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Science for South Africa ISSN 1729-830X

Antibodies and HIV vaccines Rising sea temperatures and coral reefs Gliders in the ocean: a dual robotics platform Volume 9 | Number 4 | 2013

Citizen science makes a difference to Leopard Toads History and ichthyology in South Africa

Acad e my O f Sci e n ce O f South Afri ca

Research that can change the world

Impact is at the core of the CSIR's mandate. In improving its research focus and ensuring that it achieves maximum impact in industry and society, the organisation has identified six research impact areas: Energy - with the focus on alternative and renewable energy. Health - with the aim of improving health care delivery and addressing the burden of disease. Natural Environment - with an emphasis on protecting our environment and natural resources. Built Environment - with a focus on improved infrastructure and creation of sustainable human settlements. • Defence and security - contributing to national efforts to build a safer country. • Industry - in support of an efficient, competitive and responsive economic infrastructure. • • • •



ontents Volume 9 | Number 4 | 2013

Cover Stories 3 Antibodies and the search for an HIV vaccine

Quest investigates local research into broadly neutralising antibodies

6 Will our coral reefs survive climate change?

Mike Lucas looks at the impact of rising sea temperatures on coral reefs around the world

10 Gliders in the ocean

Quest follows up on this revolutionary research into Southern Ocean dynamics

12 Flux towers

Antoinette Oosthuizen looks at research into carbon dioxide exchange on land

6 3




18 Citizen science and the Western Leopard Toad

Quest covers the work of a small group of volunteers who are making a difference to this endangered species

22 From rocks to dynamite

Paul Skelton explains the historical foundations of ichthyology in South Africa

Features 14 Clean laboratories and trace elements

Antoinette Oosthuizen looks at Africa’s first ‘clean’ laboratory and its place in oceanographic research

26 Rising Star expedition

Lee Berger leads an international team in excavating new fossil finds in the Cradle of Humankind

28 South African Space Agency celebrates World Space Week

Catherine Webster explains SANA’s contribution to space science

31 The first evidence of a comet strike on Earth

South African and international scientists investigate rocks in the Libyan desert

32 The Nobel Prize for physics

François Englert and Peter Higgs win the Nobel Prize for their discovery of the Higgs boson

36 The Nobel Prize for chemistry

Martin Karplus, Michael Levitt and Arieh Warshel are awarded the Nobel Prize for their work on multiscale models for complex chemical systems

38 The Nobel Prize for Medicine

James E Rothman, Randy W Schekman and Thomas C Südhof are awarded the Nobel Prize for the discovery of transport systems in cells

Regulars 5 Fact file

HIV and immunology

35 News

Galloping dung beetles could be counting their steps back home

41 News

Prestigious gold award for NMMU scientist • Global first as Wits researchers split pollen

42 Books 45 ASSAf news 46 Subscription 49 Back page science • Mathematics puzzle 9| 4 2013


Science for South AfricA iSSn 1729-830X

Antibodies and HIV vaccines Rising sea temperatures and coral reefs Gliders in the ocean: a dual robotics platform Volume 9 | Number 4 | 2013

Citizen science makes a difference to Leopard Toads History and ichthyology in South Africa

AcAd e my o f Sci e n ce o f South Afri cA

Images: Wikimedia Commons, CSIR, www.sciencemag.org

Editor Dr Bridget Farham Editorial Board Roseanne Diab (EO: ASSAf) (Chair) John Butler-Adam (South African Journal of Science) Anusuya Chinsamy-Turan (University of Cape Town) Neil Eddy (Wynberg Boys High School) George Ellis (University of Cape Town) Kevin Govender (SAAO) Himla Soodyall (University of Witwatersrand) Penny Vinjevold (Western Cape Education Department) Correspondence and enquiries The Editor PO Box 663, Noordhoek 7979 Tel.: (021) 789 2331 Fax: 0866 718022 e-mail: ugqirha@iafrica.com (For more information visit www.questinteractive.co.za)

Advertising enquiries Barbara Spence Avenue Advertising PO Box 71308 Bryanston 2021 Tel.: (011) 463 7940 Fax: (011) 463 7939 Cell: 082 881 3454 e-mail: barbara@avenue.co.za Subscription enquiries and back issues Phathu Nemushungwa Tel.: (012) 349 6624 e-mail: phathu@assaf.org.za Copyright © 2013 Academy of Science of South Africa

Published by the Academy of Science of South Africa (ASSAf) PO Box 72135, Lynnwood Ridge 0040, South Africa

Permissions Fax: 0866 718022 e-mail: ugqirha@iafrica.com

Human costs M any of the articles in this final issue of Quest for 2013 look at human influences on our environment, how climate change is affecting our coral reefs, how developing human infrastructure is depleting vulnerable leopard toad populations and the way in which science is measuring carbon dioxide flux – crucial to understanding the role of carbon dioxide in climate change. As a species we tend to measure the effects of what we do on our planet in our terms and there are many who say that we can simply lessen the effects of our interference using science and technology. However, a recent paper published in the Proceedings of the National Academy of Sciences makes for interesting reading. The paper highlights a new branch of environmental health that focuses on the public health risks of human-caused changes to Earth’s natural systems. The authors point out repeated relationships between changes in natural systems and existing and potential health outcomes. They speak of the link between forest fires used to clear land in Indonesia and the airborne particle pollution that is linked to cardiac and lung disease in large populations downwind, such as Singapore. They point out the risk of human exposure to Chagas disease in Panama and the Brazilian Amazon and to Lyme disease in the United States, which is related to reduced diversity among mammal species. Children in households in Madagascar who cannot find wild meat to eat have an increased risk of iron-deficiency anaemia, which increases their chances of infectious diseases and poor performance at school. In Belize, nutrient enrichment from agricultural runoff hundreds of kilometres upstream changes vegetation patterns in lowland wetlands that increases the transmission of malaria in people living on the coast. The list goes on – heat stress, air pollution, infectious diseases, as well as water scarcity, food insecurity and population displacement. As a species we have a huge impact on the ecosystems around us, many of them negative. Yes, science and technology can solve many of our environmental problems. But this must not be at the expense either of the health of our populations, or the health of the planet itself.

Subscription rates (4 issues and postage) (For other countries, see subscription form) Individuals/Institutions – R100.00 Students/schoolgoers – R50.00 Design and layout

Bridget Farham Editor – QUEST: Science for South Africa

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All material is strictly copyright and all rights are reserved. Reproduction without permission is forbidden. Every care is taken in compiling the contents of this publication, but we assume no responsibility for effects arising therefrom. The views expressed in this magazine are not necessarily those of the publisher.

❚❚❚❙❙❙❘❘❘ HIV Medicine

Antibodies and the search for an HIV vaccine HIV vaccine research has been through many phases in the past three decades. Local research is focusing on the search for antibodies that are effective against multiple strains of HIV. Quest reports.


n 21 October 2012, the journal Nature Medicine published a letter ‘Evolution of an HIV glycandependent broadly neutralizing antibody epitope through immune escape’. This letter was written by Penny Moore of the National Institute for Communicable Diseases in Johnannesburg and several colleagues from other institutions. The essence of this paper was that Moore and the team had found two women who had developed antibodies – called broadly neutralising antibodies – that were able to neutralise a large percentage of the different strains of HIV that develop in an infected individual over time. One woman, called subject CAP177, produced antibodies three years after infection that were able to neutralise 88% of 225 different strains of HIV. The other woman, subject CAP314, produced antibodies only two years after infection that could neutralise 46% of 41 different strains of the virus. Moore and her colleagues had also showed for the first time exactly how these antibodies emerged. Why is this so significant? To understand this, we need to start by looking at some of the history of research into HIV vaccines, but before we do that, let’s introduce the concept of ‘elite neutralisers’. Elite neutralisers We now know that 10 - 30% of people infected with HIV for between two and four years develop what are called broadly neutralising antibodies or bNAbs. Among these individuals there is a subset of people – around 1% – who develop the ability to neutralise an exceptional number of different HIV strains. They are called elite neutralisers. Research has shown that there are several factors that are common to those who develop bNAbs. Duration of infection is the first – this type of antibody takes years to develop. These people generally have a high viral load that drives the immune system to produce these antibodies. They have a lot of viral diversity – in other words the virus has mutated many times while replicating in their bodies. And these people sometimes have what is called superinfection – they have been infected with more than one strain of the virus, usually as a result of infection by multiple partners. What Moore and her colleagues are starting to find out is why this process takes the time it does, by looking at specific proteins on the HIV envelope. In individuals who develop bNAbs, the HIV evolutionary pathway starts with the founder virus and the antibodies that are raised in response to this specific virus. They have found that what is different about the antibody response in some elite neutralisers is that the antibody

HIV’s gp120 (red) bound by a potent bNAb (blue). Image: www.sciencemag.org

response that these people eventually mount is directed not at the original founder virus, but at what is called immune escape variants. The ‘escapees’ are the HI viruses that develop through subtle protein changes as a result of selection pressure on the founder virus and it is the immune responses to these escaped virus strains that result in the development of broadly crossneutralising antibodies. The search for a vaccine The search for a vaccine to prevent HIV has been going on for at least two decades – with little success so far. When, in 1984, it was proved that HIV caused AIDS, researchers found one major problem with making a vaccine. HIV reproduces itself so fast that its genetic code is replicated very ‘sloppily’ each time. This leads to frequent mutations – which are mistakes in the code – and a lot of these mutants thrive in the human host. All these different mutant strains of HIV have different protein antigens on their surface. So antibodies that can usually target a single antigen very accurately, cannot keep up with the ‘ever-changing virus’. The bottom line is that neither the human body nor a response induced by a conventional vaccine is effective. As far back as 2006, the International AIDS Vaccine Initiative (IAVI) launched the global hunt to find antibodies that were able to act against every known strain of the virus. They even gave the initiative a macho name – Protocol G. By the time Protocol G was launched vaccine researchers had realised that one of the most promising discoveries were bNAbs. However, very few had been discovered at this time 9| 4 2013


