventually extrapolate that data onto global maps. “Our tagline has been, ‘there’s enough data out there—we don’t need more science, we need to put science to work’.” He describes the MOW project as a matrix, with researchers in different institutions around the world working on different parts of the project. “You think of five or six different coastal marine habitats: coral reefs, mangrove forests, saltmarshes, seagrasses. Then you can think of a bunch of services: carbon [sequestration], coastal protection, fish production, tourism and even water filtration. So there is a matrix there. We started gradually ticking off the boxes. We’ve done coral reefs and tourism. We’ve done mangroves and carbon sequestration. Each one is a nice research project in its own right.” In mapping the value of coral reefs provided by tourism, for example, the team used a novel approach to determine the value of the reefs—using social media to find areas where tourism is based around coral reefs. “We used key word searches on Flickr to pick out underwater photographs. We got tens of thousands of geolocated underwater photographs... We’re now working with Microsoft. They’re thinking about using image recognition and machine learning to train a system that will go [online] and find underwater photos for us.” According to Dr Spalding, the MOW project is modular, not a “tight-knit” team. He and his colleagues provide guidance and encouragement, while different parts of the project tend to branch off and continue in different countries. He emphasises the importance of maintaining links with people at the various coastal ecosystems to implement the MOW

Michaelmas 2017

FOCUS

research. “Having people connected on the ground to do something with it afterwards - that’s critical. Otherwise we are just looking inwards—being classic academics I suppose. Writing stuff, and hoping someone else does something about it!” Dr Spalding believes firmly in the fundamental importance of the project. “Marine spatial planning is becoming quite urgent and a lot of countries are beginning to take it quite seriously. Our maps give us a place at the table in those discussions. We see it as a lever to try to encourage stronger efforts, stronger investment and more nuanced and thoughtful management and policy interventions—to try and change things really. It’s too easy to say, ‘It’s all going to hell,’ but much more challenging if you can point a finger, point to a place on the map and say ‘this is where the pressure is highest, here’s where there’s an opportunity to do conservation”

When using the MOW mapping tool, one can select the ecosystem service “recreation and tourism” for coral reefs. The amount of tourism expenditure, or the number of visitors generated through recreation and tourism as a service is shown on each and every coral reef in the world. Colour-coded categories are shown on a global atlas. The east coast of Brazil shows up predominantly dark red, meaning that it’s generating over $908 000 per km2 per year, whereas some reefs on the barren North coast of Australia, coral reefs are coloured grey - they are given no value for tourism. As well as recreation and tourism, the mapping tool shows global data sets for coastal protection, fisheries and carbon storage and sequestration.

Hayley Hardstaff is a recent graduate of the Biological Natural Sciences at Emmanuel College. Artwork by Hayley Hardstaff (p16) and Richard Johnson (p19)

Michaelmas 2017

Focus

Brexit: a Cause for ConCERN? Bruno Barton-Singer discusses the future of CERN with Professor Ben Allanach

“The fact is that with CERN, you really couldn’t do it in one country. In any one country, you don’t have the expertise"

In 1954 the UK, France, West Germany and most other non-communist European countries joined together to create the Council for European Nuclear Research (CERN). Like the European Coal and Steel community and the European Economic community set up in surrounding years, CERN was a symbol of a new spirit of European integration. It was an antidote to the nationalism that had torn Europe apart twice in the previous forty years. As the name suggests, CERN was originally devoted to the study of nuclear physics, but over the following decades it became the central laboratory of European particle physics. After many groundbreaking discoveries, CERN made international headlines in 2008 and then 2012 first for building the Large Hadron Collider (LHC), the largest particle accelerator in the world, and then for discovering the famous Higgs boson. The accelerator crosses the border between Switzerland and France, and is funded and staffed from across the world. Is it the success story of international science collaboration that it appears? Where next for CERN and the LHC, at a time when in many countries nationalism, at the expense of internationalism, seems to be on the rise? Physicists are typically divided into theoreticians, who come up with the theories, and experimentalists, who do the experiments that test them. But Professor Ben Allanach is a phenomenologist, an intermediary between the two, who works “on the boundary of data and theory”. His job is to work out how you can test particle theories by going through the data that comes out of these experiments, in particular the results coming from the LHC. Allanach is an enthusiastic champion of CERN: “it’s like the Mecca of physics”, he says. “The fact is that with CERN, you really couldn’t do it in one country. In any one country, you don’t have the expertise.” He spends most of the year in the Department of Applied Mathematics and Theoretical Physics in Cambridge, now only visiting CERN for a few days a year. He is in regular correspondence with the people who run experiments at the LHC, and tells them how to look for signs of physics beyond our current knowledge. According to Allanach, nothing compares to the atmosphere at CERN and the frequent cross-fertilization of ideas within a workplace of around fourteen thousand people. “There are too many interesting lectures going on, every day!” As an international collaboration, Allanach views CERN as a model. In fact, he thinks it’s so successful that we should consider extending its lessons to other areas of science, in particular health. “To get a drug, or a vaccine, through clinical trials costs a billion dollars. For a vaccine, pharmaceutical companies don’t want to do it... but for governments, it makes perfect sense.” Like CERN, the costs are too big to be borne by individual countries, but working as a team they could collectively reap the rewards. Allanach admits it’s a pipe dream, but who would have

Brexit: A Cause for ConCERN?

predicted where CERN would be now when it was set up in the fifties? With Brexit on the horizon, Allanach thinks that the general picture for UK-EU science collaboration is uncertain. There is the question of the free movement of people when it comes to hiring researchers and teaching students, which is so far undecided. Then there is the question of funding: the UK does the best out of any country in the EU with respect to European Research Council (ERC) grants. The UK received around 1600 ERC grants in the last decade, more than twice as many as all other EU countries excluding France and Germany. In fact, the UK gets back more than the government puts into the scheme. Allanach also points out that an EU country is unlikely to pull out of a collaborative EU research project without the agreement of the other member countries. Hence any new relationship between the UK and European science would always be viewed with suspicion when UK domestic politics could make us an unreliable partner. One example of domestic politics affecting an international collaboration in this way is the LISA project. The LISA project, a proposed satellite-based gravitational wave detector, faced a setback in 2011 when the United States pulled out of the project due to funding restrictions. At least CERN will be fine, as a wider international organisation that the UK is committed to already. “[Brexit] will be a problem for Physics but not for CERN”, says Allanach. Despite the perhaps generally gloomy forecast, we have much to look forward to with the research CERN is able to perform with the current equipment. The universe is currently explained through two theories: Einstein’s general relativity, which describes gravity, and the ‘Standard Model’, which describes everything else. The Standard Model is a theory of seventeen fundamental particles that make up all matter and carry the three other fundamental forces between them (weak, strong and electromagnetic). The Higgs boson was the seventeenth and final particle to be discovered of that theory. The model is somewhat arbitrary: the masses of the particles and the strengths of their interactions are not all predicted by the model. Instead the model must be reverse engineered to fit the physics we see. Although the model still has strong predictive power, there seems to be no reason why the Standard Model should have exactly those particles with those masses and interaction strengths. The LHC may yet provide the clue as to where physicists should look next. Allanach says that a current research focus is B meson decay, which “might make us rip up all the textbooks”. The B meson is a particle made from a quark and an antiquark, the particles that make up protons and neutrons. The B meson is unstable, so quickly falls apart (‘decays’) into other particles. However, it does not decay into the same particles every time. The problem Michaelmas 2018

Bruno Barton-Singer is a recent graduate from Physical Natural Sciences at Emmanuel College and is commencing his st year of PhD in theoretical physics at the Heriot-Watt University, @ BruBartonSinger

is that B mesons do not seem to decay as often as they should to a certain final state, hinting at some new particle, completely beyond the Standard Model, that is interfering in the process. The decay is very rare: only one in ten billion B mesons decay to this final state. The LHC is still at the stage of gathering more data before anything can be said for certain. In the next few years we should know whether this anomaly really does suggest a new particle or is just a blip in the data. To look for any new particles beyond the Standard Model, such as those required to explain B meson decay, physicists want to upgrade to an even larger accelerator, the ‘future circular collider’. It is planned to collide particles together at almost eight times the energy of the LHC, although whether the international community is willing to pay the money

Michaelmas 2018

The UK received around 1600 ERC grants in the last decade, more than twice as many as all other EU countries excluding France and Germany. In fact, the UK gets back more than the government puts into the scheme

required is doubtful. There is talk of China taking over and making the circular collider a solely Chinese project, but according to Allanach “that’s very tricky in terms of expertise”. At the same time, American particle physics is suffering from the volatility associated with national funding. “The people who work in labs in the states are struggling, there are cuts left right and centre,” says Allanach. It’s hard to see a future for particle physics that isn’t more, not less, global Bruno Barton-Singer is a recent graduate from Physical Natural Sciences at Emmanuel College and is commencing his 1st year of PhD in theoretical physics at the Heriot-Watt University, @ BruBartonSinger. Artwork by Alexander Bates

Brexit: A Cause for ConCERN?