HIV’s gp120 glycoprotein. Image: Wikimedia Commons

Long-term analysis of an HIV-infected individual was performed up to the development of bNAbs. The evolution of the HIV envelope on the virus drives the diversification of the antibody response. By isolating and sequencing the HIV envelope on the founder virus (red square) and on later stages of the viruses (light green to dark green), researchers get vital information that allows them to generate antigens that can potentially elicit a bNab response. This is the approach used to ‘trick’ the immune system into making bNAbs. Image: www.sciencemag.org

gp120 gp120 is an envelope glycoprotein that is exposed on the surface of the HI virus envelope. The 120 comes from its molecular weight. Gp120 is essential for the virus to enter cells because it plays a vital role in attachment to specific cell surface receptors – the most well-known of which is the CD4 receptor on helper T cells that are the favourite target of the virus. When the virus binds to the host’s CD4 cells a cascade of changes to the shape or conformation of gp120 occur that allows the virus to fuse with the host cell membrane. Because broadly neutralising antibodies often bind this part of the virus, gp120 has been a target of vaccine research. However, there are chemical and structural properties of gp120 that make it difficult for antibodies to bind to it. Despite these hurdles, there are antibodies that bind 91% of HIV strains in the region of gp120, making this region of the virus envelope particularly important in vaccine development strategy.

and even the best of them worked against only a few dozen of the hundreds of strains of HIV that a vaccine would have to be able to protect against. The Malawi link In April 2013 another important paper in Nature followed that of Moore et al. Two researchers from Duke University and the National Institute of Allergy and Infectious Diseases (NIAID)’s Vaccine Research Center reported the results of a long-term study that started in 2006, when a man in Malawi walked into a clinic for sexually transmitted infections. The clinic was already running a research project to try to find people within weeks of being infected with HIV. This man was recently infected and he joined the ‘acute infection’ study – donating blood frequently. This allowed researchers a ‘window’ into HIV evolution. Over time, researchers found changes in the gp120 of his virus, his antibody response and ultimately the emergence of a bNAb – as seen by Moore and her colleagues in the South African women. The collaboration from Duke University and the NIAID were able to trace the evolution of the antibody response from its beginnings in the B cell response right through to the evolution of the bNAb, which occurred after more than one year. When this Malawian was first infected, the original antibody type that his body produced bound hard to the original – called founder – virus that infected him. Over time, this ability to bind improved until eventually, his antibodies were able to neutralise the different strains of the virus as they emerged in his body. So how would this help with vaccine production? Researchers hypothesised that a vaccine could use the gp120 from the founder virus to stimulate production of a B cell lineage that 4

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can eventually produce a bNAb. Booster shots of the vaccine could then ‘guide’ the mutation of the antibody genes to expand the range of antibodies they can produce by using the same sequence of gp120 variants that naturally created the bNAb in the Malawian man and the two South African women. It is this approach that is being used by Moore and her colleagues as they elucidate ways in which to mimic how the virus changes in the infected person to try to guide the antibodies along the same pathway. bNAbs and the search for a vaccine We do know that most circulating HIV strains are sensitive to most of the bNAbs that have so far been identified in vitro. However, so far the bNAbs that are naturally circulating in those who have them have no effect on disease progression because the virus easily escapes. What is required is an effective neutralising response that is in place before a person is exposed to HIV to prevent infection. We need a way to ‘trick’ the immune system into making these broadly cross-neutralising antibodies that does not rely on many years of evolution. And it is this approach that Moore and her colleagues are trying. The idea is to take the founder virus and use that as the first immunogen, then follow it up with escapee gp120s, one after the other, in order to guide the antibodies along the pathway to becoming broadly neutralising. Moore and her colleagues have started testing this in collaboration with investigators in Oregon. Essentially, they are trying to shortcut the system and in doing so, produce a vaccine. Q Dr Penny Moore is a Senior Scientist in the Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services. She holds a joint appointment as a Senior Researcher in the School of Pathology, University of the Witwatersrand, and as a Research Associate, Centre for the AIDS Programme of Research in South Africa (CAPRISA) in Durban, South Africa. Penny obtained her PhD from the University of London, where she studied the hepatitis B virus, before returning to South Africa in 2003 to work on HIV. She is currently supported by a Wellcome Trust Fellowship in Public Health and Tropical Medicine. Penny is a founding member of the South African Young Academy of Science and has published more than 40 papers, many focused on the intersection between HIV viral evolution and humoral immunity.

❚❚❚❙❙❙❘❘❘ Fact file

HIV and immunology HIV structure

vital to our immune response – this change eventually prevents the body from mounting an immune response to the virus.

From B cell to antibody to bNAb

A diagram of HIV showing the envelope proteins and internal structure. Image: Wikimedia Commons

HIV is a roughly spherical retrovirus, with a diameter of about 120 nm, which is large for a virus. It is made up of two copies of a positive single-stranded RNA that encodes for the virus’s nine genes, which are enclosed by a ‘shell’ that is made up of 2 000 copies of the viral protein p24. This internal structure is enclosed by an evelope, which is made up of two fatty layers that are taken from the membrane of a human cell when a newly formed virus particle buds from the cell.

Let’s try to unpack the way that researchers followed the immune response of the HIV-positive man from Malawi. When he was first infected with HIV his body reacted as described above. His first response to the HIV infection is called the humoral response to infection. An infectious agent, such as a virus or bacterium, is called a pathogen and the infected person or other mammal is called a biological host. It is vital that we are able to mount a defence against infectious diseases. To do this, our bodies need to be able to eliminate the pathogen or its toxins by making them nonfunctional. The collection of various cells, tissues and organs that specialise in protecting the body against infection is called the immune system. The immune system does this through direct contact between certain types of white blood cells and the pathogen, which involves a part of the immune system called cell-mediated immunity or by producing substances that move to sites distant from where they are produced, where they actively seek the disease-causing cells by specifically binding with them and neutralising them in the humoral arm of the immune system. These substances are soluble antibodies. Now to the B cell response. Antibodies serve various functions in protecting the host against the pathogen. Their soluble forms that carry out these functions are produced by plasma B cells – a type of white blood cell. This production is tightly regulated and requires the activation of B cells by activated T cells (another type of white blood cell). The major steps involved are: n Specific recognition of the pathogen because of its antigens and then engulfing the pathogen by B cells or macrophages; this partially activates the B cell n Antigen processing n Antigen presentation n Activation of helper T cells by antigen-presenting cells n Co-stimulation of the B cell by an activated T cell, which results in complete activation of the B cell n Proliferation of B cells, which results in the production of soluble antibodies

Scanning electron micrograph of HIV (in green) budding from a cultured lymphocyte. Multiple round bumps on the cell surface respresent sites of assembly and budding of virions. Image: Wikimedia Commons

The immunology of HIV To start to understand the search for a vaccine to prevent HIV infection, you need to understand the immunology of the virus and how it affects the immune system of an infected person. When a person is infected by HIV, the virus enters the bloodstream through the mucous membranes that line the vagina, rectum or, more rarely, the mouth. Cells from our immune system called macrophages and dendritic cells, bind the virus and take it into our lymph nodes. The lymph nodes contain high concentrations of helper T cells – which are better known as CD4+ T cells. Once HIV has entered the body, the immune system starts to produce anti-HIV antibodies and cytotoxic T cells. This can take between one and six months. As HIV invades the body, it weakens many of our natural immune defences by destroying immune cells such as memory T cells. The virus replicates rapidly and is present in large numbers in the blood stream and throughout the body’s lymph tissues. HIV is so successful at establishing chronic infection because the way that our immune system works actually causes HIV replication. The body responds to HIV by producing more and more CD4+ T cells, which are then destroyed. This rapid turnover of CD4+ T cells and their destruction leads to a change in the lymphoid tissues that are

Steps in production of antibodies by B cells: 1. Antigen is recognised and engulfed by B cell 2. Antigen is processed 3. Processed antigen is presented on B cell surface 4. B cell and T cell mutually activate each other 5. B cells differentiate into plasma cells to produce soluble antibodies. Image: Wikimedia Commons

In our man from Malawi, what researchers were seeing as they examined his blood over and over again for many years following his infection was this response to each strain of HIV that evolved from the founder virus with each replication of the virus as it spread through his body. Eventually the antibodies that were produced were able to neutralise many different strains of the virus and not just the founder virus strain – broadly neutralising antibodies or bNAbs. Material for this article was sourced from Wikipedia.

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Will our coral reefs survive

climate change?

Coral reefs world-wide are being threatened by warming oceans, which causes ‘coral bleaching’, as well as by ocean acidification. In the face of such climate change impacts, the small South African coral reefs of KwaZuluNatal may provide a refuge for western Indian Ocean corals. By Mike Lucas. Hard coral reefs are home to colourful fish and other animals, such as this bright blue starfish. Image: Wikimedia Commons


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❚❚❚❙❙❙❘❘❘ Climate change

Corals belong to the Phylum Cnidaria (Class Anthozoa). The colourful polyps (right) contain symbiotic photosynthetic algae, called zooxanthellae (above), which live in the polyps.


pectacular, exotic and diverse – tropical and subtropical coral reef ecosystems such as Australia’s Great Barrier Reef provides refuge for 25% of all marine species. These include lowly sponges, sea squirts, delicate fan-worms, sea urchins, starfish, exotic molluscs and crustaceans, shoals of multi-coloured fish and reef sharks. Coral reefs are therefore some of the most biodiverse and economically important ecosystems in the world. Apart from attracting tourism, coral reefs also provide natural barriers against storm damage and coastal erosion. They also provide building materials and support artisanal fisheries, as well as being an increasing source of new biomedical compounds. Closer to home in South Africa, coral reefs of the western Indian Ocean in Kenya, the Maldives and the Seychelles have attracted recreational scuba divers from all over the world. The high-latitude reefs of South Africa represent the current southern geographical limit of western Indian Ocean reefs and are located within the iSimangaliso Wetland Park, a World Heritage Site that is perhaps better known as St Lucia, on the north-eastern KwaZulu-Natal coast. Although these reefs in Sodwana Bay between 27°23’S and 27°32’S are small by global standards, with a total area of barely 3 km2, they are of disproportionate scientific interest because they may represent a southern refugia for more tropical western Indian Ocean corals that face a sterner test as a result of of ocean warming.