RIPEning our crops for global food security Rebecca Rebis discusses the ambitions of RIPE to optimise the photosynthetic capabilities of our crops When you are a child, you are taught that plants need light to grow. While you may not understand why, you know that putting your favourite plant, grass pot or mini cactus in a cupboard will lead to a dead plant, grass pot or mini cactus not long after. Gradually you gain in knowledge (plants also need water and air!), until that fateful day in secondary school biology when you learn that, using energy from the sun, plants change carbon dioxide and water into oxygen and glucose. At last, you believe you understand the secret of photosynthesis. But it is not until Biology A-level that you realise there is more: there is RuBisCO, the enzyme which catalyses carbon fixation, the Calvin cycle where multiple reactions take place to make carbon into sugars, and a whole host of molecules you never knew existed.

RIPEning Crops for Global Food Security

The RIPE project, however, is taking photosynthesis to a whole new level. Through intense study and modelling, teams of researchers from nine different academic institutions are working together to ‘hack’ photosynthesis, in the hope that they can design plants that photosynthesize far more effectively than they can at present. By Realizing Increased Photosynthetic Efficiency (RIPE), they aim to increase crop yields, address growing food insecurity and improve the livelihoods of millions around the world. Bringing together academic institutions from across the world - from the University of Illinois, to the Australian National University, to the Chinese Academy of Science Max Planck Institute — the RIPE collaboration harnesses

Michaelmas 2018

the different experience and expertise of a wide range of researchers. In addition, with so many institutions working together, the teams can carry out far more trials than they could do alone. The project’s funding, too, has sources around the world: RIPE took root in 2012 with a $25 million grant from the Bill & Melinda Gates Foundation and continues now with additional support from the Foundation for Food and Agriculture Research and the UK Department for International Development. With so many contributors, the RIPE project has a much wider reach than that of a single institution, as each team supports and publicises the breakthroughs made by their partners. So what does hacking photosynthesis involve? After many models and much analysis, RIPE have identified seven research objectives, which they believe hold the key to making photosynthesis as efficient as possible. The objectives include improving photosynthetic carbon metabolism by increasing efficiency within the Calvin cycle, and improving mesophyll conductance – the diffusion of CO2 from the atmosphere through the inner leaf tissue. The project is also investigating the prospect of faster RuBisCO activation and copying more efficient photosynthetic strategies from algae. On a larger scale, RIPE are also hoping to adapt plant canopies by changing leaf colour and orientation, so that each leaf receives as much light as possible. As an example, take photoprotection. Plants contain defence mechanisms against high levels of light intensity, to protect their leaves from harm. Whilst these mechanisms are excellent for ensuring that the plant is not damaged, they inhibit photosynthesis and can take some time to switch off, thus reducing the amount of time the plant can spend photosynthesising. By speeding up the relaxation of the defences, once light intensity has returned to a safe level, plants can return to photosynthesising much more quickly and therefore be more productive. Theory is all very well, but RIPE’s studies show that such improvements are not just a pipe dream. Earlier this year, researchers led by Professor Stephen Long successfully increased water-use efficiency in tobacco plants by 25% by altering levels of the photosynthetic protein Photosystem II subunit S (PsbS). This protein influences the opening and closing of stomata in line with local light levels, the main mechanism by which plants regulate the amount of carbon dioxide entering and water vapour exiting the leaf. An open stoma - effectively a pore in the leaf - means more carbon dioxide for cells to photosynthesise, but also more water loss. RIPE researchers observed that increasing levels of PsbS (so that stomata partially close) does not affect CO2 entry, but does increase water retention. However, as with any experiments involving genetically modified material, the results can be unexpected. In another field study this year, RIPE managed to boost crop production in tobacco plants by 47% by tackling the energy waste caused by photorespiration. Photorespiration happens during the Calvin Cycle, when the enzyme RuBisCO binds to oxygen instead of carbon dioxide. Though it is an essential process for plant survival, photorespiration also forms ‘waste’ products Michaelmas 2018

that need to be recycled, at a metabolic cost to the plant. To speed the recycling process along, scientists engineered the tobacco plants to overexpress a photorespiratory protein used to recycle the waste, known as the H-protein. Whilst the modification did lead to greater crop productivity (more efficient photosynthesis) in the leaves, overexpression of the H-protein throughout the plant limited growth and metabolism, leading to significantly smaller crops. Perhaps a more targeted approach - overexpression in the leaves only — could lead to greater crop productivity while avoiding unhelpful side-effects. Despite the setbacks, there is hope that the modifications tested by RIPE will increase photosynthetic efficiency and lead to greater production for farmers across the world. Such engineering could even set in motion another Green Revolution, propelling a worldwide elevation in crop productivity. Once desirable changes - such as photosynthetic efficiency - have been identified in field studies on tobacco plants (excellent ‘lab rats’, as they are easy to handle and modify in both lab and field), the next challenge is to transfer the genetic changes into staple crops such as cassava, soybeans and rice. With agricultural systems already under strain from climate change, plants that are more responsive to light, more water efficient, and higher yielding offer a solution to global food insecurity. Furthermore, growing crops more productively addresses concerns that the needs of an increasing human population will outstrip the amount of land available. With a 50-70% increase in food production needed to meet the predicted population demands of 2050, innovations such as vertical farms (think of a farm, but in a skyscraper) and hydroponics (soil-less farms) are becoming more commonplace. RIPE offers another potential solution to the need to grow more food using less land. The final challenge is to ensure that the discoveries made by RIPE are available to everyone. As agriculture differs across the world, many crops will need to be considered for modification; both mainstream species and so-called ‘orphan crops’ - regionally important but not traded globally and therefore often neglected by scientific research. In the past, some companies have engineered useful crops and sold them for a high price, or modified the crops so that farmers need to buy new seeds each year. However, as a partner with the Gates Foundation, RIPE is committed to making their work as accessible as possible. It is their belief that, using their knowledge, farmers will be able to “produce more in this century than in the history of humankind”

Earlier this year, researchers led by Professor Stephen Long successfully increased wateruse efficiency in tobacco plants by 25%

Rebecca Rebis is a recently graduated student of Geography at Emmanuel College, now Marketing Coordinator at Remedy Geotechnics, @rebecca_siber. Artwork by Irene Taptas

RIPEning Crops for Global Food Security 25

Quantum Technologies for Precision Measurements Adam Barker discusses the applications of up-andcoming high-precision quantum technologies

The best mechanical watches will lose less than 100 seconds of time per year. The best caesium clock in the world maintains a precision of around 3 parts in 1015; this means it will neither lose or gain 1 second in 100 million years. A recent stronium-atombased optical clock - based on visible light rather than microwaves - will lose or gain no more than 0.1s over the whole age of the universe

Quantum mechanics describes the universe at the fundamental level, when it no longer can be thought of as continuous: energy, length, momentum and many other physical quantities must be treated in discrete chunks. In our macroscopic world, we are blind to the nature of the universe on its smallest scales, as heat and other disturbances blur it all out. It is only when we dig deeper, isolating systems from the environment or cooling them down, that quantum mechanics becomes apparent. In popular culture, quantum is a word that is now synonymous with progress. Everyone from carpet manufacturers to popular brands of dishwashing detergent are squeezing ‘quantum’ into their brand names to capitalise on its connotations with innovation and advancement, without having anything ‘quantum’ going on. One very notable exception is the quantum computer – the poster child of a quantum-enhanced future (see BlueSci Michaelmas 2016, ‘Computing’s Quantum Leap’). While the quantum computer certainly has the capability to change the way in which we do our computing and conquer previously unsolvable problems, there are many other truly quantum applications, which currently, or will very shortly, play a huge part in society. These applications may allow us to measure the fundamental quantities of the universe, such as time, distance or acceleration, to higher and higher precision. So, what are these lesser-known quantum applications, and how could they play an enormous role in our society? Clocks | Keeping time accurately has always been of profound importance to humans. Prior to the advent of satellites and radio, ships determined their longitude by measuring the inclination of the sun at a known time of day. This relied on a precise knowledge of time, to compare with measurements from astronomical charts. This was such a momentous problem for mariners in the 18th century that the British government offered a prize to anyone who could design a clock capable of withstanding the turbulence of a marine journey. Nowadays, we have a whole range of clock technologies at our disposal. The best mechanical watches will lose less than 100 seconds of time per year, while quartz-based clocks may be even better. However, keeping accurate time has never been so important. The satellites that are responsible for supporting the Global Positioning System (GPS), which is in turn responsible for keeping cars and planes on track, are