What are corals? Corals are animals consisting of colonies of identical individual ‘polyps’. The most common corals are reefbuilding hermatypic corals found in clear, shallow, sunlit but nutrient-poor tropical waters. Reefs are built from the calcium carbonate (aragonite) skeletons of corals stacked on top of each other, where reef growth and physical erosion are finely balanced. Each polyp feeds by capturing scarce and minute suspended food particles with their sticky tentacles. Corals supplement this food ration with organic carbon produced by photosynthesising symbiotic algae that live within the polyps, collectively called zooxanthellae (e.g. Symbiodinium). It is their differing photosynthetic pigments that create the colourful tapestry of coral reefs. The coral-zooxanthellae symbiotic relationship is an

The 2 600 km long Great Barrier Reef, off the Queensland coast, consisting of about 2 900 reefs scattered among over 900 coral atolls. Image: Wikimedia Commons

uneasy one. Zooxanthellae produce O2 from photosynthesis, which the corals must ditch to avoid oxidative stress, yet 90% of the energy corals need comes from their zooxanthellae. In exchange, the polyps provide their guests with a home and CO2 for photosynthesis, as well as excreted ammonium to build protein. Without zooxanthellae, the corals die. The fate of corals Modern corals first appeared in the Jurassic Period (~200 million years ago), surviving Earth’s many cataclysmic events since then. But now coral reef ecosystems are in serious trouble due to rapid climate change. Coral reefs are dying because of ocean acidification, increasing sea-surface 9| 4 2013


The global distribution of hard coral reefs. Most corals live in shallow clear waters warmer than 20 °C, marked by the 20 °C isotherm boundary between warm subtropical and tropical waters (dark blue) and cooler waters (light blue). Image: Wikimedia Commons Left: When SSTs exceed about 29 °C, the corals expel their zooxanthellae and the corals turn white (bleached) without them. Image: Wikimedia Commons

temperature (SST), pollution, sea level rise and disease, leaving dead reefs bereft of life. During the 20th century, average global SST has risen by 0.74 °C. Coral bleaching generally occurs when summer SST exceeds 1 - 2 °C for 3 - 4 weeks, although some coral species are more resilient than others. At the same time, average ocean pH has fallen by about 0.1 pH units – enough to affect the coral’s ability to form their calcium carbonate skeletons. As a result, about 10% of coral reefs world-wide have already died, and a further 60% are acutely at risk. Coral reefs in the Indo-Pacific are disappearing faster than tropical rain-forests. In the early 1980s about 40% of reefs were covered by live coral, but this was just 20% by 2003. Today only 2% of Indo-Pacific reefs have as much live coral as they did in the 1980s. Caribbean reefs are declining even faster, annually losing 1.5% of the area they once covered. South African reefs remain relatively secure for the moment, and largely escaped the mass bleaching event of 1998 that severely affected Indian Ocean reefs. Even so, recent research by Mike Schleyer and his colleagues in Durban has revealed that the intensity and frequency of bleaching events have increased over the last decade as sea temperatures have risen. The effects of ocean acidification and high temperature on corals Corals grow and calcify normally at an aragonite saturation state of greater than 4.5. However in 2011, Australian scientists working on the Great Barrier Reef found that aragonite saturation state is now less than 3.5, a value where aragonite should begin to dissolve. But surprisingly, the corals still appear healthy, although perhaps close to a critical ‘tipping point’ of aragonite saturation state of 2.8 recorded in the Red Sea, where corals are beginning to dissolve. Even so, some corals are able to survive at low aragonite saturation state by physiologically controlling their internal pH and aragonite saturation state, but this uses extra energy. Although this ability does allow such corals to survive, ‘coral bleaching’ poses another serious threat. Corals thrive best in waters of 25 - 27 °C, but if SST rises to 29 °C or more, even for a few days, the coralzooxanthellae relationship becomes unbalanced, so the zooxanthellae are expelled and the corals turn white. 8

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Without their major source of nutrition, the corals soon die unless SST falls and the zooxanthellae are replaced. Current trends in tropical SST warming may mean that the Great Barrier Reef will be in serious trouble in less than 10 years. Moreover, El Niño events compound rising SST, and during the 2010 event 16% of the world’s reefs died, including 80% of Indonesia’s corals. Coral survival strategies One way corals might escape warming is for reefs to ‘migrate’ into cooler waters fast enough to offset local SST warming. For the Great Barrier Reef, the required migration rate is about 15 km per year. Unfortunately this is much faster than corals grow, although their planktonic larvae could re-colonise suitable new areas. It is the southern geographic range of the South African reef systems that makes them a potential refugia for Indian Ocean corals. The downside is that ocean acidification impacts are more severe in cooler waters. Coral reefs may therefore be squeezed into a narrower latitudinal distribution by tropical ocean warming and greater ocean acidification impacts in cooler, more pole-ward oceans. Adaptation to rising SST may, however, be possible. Corals in the Arabian Gulf tolerate temperatures that exceed near-term climate change predictions. It seems that some corals can host different types of zooxanthellae with differing tolerances to elevated SST. This could lead to the evolutionary selection of more heat-tolerant corals over several decades, although recent (2011) evidence suggests that only 25% of corals have this option. Sea level rise (SLR) poses yet another threat, but also an opportunity. Current SLR is about 2 - 5mm per year, with a potentially catastrophic rise of 3 - 7m if the West Antarctic and Greenland Ice sheets melt in the future. Since many reefs have grown upwards to the point where they are sealevel-limited, a modest rise in sea level would be beneficial. Unless the worst-case scenario prevails, most coral reefs can certainly keep up with SLR. However, the increasing frequency of tropical storms and storm surges does pose a physically destructive threat, while any increase in coastal erosion could smother reefs with sediment. Multiple stresses have made corals more prone to diseases over the last 20 - 30 years. Rising SST compromises coral immune systems, leading to bacterial and viral infections

The structure of corals Corals are marine invertebrates of the Class Anthozoa and phylum Cnidaria. They usually live in compact colonies of many, many identical individual polyps. Some corals can catch small fish and plankton using stinging cells on their tentacles, most corals get their energy and nutrients through the photosynthetic single-celled algae – zooxanthellae – that live with the coral’s tissue. These corals need sunlight and grow in clear, shallow water, usually at depths of less than 60 m.

by, for example, herpes-like viruses in the coral Porites compressa. Even so, new evidence suggests that corals are fighting back with improved immune systems and pathogen-fighting bacteria. Is there hope? So, is there hope? Primitive corals first appeared in the Cambrian Period, 542 million years ago. ‘Modern’ Scleractinian corals appeared in the Jurassic Period, ~200 million years ago, surviving and adapting to Earth’s natural and relatively slow climate evolution, including the advance and retreat of the Ice Ages. Corals are therefore clearly ‘survivors’, but adaptation to rapid climate change represents a far more severe test of survival. Unless CO2 emissions are reduced to lessen their oceanic impacts, the future of corals looks stark, but don’t bet on their extinction. Q Associate Professor Mike Lucas is employed within the University of Cape Town’s Zoology Department. He is also an Honorary Research Associate at the National Oceanography Centre (NOC) in Southampton, UK. He conducts much of his research in the North and South Atlantic, as well as in the Southern Ocean and in the Benguela upwelling system.

Top: Many beautifully coloured corals in a coral reef. The colour is derived from symbiotic zooxanthellae. Image: Wikimedia Commons

Above: In this photograph you can see a close-up of the individual polyps that make up a coral colony. Image: Wikimedia Commons

A diagram of a coral polyp. Image: Wikimedia Commons

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A glider is deployed from the stern of the SA Agulhas II in December 2012 on the way to Antarctica. Image: Dave Scott

In 2012 the first five buoyancy gliders were deployed in the Southern Ocean. Now, South African researchers are using both wave and buoyancydriven seagliders. Quest explores further.

Gliders in the ocean

L Salinity data from the surface to 1 000 m from one of the gliders in the Southern Ocean.