Quantum Technologies for Precision Measurements

hurtling through space, 20 km above us. To keep in orbit, these satellites must travel at several km per second and thus a small error in timekeeping results in a large error in position. To rub even more temporal sand into the eyes, effects described by special and general relativity play their part in satellite timekeeping. Time dilation is the property of a moving observer measuring a slower rate of time, as compared to a stationary observer —“moving clocks go slow”. This effect is practically immeasurable when travelling at our terrestrial speeds but becomes significant for objects travelling nearer to the speed of light, such as a proton in a particle accelerator. GPS satellites are travelling at very high speeds and ignoring the corrections due to time dilation would lead to an error of a few microseconds per day. Furthermore, the slightly reduced gravitational pull felt by the satellites leads to a minor speed-up which, if left uncorrected, would also lead to a few microseconds of error. Atomic clocks have played a huge part in accurate timekeeping since the mid-1970s and caesium atomic clocks have been the ‘gold standard’ for decades (actually, we refer to this as the caesium standard). Here, a specific cycle of an electron in caesium defines the second; the exact definition is “the duration of 9,192,631,770 periods of the transition between the two hyperfine levels of the ground state of the caesium-133 atom”. This sounds complicated, but it essentially describes an electron in a caesium atom jumping from its quantum energy level to a slightly higher level and subsequently falling back again. It is 9 billion or thereabouts of these round trips which defines the second. The best caesium clock in the world maintains a precision of around 3 parts in 1015; this means it will neither lose or gain 1 second in 100 million years. Most recently, scientists in JILA, Boulder were able to synchronise 1,000 strontium atoms packed into a 3-dimensional lattice made from light in order to achieve a precision of 3 parts in 1019. This clock would lose or gain no more than 0.1s over the whole age of the universe. Owing to these quantum leaps in time keeping, satellites, stock markets and many other human pursuits are able to operate in harmony across the world. Accurate timekeeping may become even more important when communicating over astronomical distances, such as to other planets: time will tell. Accelerometers and Gravimeters | Just as important as measuring time, is measuring distance. This is especially Michaelmas 2018

important for navigation without GPS, a problem faced by submerged craft away from sonar beacons or other ships. Submarines cannot use GPS owing to the reflection of radio waves at the water-air interface and instead use a system of very precise devices which measure acceleration. The results of these accelerometers are integrated twice to determine position in a process called ‘dead reckoning’. This leads to uncertainties in the position of the submarine up to several km when submerged for weeks. Several groups around the world have constructed extremely precise accelerometers using Bose-Einstein condensates (BEC) – a very cold state of matter predicted by Einstein and Bose in the 1920s that was only realised experimentally in the 1990s. These novel objects consist of thousands of atoms in the same quantum state and behaving identically, like an army marching in lockstep. The coherent nature of these objects means interference fringes can form when one BEC is overlapped with another, like a laser passing through two slits. The interference fringes are a direct consequence of the quantum mechanical nature of these objects, which becomes apparent when the atoms are cooled to a few billionths of a degree above absolute zero – a regime previously inaccessible before major leaps in laser technology. The location of these fringes is extremely sensitive to the velocity and hence acceleration of the interfering BECs and acceleration can be measured as precisely as to 10-8 m/s2.

Michaelmas 2018

The same technology can be used to measure gravity, by allowing the atom clouds to fall vertically. Einstein’s equivalence principle states that acceleration upwards at 9.81 m/s2 cannot be distinguished from gravity. A precise measure of gravitational acceleration could be used to detect small local fluctuations in the density of the earth below, such as those produced by iron deposits or oil fields. Conclusions | While quantum computers promise an enormous leap forward in our ability to solve problems, such as the ability to search large datasets or even simulate other quantum systems, they are by no means alone in their ability to provide a quantum leap. Within our lifetime, we will experience several orders of magnitude improvement in our ability to measure time, acceleration and distance. In the not-too-distant future, the physics describing the universe on its smallest scale has the potential to make a huge impact on our lives Adam Barker is a DPhil student in Atomic and Laser Physics at Magdalen College, Oxford, @ox_ultracold. Artwork by Alexander Bates

Quantum Technologies for Precision Measurements

Autonomous Vehicles: Looking at the Road Ahead James Macdonald interviews Professor John Miles and Wayve start-up founder Amar Shah about the future of autonomous vehicles In the UK there are 48 million driving licence holders, around threequarters of the population. The car has been a huge enabler of personal mobility across society and the ability to travel is a large part of the quality of life we now enjoy. But for such an embedded part of our culture there are many negative effects of driving, for instance, the average worker spends 54 minutes of their day commuting and in 2015 there were nearly 200,000 casualties due to road accidents. It is no surprise then, that the field of driverless cars – or autonomous vehicles, which drive using computer systems with artificial intelligence (AI) built in – has attracted research and investment on a global scale. The advent of self-driving cars could reduce road fatalities by a factor of 10 and cause the most disruptive technological change in transport since horses were outpaced by internal combustion engines. However, there are substantial risks to the development of the technology such as stifling regulation and potential downsides such as job losses. This article route-checks the path to mainstream adoption of autonomous vehicles, explores some of the challenges on the way and looks at how they could be overcome to benefit society and enable environmentally efficient mobility. BlueSci speaks to Professor John Miles whose research into Transitional Energy Strategies at the University of Cambridge explores the potential to reduce urban emissions through radical alternatives to conventional transport systems. The potential transformative effects described by Professor Miles have created a race to develop both the hardware and the software underpinning these future autonomous vehicles. BlueSci also interviews Amar Shah, founder and CEO of Wayve, a Cambridge start-up that develops and tests machine learning algorithms for autonomous vehicles.

Autonomous Vehicles

John Miles, Professor of Transitional Energy Strategies at the University of Cambridge JM | Why is autonomous transport an important topic for research? Prof. Miles | There is a dim view of transport currently, the politically correct view is that it’s not sustainable to travel and that we should travel less. However, mobility is a fundamental part of the quality of life we all enjoy, therefore we should get rid of the side effects of transport. Electric vehicles and autonomous vehicles have the ability to ameliorate these bad side effects. It is obvious that electric vehicles stand to reduce emissions, noise and other unpleasant side effects. Autonomous vehicles offer additional benefits such as more efficient fuel consumption, reduced congestion and increased safety. JM | A lot of people in the UK are employed as professional drivers or in taxi companies. Does this make the emerging technology a threat or an opportunity? Prof. Miles | I think superficially it’s a threat because of the very large number of drivers. For example, in Milton Keynes there are around 1400 taxi drivers representing a big local employer. If you made all these vehicles autonomous you’d suddenly put 1400 people out of business overnight. If you multiply that up across all the cities in the UK you end up with a very large number of people. The counterargument is that if autonomous vehicles became ubiquitous because they were cheap and flexible, everyone currently using their own cars would start to use taxis as well. With this demand the ridership of these vehicles would shoot up and the associated duties of maintaining that fleet would create new jobs. In an ideal world, the people displaced from being drivers might be employed as mechanics, service clerks and centre answerers. There’d just be different jobs. Whether that’s true or not remains to be seen… Michaelmas 2018

But there will be jobs created by this transition. JM | According to Bill Gates, although the technology underpinning autonomous driving is good, the actual adoption will be slower due to the slow rate of regulation and policy making. Do you think the transition will be incremental or would you expect a more sweeping change? Prof. Miles | I think social acceptance of new technology is very much based on the perception of utility. I think the time between making the technology available and widespread public uptake will be relatively short. To qualify, I don’t think fully autonomous vehicles will be available any time soon; perhaps 2040-2050. But we should see limited autonomy fairly soon. At the moment even with automated lane change you’re still the driver in the hot seat – but once you can turn your brain off and read a newspaper driving three hours down the M1 everyone is going to want to do it. Amar Shah, founder and CEO of start-up Wayve JM | What does Wayve do? AS | We are aiming to build the AI brain of autonomous vehicles, all the way from sensing the world with cameras to decision-making on steering, accelerating and braking. Many of the people working on the technology have good algorithms but can’t gain the last few percentage points of accuracy to have sufficient safety and confidence. We are using an end-to-end approach, which means directly optimising the entire pipeline in one algorithm. Many of the established companies use a modular approach, which separates the problem into multiple blocks and then stitches together the solutions in each block. Although the modular approach makes the algorithm interpretable there are problems with errors that can propagate into the end decision. We think end-to-end training is a potential way around this, which means focusing on our end goal and training our entire model to fit the end goal. JM | What are the big challenges in implementing this technology and seeing autonomous vehicles on the streets? AS | If you look at some of the early self-driving cars they often looked like tanks with all sorts of sensors and spinning things. For example, it’s common to have a sedan with 12 LIDAR (light detection and ranging) sensors and 12 cameras. Then different teams take these inputs and try to fuse them Michaelmas 2018