The Liquids Robotic Wave Glider waiting to be deployed. Image: CSIR


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ast year (2012) saw the start of the revolutionary glider programme in South Africa - see Quest 9(1) 2013;15-17. Seb Swart and other scientists from the CSIR launched five buoyancy-propelled gliders. In September 2012, the first two gliders were deployed from the SA Agulhas II, marking the start of the Southern Ocean Seasonal Cycle Experiment (SOSCEx) which takes place from the austral spring 2012 to autumn 2013. These two gliders were deployed into the heart of the world’s largest ocean current, the Antarctic Circumpolar Current and this was the first time that gliders were used in this region of the Southern Ocean – the most under-sampled ocean in the world. Two months later, during the annual South African voyage to Antarctica, another three gliders were deployed 2 000 km downstream from the first two in order to continue the experiment. Glider pilots back in South Africa navigated these five gliders through the turbid Southern Ocean, where strong ocean currents and eddies threatened to push the gliders off course. These five gliders were retrieved in February and March this year and the full set of data from them is being analysed by Masters and Doctoral students at the CSIR and the Unversity of Cape Town. An integrated platform Now the glider programme is being expanded by using a dual robotics platform that will deploy both wave- and buoyancy-driven sea gliders. The new liquid robotics wave

The Southern Ocean Seasonal Cycle Experiment (SOSCEx)

Above: The Liquid Robotics Wave Glider on the surface of the ocean. Image: CSIR Above right: The crew of the SA Agulhas II preparing to deploy the Liquid Robotics Wave Glider. Image: CSIR

glider is designed to ride on the surface of the ocean using the vertical movements of the waves to propel it forward. The specialised instruments that this glider carries measure CO2, ocean acidity and other oceanographic physical variables. The data generated are sent via satellite and seen in real time by climate scientists at the CSIR. In October this year the SA Agulhas II was chartered for a short trip to the sub-Antarctic Zone of the Southern Ocean, where a wave glider was deployed along with a buoyancydriven glider. This deployment is unique since the 1 000 m profiling sea glider will be deployed together with the surface wave glider. This twinned deployment on the Good Hope Line will provide valuable insight into the relationship between the interior of the ocean, the mixed layer and the atmosphere – all at the same time. The team are intending to try to keep the two gliders within 1 km of each other – a demanding exercise in the stormy Southern Ocean. Seb Swart says, ‘For the first time, we are deploying a wave glider in the Southern Ocean, but of more significance to climate researchers, we have twinned it with a sea glider that dives below the wave glider. This will allow us to acquire valuable information from both gliders using an integrated approach, but more importantly, this means that we can link CO2 flux between the ocean and the atmosphere at the surface with understanding of the connected physical and biogeochemical processes that are occurring below the surface and in the ocean interior’. More buoyancy gliders will be deployed in December 2013 during the SA Agulhas II’s annual voyage to Antarctica to expand SOSCEx’s observational coverage. q Additional material for this article courtesy of Tendani Tsedu, CSIR.

SOSCEx has four main themes, linking the carbon cycle to climate variability: 1. The dynamics of mixed-layer stratification – the role of breaking surface waves, wind-driven currents and convection in the formation of the oceanic mixed layer 2. CO2 and O2 gas exchange with the atmopshere 3. Carbon export from the mixed layer 4. The bio-optics linking the inherent optical properties of the water column to visible irradiance seen by satellite observations The experiment will take place around the three annual logistical trip of the SA Agulhas II, starting with the spring voyage to Gough Island, the midsummer voyage to the South African National Antarctic Expedition (SANAE) base and the autumn voyage to Marion Island, with only around five to ten additional days over and above the existing schedule. Sampling started in September 2012 during the austral spring relief voyage from Cape Town to Gough Island. The four iRobot® SeagliderTM units were deployed south of the Subtropical Front, in the Subantarctic Zone, at the Subantarctic Front and in the nothern Polar Frontal Zone. They were programmed to profile the water column from the surfae to 1 000 m every 4 km in four dives a day. Carbon explorer floats were also deployed at the same location as each glider and the Liquid Robotics wave-glider units are now being deployed in the Subantarctic Zone and the Polar Frontal Zone to sample CO2 and O2. Each of the units will be intercepted during the summer SANAE poleward or equatorward legs and finally retrieved in the autumn on the Marion Island trip. Full water column profiles, taken at each release and intercept location, will provide biogeochemical and physics boundary conditions of the system, such as CO2 levels, nutrients, iron concentrations, phytoplankton species composition and bio-optics.

The SOSCEx oceanographic sampling strategy overlaid on the region's topography (in meters below sea level). Green line: Marion Island underway transect in April; red line: Gough Island underway transect in September; yellow line: GoodHope underway transect to Antarctica completed in December and February; magenta line: Buoy Run transect to South Georgia Island where underway and subsurface CTD measurements are taken. Image: CSIR

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Flux towers Along with ocean gliders, CSIR researchers have been looking at carbon dioxide exchange on land. By Antoinette Oosthuizen.


esearchers have also been keeping tabs on CO2 exchange on land. According to Dr Bob Scholes, CSIR Fellow and systems ecologist, it is difficult to achieve representative measurements over land, as the surfaces vary so much (as opposed to the ocean). Measurements in particular areas could be greatly influenced by a nearby sink or source of CO2. By measuring CO2 flux and concentrations at different places, and combining it with modelling and satellite observations, researchers hope to get a more accurate idea of carbon exchange from land ecosystems. The Skukuza flux tower in the Kruger National Park is one of the longest-running flux towers in Africa. There are only a few in savannas, those areas typified by grassland and scattered trees, covering 20%

Flux towers These are tall steel structures fitted with eddy-covariance sensors that measure the upward and downward movement of gases above the vegetation canopy due to air turbulence, 20 times per second. A flux tower in the African savanna. Image: CSIR


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❚❚❚❙❙❙❘❘❘ Climate change

Why invest in infrastructure to measure CO2? The uptake and release of CO2 between the atmosphere, oceans, plants, animals, soil and micro-organisms is part of Earth’s natural carbon exchange cycle which is approximately balanced in the long term, but has been disturbed by human activities since the Industrial Revolution. CO2 is the primary greenhouse gas emitted through human activity, such as the burning of fossil fuels for electricity, transport and industry and the clearing of land for agriculture. Too much CO2 in the atmosphere increases the absorption of heat from the sun, almost like a blanket, causing the lower atmosphere, land surface and ocean temperature of the Earth to rise. This is the main cause of modern climate change, prompting international attempts to limit the rise in CO2 and other greenhouse gases. To improve climate models, researchers need to understand and predict both how the ocean and terrestrial uptake of anthropogenic and natural CO2 might be affected by climate change, and how they drive longterm risk to economic development.

of land areas worldwide. An additional flux tower has been operated at Malopeni near the Phalaborwa gate in Mopane veld. This differs from the vegetation at Skukuza which is dominated by Acacia and Combretum trees. Thus, CO2 exchange in two of the major types of southern African savannas is covered. These towers have been taking detailed measurements of the exchanges of energy, water, CO2 and other substances between the land and the atmosphere since 2000. Q Material for this article is courtesy of the CSIR’s ScienceScope, Volume 6, Number 4, November 2013, South Africa’s Council for Scientific and Industrial Research. Antoinette Oosthuizen is a Research Communication Practitioner for the CSIR.

Acacia trees in the savanna. Image: CSIR

Dr Bob Scholes Scholes leads the CSIR’s research in respect of global change and ecosystem dynamics and is a CSIR Fellow. He has been with the CSIR since 1992. Before that, he led the South African Savanna Biome Research Programme. He is a systems ecologist who studies how global change processes, such as climate change, affect ecosystems, especially the terrestrial ecosystems of Africa. ‘Africa is regarded as approximately balanced between being a source and sink of CO2, but we need to understand the processes of photosynthesis and respiration from the continent’s ecosystems to be able to predict the carbon cycle. The data generated by the flux towers will be compared to atmospheric measurements and collated with oceanographic findings, information which can help us to fine-tune the models we use to make these predictions,’ he says. These data are part of a global repository known as FluxNet. Dr Bob Scholes. Image: CSIR

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Clean laboratories trace elements


Thato Mtshali sets up Africa’s first ‘clean laboratory to measure trace elements in seawater. By Antoinette Oosthuizen.

P At work in the clean laboratory. Image: CSIR

Dr Thato Mtshali working in a biochemistry clean laboratory. Image: CSIR

hytoplankton in the oceans absorb atmospheric carbon dioxide (CO2) through photosynthesis. We need to learn more about this process and its possible sensitivity to climate change and impact on global warming. This is why the recently established ‘clean lab’ at Stellenbosch University has been welcomed by local environmental researchers. Until recently South African researchers did not have the facilities to measure bioactive trace elements, like iron, in seawater in very controlled, sterile conditions. This is important as the trace levels of iron in seawater are so low that the slightest contamination due to human error or contaminated equipment – for example by rust on a ship – could lead to false positive test results or experimental bias. Before the establishment of the trace and experimental biogeochemistry clean laboratory, scientists had to send their samples to laboratories in the US and Europe for analysis, which was costly and time consuming. Scientists are now able to collect and test their own samples locally, putting them on a par with their international peers in being able to design and run experiments that advance our understanding of the trajectory of climate change in the 21st Century and will help assess the feasibility of iron-linked geoengineering options to reduce atmospheric CO2. They are also able to participate in long-term international observational programmes, such as GEOTRACES, which aim to

THE INFRASTRUCTURE Trace and experimental biochemistry clean laboratory This is a sterile environment and the air is virtually free from any form of contamination – only 10 000 (≥ 0.1 µm) particles per 1 m3 of air – which enables scientists to measure minute quantities of trace elements in seawater. The 20 m2 laboratory consists of three separate rooms with air pressure from high to low, to ensure that contaminated air does not flow into, but rather out of the third ‘clean’ room when the door is opened.

Sampling equipment The titanium frame GEOTRACES CTD rosette is a piece of equipment used for sampling It is fitted with 24 12 l GP-FLO bottles and weighs more than 300 kg. This rosette is used to collect seawater samples for trace metal


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analysis at different depths. It is deployed using a Kevlar/Dynema nylon rope instead of a steel cable to prevent metal contamination.

Trace metal clean containers The CSIR houses two clean containers (sampling and flow injection analyser (FIA) containers). The sampling container is used to store GO-FLO bottles and collect and filter clean seawater subsamples, while the FIA container is used for measuring low levels of iron concentrations in seawater using an FIA with chemiluminescence detection. These containers weigh 60 tons each and can be used during fieldwork at sea, or on land at the CSIR. The units are fitted with laminar flow hoods which ensure that the air circulation inside remains clean.

❚❚❚❙❙❙❘❘❘ Natural Environment

Dr Thato Mtshali. Image: CSIR

Meet ‘iron man’ Dr Thato Mtshali Mtshali obtained a PhD in organic chemistry at the University of the Free State and lectured there for two years before joining the CSIR in July 2009. He is a senior researcher who studies the biogeochemistry of iron in seawater. Mtshali and his colleagues collected samples during a recent cruise as part of the Southern Ocean Seasonal Cycle Experiment to investigate the influence of light and iron supply on phytoplankton processes. Seawater samples containing phytoplankton were spiked with iron and incubated in specialised incubators at different light and temperature conditions. This enabled researchers to investigate the impact of changing iron concentrations on phytoplankton physiology (how they react to light). ‘Our aim is to understand how Southern Ocean phytoplankton species adapt to iron and light deprivation. Access to the clean laboratory in Stellenbosch also means that we are now able to set up and grow specific plankton species using our own prepared trace metal clean seawater solution (AQUIL) and allow it to adapt to different iron and light conditions, similar to those of the Southern Ocean. We can now measure specific parameters in a way which not possible locally before,’ Mtshali says.

Dr Thato Mtshali with a fast repetition rate fluorometer used to measure phytoplankton physiology. The equipment helps researchers to understand how the phytoplankton responds to environmental changes in the ocean. Image: CSIR Phytoplankton form the bottom of the oceanic food chain. Image: Wikimedia Commons

The importance of iron improve the understanding of biogeochemical cycles and large-scale distribution of trace elements and their isotopes in all major ocean basins over the next decade. The R2.2 million laboratory was co-funded by the Department of Science and Technology through the CSIR’s Southern Ocean Carbon-Climate Observatory (SOCCO) programme, as well as the Stellenbosch University Rector’s strategic fund. Based at the university, a SOCCO participant, it is part of a broader strategy to integrate research infrastructure development. This includes the provision of new analytical equipment, for example, the titanium frame GEOTRACES CTD rosette, which is used to sample sea water to measure trace metal, and mobile clean laboratories that can be fitted in the polar research ship, SA Agulhas II. These trace metal containers are the first of their kind in South Africa and can also be used on land. This means that samples are kept under prescribed conditions from when they are collected at sea, until they can be analysed on board or stored for analysis on land. Dr Pedro Monteiro, head of SOCCO, says recent estimates

Phytoplankton grows in the upper layers of the oceans, because it needs light for photosynthesis to create food and energy for itself. It absorbs CO2 and plays an important role in the carbon cycle. Iron is a micronutrient which assists with photosynthesis and researchers have found that phytoplankton does not grow that well in open ocean regions such as the Southern Ocean, which are low in iron. ‘These tiny microscopic plant-like organisms form the bas of the marine food chain and they need iron for growth as it plays an important role in their different metabolic processes. Elevated iron concentrations can result in phytoplankton blooms which influence the carbon cycle through the biological pump which transports carbon into the deep ocean,’ says Mtshali.

indicate that approximately 50% of all CO2 emitted by humans and absorbed by oceans, is stored in the Southern Ocean. An estimated 85% of non-polar ocean productivity is supported by nutrients derived from the Southern Ocean, yet researchers know little about the sensitivity of its carbon and nutrient fluxes to climate change. Q Material for this article is courtesy of the CSIR’s ScienceScope, Volume 6, Number 4, November 2013, South Africa’s Council for Scientific and Industrial Research. Antoinette Oosthuizen is a Research Communication Practitioner for the CSIR. 9| 4 2013



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& Western Leopard Toad Citizen science


A small group of volunteers from the Western Cape are making a big difference to the fate of the endangered Western Leopard Toad. Quest investigates their efforts.


very wet, windy and unpleasant winter night, volunteers from the communities around the Cape Flats, southern suburbs and the south peninsula of Cape Town in the Western Cape patrol the roads in an effort to prevent Western Leopard Toads (Amietophrynus pantherinus) from being killed as they cross roads in their annual migration to mating ponds. Toad NUTS At least, that is part of what Toad NUTS is all about. Toad NUTS (Noordhoek Unpaid Toad Savers) are an ‘exciting group of volunteers with the aim of saving the endangered Western Leopard Toad from extinction’. They work together with all toad volunteers in the greater Cape Town area and are supported by the Western Leopard Toad Conservation Committee (WLT-CC). Toad NUTS was started in 2008 by Noordhoek residents, Suzi J’Kul and Alison Faraday, after they realised the extent of the damage being done to the toad population by cars on the Noordhoek roads. The group identified three main challenges to the species’ local population – migration hazards and alien fish and ducks in the local breeding dams and wetlands. Initially, their focus was on preventing road mortality in the main breeding areas by patrolling the roads on dark, wet nights to try to slow motorists down to prevent ‘splatter’ – dead toads on the road. But in the main migration areas such as the section of Noordhoek Main Road, running past the Lake Michelle wetland, up to 29% of all toads seen were killed on the road. And it was not only the toads that were in danger. Toad NUT patrollers took their lives in their hands as well – confronting motorists, often worse the wear for drink, on dark, wet nights. One volunteer was rammed by a drunk driver in a bakkie as she stopped to examine a dead toad on the road. Something more than road patrols was needed.

International solutions to the problem of ‘road kill’. Image: Alison Faraday


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Fauna barriers Road kill is not just a local problem and it is not just amphibians that are endangered by road kill. Large mammals such as moose, caribou and mountain goats are killed on roads in Canada for, example. In response, Canadian conservation authorities have constructed overpasses over the Banff Trans Canada Highway. There are even bridges for red crabs in Australia. But what can we do here? In more affluent parts of the

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Right: Barriers were constructed along Noordhoek Main Road and inside the residential Lake Michelle complex. Image: Alison Faraday Below: It was not just the toads who were in danger on wet, winter nights. Image: Toad NUTS

the toads heading over the road to Lake Michelle to breed. On the west side of Main Road, volunteers found 27 toads behind the barrier and in buckets – assumed to be toads who have bred and were returning to their home ranges. All toads found behind the barrier and in buckets were carried to the opposite side of Main Road and placed safely behind the barrier.

A graph showing road kills before and after the construction of the barrier. Image: Alison Faraday

world, specially constructed amphibian tunnels, drift nets and pitfall traps have been placed permanently in areas where amphibians are known to cross busy roads. All of these solutions were impossibly costly for this self-funded local initiative. But this did not deter the brains and energy behind Toad NUTS, Suzi J’Kul and Alison Faraday. With the help of Endangered Wildlife Trust (EWT) Toad NUTS constructed barriers using the emergency-coloured netting similar to that used in road construction projects in South Africa. On particularly busy migration areas such as the 500 m stretch of Noordhoek Main Road past Lake Michelle, these barriers lead the toads into bucket pitfall traps, from which they were carried by volunteers, across the road and into their breeding wetland areas. Was the barrier successful? The graph above shows that road kills were substantially reduced following the introduction of the barrier. Before the barrier was erected on 4 August 2013, 70 toads attempted to cross this stretch of Noordhoek Main Road. A relatively large number (19) of these were found dead on the road, in spite of regular road patrols trying to prevent this. The eastside barrier was erected on 4 August 2013 and the west-side barrier on 5 August. Since the construction of the barrier, no toads have been found on this stretch of road – either dead or alive. Volunteers manning the buckets found 61 toads behind the barrier and in buckets on the east side of Main Road –

Did the barrier reduce the death toll? The number of toads, dead and alive found on the 500 m stretch of road in 2013 is shown in the following table – before and after the barrier was erected on the east side of the road (to catch the migrating toads) and on the west side (to catch the returning toads).

Alive Dead Total % dead

Total migrating before barrier – east side





Total migrating after barrier – east side









Total migrating to breeding ponds Total returning before barrier – west side





Total returning after barrier – west side





Total returning from breeding ponds









Total (east and west)

The table below shows the comparative statistics from this section of road in 2011 and 2012 and before the barrier was erected in 2013.

Alive Dead Total % dead

2011 (no barrier)





2012 (no barrier)





2013 (before barrier)





2013 (after barrier)





The numbers speak for themselves. A spin-off of the barrier was that volunteer patrollers could focus on other migrating areas where there were no barriers because the barriers were monitored either early in the evening or early morning, when toads were no longer crossing the roads. As 9| 4 2013


Many other species were found in the buckets. Image: Alison Faraday

Leopard toads waiting to be transported across the road. Image: Alison Faraday

a result, live toads were rescued from roads in other areas by people who would have been patrolling this busy section of Noordhoek Main Road if the barrier had not been in place. Toad NUTS plan to erect barriers before the start of the 2014 breeding season.

An amplexing pair. Image: Stan Hannath

LIFE CYCLE The Western Leopard Toad only breeds in short bursts during the breeding season for around a week at a time. Breeding usually takes place during August, but has also been recorded during July and as late as September – particularly this year (2013), when the winter rains were very late. The start of the breeding season depends very much on rainfall and temperature. The start of the breeding season is signalled by large numbers of adult toads appearing after dark, particularly on rainy nights, when they converge on selected breeding sites, some of which are many kilometres from the toad’s normal range. The toads return to the same breeding sites each season. The calls of male toads signal their arrival at the breeding sites, usually at night, and in large groups – up to 200 have been recorded. The males will call from the shelter of wetland vegetation, but also from open water, particularly at night. Mating pairs – called amplexing pairs – use open water for spawning. The female deposits thousands of eggs in strings of jelly. Metamorphosis takes around 10 weeks and to begin with the tadpoles stick to the bottom of the breeding water. They develop into tiny 11 mm long toadlets that leave the water in October to December in their thousands. Many fall foul of predators and other hazards and relatively few develop into adults, which takes about one to three years for the males and two to six years for the females.