together to make a single cohesive representation of what’s going on and then try to decide thereafter what to do with these modules. This creates redundancy and you spend a lot of human and computational resources collating all this information and figuring out what to do with it. We think our approach - which is lean on both the hardware and software side - allows us to simplify the machine learning part of the problem, as well as testing and modelling. Our recent demonstration in June had a model with a very small neural network, only 10,000 parameters. For context, today’s top image classification models have tens of millions of parameters. This car was able to learn to follow lanes in 15-20 minutes, so we think we can do a lot with very specialised small models.”

In Wayve’s protoype car, eight cameras capture video in real time.This feed is classified into different types of objects relevant to driving and used to make driving decisions

JM | How can a startup fit into a landscape dominated by huge tech firms who are investing billions into the technology? AS | I don’t think anyone has a very clear idea of what the business models will look like. I certainly think there will be partnerships and collaboration between companies who are good at making cars and others who are good at making intelligent algorithms. One way we could enter the market is by partnering with a fleet provider who leases us cars that we program with our algorithm and operate as an autonomous fleet. Alternatively, a company like ours could simply licence algorithms to automakers who are less specialized in creating intelligent algorithms. JM | What would you say to others with ideas to start a business in technology? AS | I think you need to have a vision and really test it by looking at what’s around and why you want to build this company. I think building up experience and credentials in the tech world also helps to convince potential stakeholders. I hope more people from Cambridge do stuff like this because we have great talent here and investment in the UK tech scene has really risen over the last five years. But I think really believing in your vision and your ability to execute is key James Macdonald is a PhD student in the Department of Engineering at Darwin College. More with @wayve_ai @Cambridge_Eng. Artwork by Tamsin Saunders

Autonomous Vehicles

Map of Health Honor Pollard explores Odra Noel’s Map of Health, which portrays the main causes of death worldwide

Odra Noel is a London-based artist who uses her scientific background to infuse her artwork with facts. Based on 2008 WHO disease prevalence data, this particular piece showcases Noel’s interest in making human health aesthetically beautiful and informative.

Can you match the cell type depicted in each region to the most common health problems? There are no points for guessing that North America is represented by adipose (fat) cells. These cells are linked to conditions including high blood pressure and heart attacks. Africa’s cell type is another unsurprising result; you might recognise the red blood cells from their lack of a nucleus, or their biconcave dip. Africa is the only region where infectious diseases such as HIV and malaria, which infect red blood cells, present a significant threat to the population’s health.

The flower-like green blooms in the Pacific are structures found in the pancreas. Each ‘bloom’ is a collection of acinar cells, which synthesise and secrete digestive enzymes. Faulty pancreatic tissue can lead to diabetes; more than 80% of the people with this condition live in developing countries. Lung diseases are a major problem in Latin America, where over half of countries reported a prevalence of childhood asthma greater than 15% (the US average is 9.3%) as of 2015. Therefore, Noel represents Central and South America as pulmonary (lung) tissue

Ten years of revolutionary medicine later, is the map still accurate? As of 2017, the leading cause of death in Africa was no longer HIV/ AIDS, but instead lung infections. What will the future of this map look like? As medical interventions improve, will the world ever be represented by a homogeneous cell type?

For an extra challenge, Noel has hidden five mitochondria across the globe: a prediction of what was to come. Mitochondria generate energy for cells. Diseases associated with their misfunction have gained increased attention from medical researchers and the media in recent years. This includes the approval and discussion of three-parent babies (a therapeutic technique similar to IVF) in some countries. As we get older, mitochondria do not work as efficiently, which is thought to lead to signs of ageing.

Across the ocean, in the Middle East and Central Asia, heart muscle cells are laid down like building blocks. These reflect the regionâ&#x20AC;&#x2122;s rising levels of hypertension, a condition in which blood pressure is consistently high. In Europe, the most pressing health problems are neurodegenerative diseases, which go hand in hand with an ageing population. These diseases are represented by the star-like cell bodies of neurones, with projecting dendrites that connect to one another to make up the networks of nerves in the body. In Greenland, an additional issue is portrayed by sperm cells: a high infertility rate. In 2014, there were 2.01 children born per woman, below the approximate rate of 2.1 needed to maintain the population level