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The bucket list ‘Bucket runs’ were done at least once a day and 105 runs were done by 24 dedicated volunteers. Not only toads were found in the buckets. The species list included sand frogs, clicking stream frogs, sand toads, common platannas, slugeating snakes, Cape river crabs, skinks and terrapins. How did other suburbs do? Although the work done by the volunteers cannot provide an accurate picture of how many Western Leopard Toads there are in the volunteer area, it is useful to look at the numbers of toads seen. By far the largest number of toads were seen in the Noordhoek Main Road area. This may be a function of the numbers of volunteers patrolling that stretch of road but there are dedicated groups in other areas as well and general awareness is rising, particularly after the barrier was constructed. The larger breeding ponds are also around Noordhoek Main Road, which explains why there are many more toads crossing there. Challenges The story of Toad NUTS is one of the importance of passion and dedication and a willingness to take conservation matters into the hands of individuals. Toads have been saved – there is no question of that. But Western Leopard Toads are an endangered species for a number

The Western Leopard toad. Image: Wikimedia Commons


Citizen science. Image: Alison Faraday

The numbers of toads seen in other areas of the south peninsula. Image: Alison Faraday

of reasons. The main problem is that their range overlaps with that of humans, who also enjoy living in fynbos areas, close to the sea and around the toad’s wetland breeding areas. The fragmentation of toad populations as a result of human activity is another danger in itself. Small, isolated populations will not have enough genetic variability to breed successfully and will die out – further reducing the numbers available to breed in the entire population. While the efforts of Toad NUTS and other similar groups are certainly preventing deaths, only scientific studies of subsequent breeding success after these interventions will tell us just how successful these efforts are. This is where citizen science comes up against its greatest limitation. What is now desperately needed is intervention from the scientific community to guide further initiatives and do the research required to accurately guage the success or otherwise of conservation efforts. Q

The Western Leopard Toad is listed by the IUCN’s Red List of Threatened Species – popularly known as the Red Data List – as ‘endangered’. The species is listed as endangered because it occurs only in a very small range – across 1 750 km2 and occupies an area of only 440 km2. Its distribution is severely fragmented by human use of its environment and its environment is under ongoing threat from encroaching human development. The species is only found from the Cape Peninsula eastward to the westernmost part of Agulhas National Park. This area is constantly being reduced by development and habitat change within the City The distribution of the Western Leopard of Cape Town and Overstrand. Toad. Image: IUCN Western Leopard Toads only breed at low elevations within 25 km of the sea, although adults have been found ranging in the mountains up to 500 m. The subpopulations from the City of Cape Town are genetically distinct from the populations in the eastern area of the species’ distribution. The subpopulations in Kleinmond, Betty’s Bay and Pringle Bay in the Western Cape are now thought to be extinct.

Population Western Leopard Toads are common in the areas where they still occur and are fairly easily seen during the winter breeding season. But, within the last 20 years there have been drastic drops in numbers in the urban areas where they were once abundant. Because the populations are so fragmented by human development, only about half of the occupied habitat area is available to the toads and more than 50% of the subpopulations are unlikely to be able to replace themselves through successful breeding.

Habitat and ecology Western Leopard Toads breed in large wetlands, vleis, dams and slowmoving water in lowland fynbos heathland. They also breed in altered habitats with permanent water bodies and sometimes in temporary water bodies that retain water well into summer. The species prefers deep water with floating plants. Females lay up to 25 000 eggs. The species forages in fynbos heathland, farmland, suburban gardens and urban open areas, although always close to fresh water. And herein lies part of the problem – an ongoing decline in the quantity and quality of suitable habitat for foraging and breeding.

Find out more about Toad Nuts at http://toadnuts.ning.com

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Figure 4: Sketch of a yellowfish made by William Burchell at the Sak River, a Karoo tributary of the Orange River, on 3 September, 1811. Image: Copyright MuseumAfrika, Johannesburg

From rocks to dynamite Paul Skelton tells Quest about the historical foundation of freshwater ichthyology in southern Africa.


ish have always been interesting to humans. They have been used for food, as cultural icons and recently as pets in aquaria or ponds. Fish have been illustrated in rock art, on the walls of caves and on other hard objects such as bone or horn. Pictures of fish have even been found in ancient Egyptian tombs. In southern Africa there are many stone-age rock etchings and paintings of fish often showing fish shoaling, e.g. in Lesotho and the Eastern Free State close to the Caledon and the upper Orange rivers. A rock etching of the mudfish

Figure 1: A ‘rubbing’ impression of the rock etching of a mudfish (Labeo capensis), from near Schweizer-Reneke in the North-West Province, South Africa, as described by Schoonraad (1961). Image: Paul Skelton

Figure 2: Painting of Barbus capensis in the South African Museum, done by Heinrich Claudius in September 1685, during Simon van der Stel’s expedition to Namaqualand (Waterhouse, 1932). Image: Copyright South African Museum


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(Labeo capensis) from a site near Schweizer-Reneke in the North West (Figure 1) records a species that occurs in the Vaal River. Local knowledge of fish and their habits was clearly important to early humankind. 1652 - 1805 – the Cape Colony Europeans first arrived in southern Africa when the Portuguese were exploring the world in the late 16th Century. In 1652 the Dutch East India Company established a base at the Cape to restock the ships that were making the trip to the then Dutch East Indies (modern Indonesia). Jan van Riebeeck was the governor of the Cape at this time. Many of these early settlers and explorers were naturalists and it was common in those days for people such as Van Riebeeck and Simon van der Stel to take expeditions away from the settled areas to explore the local flora and fauna. One of the first illustrations of a freshwater fish from the region is a Clanwilliam yellowfish from the Oliphants River (Figure 2). This can still be seen in the South African Museum. 1805 - 1815 – the start of scientific ichthyology You have probably heard of Burchell’s zebra and Burchell’s coucal. There is also a genus of indigenous Cape plants, Burchellia. All these are named for William John Burchell, who travelled extensively in South Africa between 1810 and 1815. He collected over 50 000 specimens, including fish. His four-year expedition left Cape Town in June 1811, and returned in April 1815. The expedition started in Cape Town, travelled via the Berg River pass to the Breede River valley, up the Hex River pass and into the Karoo. From there it climbed the Roggeveld escarpment to the Great Karoo and proceeded on to the Orange River and beyond to the Vaal before turning south. It crossed the Orange, proceeded on to Graaff-Reinet, and then proceeded eastwards through the Camdeboo plains and down the Fish River valley to the Great Fish river mouth. From there it turned westwards and proceeded along the coastal plain to Algoa Bay and beyond via Tsitsikamma, Swellendam and back to Cape Town (Figure 3). In late August, early September 1811 he had reached and camped at the Sak River above the Roggeveld escarpment,

Figure 3: Burchell’s expedition, descending from the Sneeuberge near Graaff-Reinet. Image: Wikimedia Commons

Figure 6: The title page of the edition of the South African Quarterly Journal, the first South African publication in which southern African freshwater fishes are described by Andrew Smith. Image: The South African Musuem

where he saw and sketched a large species of cyprinid fish, that he described in 1822 as ‘Cyprinus aeneus’. The name depicted the beautiful golden yellow of the fish, as reflected in his original sketch now housed in the MuseumAfrika in Johannesburg (Figure 4). This description was the first of any freshwater fish from southern Africa. It is now called Labeobarbus aeneus. Sketching was an important way of recording nature and the environment before the advent of photography. Burchell’s excellent illustrations of the fish are good examples and are easily identified as species that we recognise today. Another little-known painting in the MuseumAfrika is a sketch made by Ensign Robert Dingle of the Cape Corp on the banks of the Koonap River in 1815 (Figure 5) which shows two species formally described many years later, the one labelled as ‘Carper’ (Sandelia bainsii Castelnau, 1861) and ‘Whitefish’ (Labeo umbratus (A Smith, 1841). The first museum specimens Which is the earliest collected museum specimen of a southern African freshwater fish species? As far as I can establish there are two possibilities. The one, the holotype of Barbus serra Peters, 1864, is in the Berlin Natural History Museum (also known as the Humboldt Museum), and the other possibility is the sample of the two syntypes of Spirobranchus capensis Cuvier, 1829, in the Museum National d’Histoire Naturelle, Paris. A holotype is a single physical example (or illustration) of an organism that is known to have been used when the species was formally described. A syntype is any one of two or more biological types that are listed in a description of a taxon where no holotype was designated.

Figure 5: The sketch made by Ensign Robert Henry Dingle of two fishes (Sandelia bainsii and Labeo umbratus) from the Koonap River, a tributary of the Great Fish River, Eastern Cape, on 27 October 1815. Image: Copyright MuseumAfrika, Johannesburg.

Andrew Smith – freshwater fish and the father of South African zoology Sir Andrew Smith, known as ‘the father of South African zoology’ arrived in South Africa in 1821 as a British Army medical doctor, and was posted to Grahamstown, Eastern Cape. As was the case for many doctors in the 1800s, Smith was a keen naturalist. He was stationed in the eastern Cape and Grahamstown until 1825 when he was sent to Cape Town to establish the South African Museum. He was a prominent scientific presence in Cape Town and was ‘the moving spirit’ in founding the South African Institution in 1829. This formed the roots of the Royal Society of South Africa. The Royal Society of South Africa was founded in 1908. The Society is one of South Africa’s premier multi-disciplinary scientific organisations. Some of the aims of the Royal Society of South Africa are to foster and advance pure and applied science through the exchange and development of scientific ideas and knowledge, especially between disciplines, to recognise and reward excellence in research and scholarship, to initiate debate on matters of public importance that affect science or arise from its application, to foster science education and to encourage the study of the history of science in South Africa.

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Figure 7: Stuffed type of B. capensis – bought by the Natural History Museum in London in 1845, most probably collected by Andrew Smith during his expedition to Namaqualand in 1828, and possibly stuffed by Jules Verreaux. Image: Copyright NHM, London.