Weird and Wonderful A selection of the wackiest research in the world of science

Making waves: mega-tsumanis take form Tsunamis have caused devastation in coastal regions for millennia; many of us will remember the 2004 Boxing Day tsunami or the more recent 2011 Tōhoku tsunami in Japan. A tsunami is defined by a number of waves, generated when a large volume of water is rapidly displaced. However – then came the phrase “megatsunami”. Punchy and dramatic, the media loved it; but how do scientists use the word? It has been proposed that a mega-tsunami should be characterised by the height of the initial wave at the source (where the phenomenon was generated): the height must exceed a whopping 100 m. This restricts the formation of megatsunamis to highly rare events on geological timescales, such as large meteorite impacts, volcanic eruptions or even the collapse of huge flanks of oceanic islands - a single earthquake at sea is not enough to form a mega-tsunami. The most recent mega-tsunami recorded was only last year and occurred in Greenland.Yet in such a sparsely populated area, the societal effects were limited. Of greater significance to a larger populace is the risk posed by volcanic collapse on the island of La Palma, in the Canary Islands. It is predicted that the water displaced by so much rock suddenly collapsing into the ocean, could result in large-scale destruction wherever the wave makes landfall. If the wave reaches the east coast of the United States, some 6000 km away, it could be up to 50 m high. While scientists do not believe that an imminent collapse of La Palma is likely, longterm monitoring is essential. There are a range of tools to monitor the likelihood of a tsunami, including seismic stations, deepocean buoys and tidal gauges. In our connected world, globalised monitoring networks such as the Pacific Tsunami Warning Center are dramatically increasing our ability to identify potential tsunamis and mega-tsunamis. So, there is hope, at least, that we will have a bit of forewarning before such a monstrous wave descends upon our shores vh Illustration by Alex Hahn

The Bletchley Blunder that Saved the Enigma Codes Ever felt out of your depth in a new job? That’s exactly how Geoffrey Tandy felt when he was unexpectedly called to Bletchley Park in World War II. Formerly a volunteer in the Royal Navy Reserves, Tandy was unexpectedly asked to lend his expertise in breaking the infamous Enigma code used by the German Navy to send their messages. Unfortunately, however, it soon became clear that something — ironically — had been lost in translation. Tandy was a cryptogamist (an expert in non-flowering, spore-reproducing plants such as seaweeds, mosses and ferns) but the Ministry of Defence thought that Tandy was a cryptogramist (a code decipherer). Tandy tried hard to master the code-breaking skills, but struggled. He came into his element, however, when the Allied forces managed to salvage something from a torpedoed U-Boat that would change the course of the war: bigram tables used by the Germans to unscramble the Enigma messages. Tandy often had to dry wet plant specimens for preservation and could apply his methods to save the tables from a watery grave. His contribution to the work at Bletchley ultimately shortened World War II; so next time an employer asks for a transferable skill — think of Tandy jmd

Magnetoreception may be our sixth sense Over the past 30 years, debates have raged over whether humans can sense the Earth’s magnetic field. Many animals from birds and fish to mole rats and even dogs use it to migrate and orientate. Conflicting experiments trying to find our inner compasses, however, have yielded inconsistent results and have lacked in direction. Over 30 years ago, an article by Robin Baker et al. published in Science showed that a magnet disrupted the sense of direction in blindfolded students, but the experiments could not be replicated and the research floundered. In 2011, Foley et al. found that human cryptochrome (a light-sensitive protein found in our retinas) responds to magnetism. In 2016 Qin et al. went on to discover that fruit flies lacking cryptochrome lost their magnetic field-detecting abilities. When transplanted back into the flies’ eyes, a form of this protein reinstated their mental map. Back in 1990, a highly magnetic material ‘magnetite’ was discovered in human brain cells by Kirschvink et al. This mineral is also found in huge concentrations in bacteria which (surprisingly!) also use it to navigate. Earlier this year at the Royal Institute for Navigation conference, Kirschvink demonstrated that alpha waves in the human brain drop sharply in response to magnetic field shifts, suggesting that neurones in our brains are responding to the change. Ultimately, then, our inner compass may exist! However, the degradation of this ability through lack of use may make it elusive; especially so in a world filled with field interference from electronic devices jmd

All your journals in one app

Everything you need to keep up-to-date with the latest academic papers.

Use RESEARCHERâ&#x201E;˘ across all devices

DOWNLOAD FOR FREE

Filter your feed using keywords

Synchronise with your reference manager

or use at www.researcher-app.com