In 1830 the South African Museum came under the care of the newly established South African Institution. At the same time the South African Institution also published a new periodical The South African Quarterly Journal, probably edited at the time by Andrew Smith, who was one of the new journal’s first authors. One of the early papers (Figure 6) described various animals including mammals, birds, reptiles, fish and invertebrates. The fish included two freshwater species in a new genus ‘Diacopoma’ – D. typicus and D. typicoides, which are clearly recognisable as the Cape kurper Sandelia capensis and the Rocky, Sandelia bainsii. The historical significance is that these are the first descriptions of freshwater fish from South Africa by a scientist working in a South African institution, and published in South Africa. However, Smith’s contributions to South African ichthyology did not stop there. In 1834 he led an 18-month exploratory expedition to the interior, returning to the Cape in 1836. The expedition began in Graaff-Reinet, travelled north to cross the Orange River and then followed the Caledon River into what is now Lesotho. It then retraced its path westward to as far as Kuruman before striking north again to the western reaches of the Limpopo, and the Waterberg and Magaliesberg ranges and then returned to Graaff-Reinet. Smith described many of the species discovered and collected on his expeditions and travels in Illustrations of the Zoology of South Africa between 1838 and 1849. These included descriptions of several well-known freshwater species – Labeobarbus capensis, Labeobarbus marequensis, Labeo capensis, Labeo umbratus, Pseudobarbus burchelli, Barbus pallidus and Tilapia sparrmanii. The type specimens of the two Labeobarbus exist as ‘stuffed specimens’ in the Natural History Museum in London (Figure 7) but types of the other species mentioned are not known. 1840 - 1900 – the extension of ichthyology in Africa During the later part of the 19th Century many species of freshwater fish were described as a result of major expeditions, as far afield as the lower Zambezi region of Mozambique. One of the most industrious explorers was Wilhelm Peters, who made extensive collections of mammals, birds, reptiles, fish and amphibians, which he sent back to his museum in Berlin, Germany. An interesting twist in the way specimens were collected occurred in the late 1800s. In 1876 an army officer, Lt. Trevelyan, stationed at King William's Town submitted 24

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fish and other animals to the British Museum in London. The fish had been collected by using a dynamite explosion to stun them – only 13 years after Alfred Nobel invented dynamite in 1863. Exploration by European naturalists continued to the very end of the 19th Century in southern Africa, with their specimens being deposited in European museums. Conclusions – on the value of archives, art, museums and history to science Archives, libraries and museums all are places where historical items are preserved in collections of documents and specimens and are therefore irreplaceable treasures of a nation. Such treasures must be maintained over long periods of time in as good a condition as possible if their value is to be retained. The items need to be properly catalogued and recorded for retrieval by a researcher, all needing sustained expertise and resources. This article illustrates just how important such resources are if history is to be recalled accurately, especially a while after the item was deposited in a collection. And institutions themselves undergo varied fortunes – sometimes in strong health and condition and at other times in a state of neglect and decline. The interaction of individuals with collection institutions of different nations as determined by the ebb and flow of history is a healthy aspect for any disclipline, as in that way there is a better chance that the treasures of humanity will survive in spite of local loss that might befall a particular collection. q Professor Paul Skelton was previously the Managing Director of the South African Institute for Aquatic Biodiversity. He has now retired to pursue his interest in systemic icthyology, describing a number of species that have been discovered through molecular studies as part of a general revision of the freshwater fish of southern Africa. Acknowledgements My interest in historical ichthyology was initially sparked by discussions with Dr Rex Jubb and Dr Jack Skead in the 1970s. I have been fortunate to visit many museums over many years and I acknowledge all the curators who gave generously of their time and energy to assist me in my enquiries. Most recently I have been helped in my enquiries by James Maclean at the Natural History Museum in London, by Dr Peter Barsch, at the Museum fuer Naturkunde, Humboldt University, Berlin, and Patrice Pruvost and the MNHN, Paris. I am grateful to Sally Schramm, of SAIAB for locating obscure literature.

❚❚❚❙❙❙❘❘❘ News

Turning coal dust into ‘green’ gold NMMU algae researcher aims to turn SA’s 70 million tons of annual coal waste into green coal – which can also be used in the production of eco-friendly aviation fuel. By Nicky Willemse Environmentally-conscious inventor Professor Ben Zeelie – the winner of Nelson Mandela Metropolitan University’s top innovation award for 2013 – is the driving force behind an algae-to-energy initiative which is paving the way towards cleaner coal and also yielding bio-fuel good enough to be used as jet fuel. Zeelie, who heads up NMMU’s internationally recognised institute of chemical technology, InnoVenton, said the university’s cutting-edge algae-to-energy project had reached the R7 million design phase for a one-hectare technical demonstration facility in Gauteng to prove the technical and economic viability of the algae cultivation system. Such a facility will probably cost around R30million to construct and should be up and running by the end of next year. The algae at the demonstration site will be used for fine coal recovery – a process that is attracting interest from the coal mining and energy generation industries, both here and abroad. ‘Each year, South Africa’s mines produce about 70 million tons of coal waste, mainly in the form of very fine coal dust – enough to run about 25 one thousand megawatt power stations. The estimated stockpile of discarded coal in South Africa is estimated at over 2.5 billion tons – enough to run 10 one thousand MW power stations for more than 100 years, if we can find a way to recover and use this coal waste.’ What Zeelie and his team have found is that ‘if you mix coal dust and algae biomass, the algae adsorps [collects] onto the surface of the coal and binds the dust together’. The result is a coal-algae agglomerate [briquette or pellet], for which they’ve coined the name CoalgaeTM, which enables the handling of the waste coal using normal mechanised equipment. The ‘green’ coal could potentially save companies huge amounts of money. ‘In Europe, coal-fired power stations burn approximately 10% biomass every year in an attempt to reduce greenhouse gas emissions. Previously, the whole power station had to be changed, allowing one feed for coal and another for wood and other biomass. With this product, there is only one feed, which for all practical purposes is still coal.; InnoVenton is also putting up a 15KW coal burner at its Gomery Avenue, Summerstrand site in Port Elizabeth. ‘We will burn the coal, producing sufficient amounts of carbon dioxide to feed the algae [in InnoVenton’s own algae cultivation system]. This will give us the data to make sure this process will work on a bigger scale, i.e. using flue gas from power stations to grow algae. We estimate that this will reduce greenhouse gas emission from power stations by well over 20%.’ ‘If we can show we can do all this [at the technical demonstration site], and we are confident we can, it will be a world stunner. The biggest coal companies in the world are extremely interested. The number of jobs opportunities this can create is enormous.’ A second critical algae-to-energy project is the production of aviation bio-fuel. ‘The government, through the department of public enterprise, has set a target for the production of 50% aviation bio fuel by 2020.’ ‘We’ve made recommendations about how to achieve that, using CoalgaeTM to produce the biofuel,’ said Zeelie. A third project driven by Zeelie is in the field of bio-plasticisers to replace phthalates – which have been banned in many applications in the northern hemisphere over health issues, but continue to be found here. They are added to plastics to increase their flexibility, transparency, durability, and longevity and are found in personal care products, baby products, pharmaceutical products, and so on. Zeelie said a natural oil from the leaves of certain Eucaluptus trees can be modified to function as an alternative to these traditional plasticisers. InnoVenton has tested it successfully in various forms, such as nail polish, perfume and capsules for pills. ‘In all the tests, it has performed as well or better than phthalates.’

Zeelie has about 20 national and international patents under his belt, maintains that ‘Every person has one role in life they’re supposed to be living. I was lucky enough to find that role.’

Professor Ben Zeelie, Image: NMMU

Celebrating 75 years since the Discovery of the Living Coelacanth 1938-2013

Photo: Laurent Ballesta / www.andromede-ocean.com

Somerset Street, Grahamstown, 6140 Tel: 046 603 5800 Fax: 046 622 2403 E-mail: saiab@saiab.ac.za Web: www.saiab.ac.za

Camp is set up outside of Johannesburg in the World Heritage Site of the Cradle of Humankind. Image: National Geographic

Rising Star Expedition Professor Lee Berger is leading an expedition to excavate fossils in the Cradle of Humankind World Heritage Site.


Peter Schmid from the Evolutionary Studies Institute at Wits examines one of the fossils. Image: Andrew Howley, National Geographic


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n international team of researchers, led by Professor Lee Berger, are starting excavations on a new site that may contain evidence of early human fossil remains in the Cradle of Humankind World Heritage Site (COHWHS) – around 40 km from Johannesburg. Berger is a Research Professor in Human Evolution from the Evolutionary Studies Institute at the University of the Witwatersrand and a National Geographic Explorerin-Residence. He is best known for the discovery of Australopithecus sediba at the Malapa site in the COHWHS. The latest discovery was made by an expedition team sent out by Berger to search the deepest recesses of the caves in the Cradle. ‘The exploration team leader Pedro Boshoff and his two assistants, Steve Tucker and Rick Hunber, were able to access a chamber deep underground that was nearly impossible to get to, where they have found some significant fossils on the surface of the cave floor,’ says Berger. The first step in the Rising Star Expedition is to get the fossils out of the cave and to study them thoroughly before any conclusions can be drawn. ‘We do not know as yet what species of hominin we have found and we will not speculate. Our aim is to get the fossils out carefully, study them, compare them to other

❚❚❚❙❙❙❘❘❘ Palaeosciences

Lee Berger watches the live feed from cameras 30 metres below ground. Image: Andrew Howley, National Geographic

Steve Tucker, Gerrie Pretorius and Andrew Doussy installed equipment in the cave and assist as guides and rescue support. Image: Wits University

Six cavers of Rising Star Expedition: L-R Hannah Morris, Marina Elliott, Becca Peixotto, Elen Feuerriegel, Alia Gurtov and Lindsay Eaves. Image: Wits University

fossil material from around the world and then proceed to analyse and describe them. This is part of the scientific process and we are hoping to publish our findings – if all goes well – late in 2014,’ explains Berger. To do this, Berger called on his community of friends on Facebook, Twitter and LinkedIn to help him find ‘tiny and small, specialised cavers and spelunkers with excellent archaeological, palaeontological and excavation skills’. Within days, Berger had a list of 57 qualified candidates, out of which six scientists, all women, were selected to participate in the excavation. ‘These are highly trained scientists with caving experience from the USA, Canada and Australia who are currently in South Africa preparing for the excavation,’ adds Berger. ‘Only a limited number of people will be allowed access to the site, as one of my key priorities is the safety of our scientists and researchers.We also have to do the best that we can under the circumstances to get the fossils out of the cave, through a complex recovery process.’ Members of the Speleological Exploration of South africa will assist the expedition. According to Professor Adam Habib, Vice-Chancellor and Principal of Wits University, ‘The university is home to the richest collections of hominid fossils in the world and discoveries made by Wits scientists in the Cradle of Humankind are some of the most significant in the palaeosciences record. Professor Berger and his team have already added to this valuable collection with the discovery of A. sediba and the latest find to be excavated by the Rising Star Expedition will once again demonstrate the tremendous promise of palaeosciences on the continent’. Access to the site will be restricted, but updates will be provided through a blog managed by National Geographic

Lee Berger welcomes caver Hannah Morris back above ground. Image: Andrew Howley, National Geographic

Professor Lee Berger with his Rising Star Expedition team address a media briefing. Image: Wits University

at http://newswatch.nationalgeographic.com/tag/rising-starexpedition/ This is the first exploration that Berger is undertaking after being named a National Geographic Explorer-inResidence earlier this year and the expedition is supported by the National Geographic Society. Q Issued by: Erna van Wyk, Communications Officer, University of the Witwatersrand, Johannesburg and Barbara Moffet, Senior Director of Communications, National Geographic Society, Washington DC. 9| 4 2013


SANSA’s SuperDARN Radar array located at the South African research base SANAE IV in Antarctica will be upgraded to a digital system later this year. Image: SANSA

South African Space Agency

celebrates World Space Week Catherine Webster focuses on SANSA’s contribution to space research.

T SANSA’s new Ku-band In-Orbit Test (IOT) limited-motion antenna. Image: SANSA

Dr Sandile Malinga (SANSA CEO), Dr Phil Mjwara Director General DST, Dr Woodrow Whitlow NASA and Raoul Hodges SANSA Space Operations MD during the inauguration of the new Antenna. Image: SANSA


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he United Nations commemoration of World Space Week (4 - 10 October) is in its fourteenth year and is a global celebration of space. This initiative aims at educating people about the benefits received from investment in space science and technology, and promotes the greater use of space for sustainable socio-economic development. It also encourages public support for space programmes, gets children excited about space, raises awareness of institutions around the world that are involved in space, and fosters international cooperation in space outreach and education. Space may seem a distant reality, but we only have to look around us to see the benefits it has brought to our daily lives. Images from space are now commonly used in plenty of sectors such as weather forecasting, agriculture (smart farming), urban planning, monitoring de-forestation or supporting crisis management in case of flooding or large forest fires. Space also creates unique opportunities to boost the economic performance of our continent. For one, it drives innovation. We can transfer technology from the space sector and create smart technologies and smart production. Spin-offs create further commercial uses, which contribute to industrial growth. The South African National Space Agency (SANSA) in partnership with the Department of Science and Technology (DST) hosted various World Space Week events across the country. The official opening of World Space Week took place at the SANSA facility in Hartebeesthoek with the inauguration of a new In Orbit Test (IOT) antenna. Another event was held in Pretoria at the National Botanical Gardens to launch a new educational resource for high school learners utilising satellite data from SANSA. SANSA also hosted a ceremony to unveil a new high frequency digital radar built by a team of SANSA engineers in Hermanus, Western Cape. Let’s take a closer look at each of these new developments shaping the South African space industry.

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SANSA engineers who built the new HF digital radar system during the unveiling ceremony in Hermanus, Western Cape. Image: SANSA

New antenna for South Africa The ever-increasing need for information generated from space requires a number of satellites to orbit the earth, which require more antennae all over the world to track and monitor their orbits and functions. This provides a great opportunity for South Africa to invest in and develop space programmes and projects. SANSA’s new Ku-band In-Orbit Test (IOT) limitedmotion antenna is an important addition to its growing number of technologically advanced antennae at its Space Operations facility, in Hartebeesthoek, near Brits. The new R17-million facility, internally funded by SANSA, is made up of a 10 m Ku-direct broadcast satellite band antenna and an equipment room fitted with IOT equipment and infrastructure to assist clients to successfully commission new satellites. SANSA has years of experience and knowledge in the operation of IOTs. The facility will have a useful life stretching beyond the next decade and will be upgraded continuously to ensure the best possible service to both the national and international space industry. ‘The new antenna was built in response to the growing demand by satellite owners for ground facilities that are essential to test the in-orbit communications performance of new geostationary satellites,’ says SANSA chief engineer Eugene Avenant. Speaking at the World Space Week inauguration event, Department of Science and Technology (DST) Director General Dr Phil Mjwara said ‘Nowhere do you see how exciting the interaction of science and technology can be than in space. Often our scientists set challenges which drive extraordinary engineering achievements. Being part of another South African achievement as SANSA inaugurate another successfully completed antenna is humbling and shows why SANSA continues to excel in this industry’. He also expressed his pleasure in the progress the Agency has made since its formation in 2010, saying that it is great that space exploration is becoming part of a national mission. He further pointed out that government can do more and will push our space industry activity to a new level.

Dr Jane Olwoch, SANSA Earth Observation MD, handing over a satellite image to Mr Mudau, Chief Director of the DST. Image: SANSA

Launch of Fundisa resources SANSA launched the latest resource to aid school learners to understand and utilise satellite data and tools in their geography curriculum. The Fundisa School Education and Fundisa Disk are set to help increase understanding of Earth observations among Grade 10 - 12 learners. These resources, which include a portal for students, will also help to raise awareness about the value satellite imagery adds to geographic information systems (GIS) analysis. These tools are aligned to SANSA’s goal of building intellectual capital through cutting-edge research, development, innovation, technology and applications in the country. The disk contains numerous Earth observation satellite images over South Africa from different satellites as well as tools and applications for the learners to gain practical experience in utilising such data in their school projects. Many schools do not have computers and computer-based GIS software – the Fundisa resources will provide scenes relating to the school's areas of interest and surrounding communities. SANSA will complement the data with material customised for FET and as much as possible align to the curriculum. By the time the learners graduate in Grade 12 they will have a greater understanding of Earth observation and can proceed to more focused studies at tertiary level.

The Fundisa resources aim to help increase understanding of Earth observation among Grade 10 - 12 learners. Image: SANSA

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SANSA engineer Jonathan Ward with the new digital SuperDARN radar transceiver system which will be shipped to Antarctica later this year. Image: SANSA

The Fundisa Student Portal was created to assist research and learning by providing useful information, links and course material in earth observation, enable communication between students and the earth observation team at SANSA through a community web forum and inspire, excite and leverage research and learning through web mapping applications and other technologies. Check out the Fundisa Student Portal at http://fundisa. sansa.org.za/ Keeping an eye on weather in space Just as there is weather on Earth, so too is there weather in space and it can interfere with and cause damage to satellites that we rely on every day. Satellites are important to us in many ways that we often take for granted. They provide us with cable television, internet, cellular communication, global positioning systems and even observe the Sun, providing us with early warnings of upcoming solar flares. As host to the only Space Weather Centre in Africa, SANSA operates a wide range of space weather monitoring instruments and provides an important service to the nation by monitoring the sun and its activity to provide information, early warnings and forecasts on space weather conditions. SANSA’s new high frequency digital radar system is part of the super dual auroral radar network (SuperDARN), an international network of over 30 radars used to monitor the dynamics of space weather. ‘The Agency’s new radar not only marks a milestone for national and international space weather research but has also provided a unique platform for developing skills in space science and technology,’ said SANSA CEO, Sandile Malinga during the unveiling ceremony held during World Space Week in Hermanus, Western Cape. Understanding space weather, a term used to describe the effects the Sun has on Earth and the planets of our solar system, is a global priority. SuperDARN data provide 30

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scientists with information regarding the Earth’s interaction with the space environment. ‘Communication and navigation technology, town planning, resource and disaster management are highly dependent on satellites operating in our space environment. Understanding this environment has become vital in order to protect technology in space and on Earth from the devastating effects of space weather’ said Dr Lee-Anne McKinnell, SANSA Space Science MD. SANSA decided to undertake the ambitious project of constructing the radar in-house to take advantage of the training opportunities offered by a project of this magnitude as well as the opportunity to develop a radio frequency laboratory. ‘Through the development of the SuperDARN Radar, SANSA is able to provide a state-of-the-art radar platform for space science research to take place nationally and internationally, further enhancing South Africa as a global space player’ said McKinnell. The new SuperDARN radar transceiver unit will soon be shipped to Antarctica, where it will be installed at the South African research base. It will replace the ageing analogue transceiver unit currently located in Antarctica and will function together with a 16-element antenna array which has been built near the SA research base. Antarctica is a prime location for space weather research because Earth’s magnetic field lines converge at the poles and act as a funnel, channelling space plasma into the atmosphere. The radar measures the position and speed of plasma in the Earth’s ionosphere, allowing scientists to study the Earth’s interaction with the space environment. Probing the space environment allows scientists to make new breakthroughs in the fascinating world of space weather research and find novel ways to protect our technology in space and on Earth. New satellite for South Africa The Agency is also undertaking the construction of South Africa’s third Earth observation satellite, which will be launched in about four years’ time. This is being funded by the Department of Science and Technology. The design and development will involve contributions from the South African industry and scientific communities, thus enabling the development of a local space industry and the necessary skills and knowledge needed for an effective space programme. The satellite will be different from the previous two South African satellites, which were technology demonstrators. The new satellite will have a clear primary mission, and secondary missions and ancillary missions similar to international Earth observation satellites. ‘The new satellite will be used to take pictures of the African continent that are vital to food security, land use and disaster recovery. A dedicated satellite is important as it makes the African continent less dependent on the rest of the world with regard to procuring this information’, says SANSA Acting Space Programme Manager, Shravan Singh. Space brings us many benefits and SANSA is committed to keep up with the latest developments in the industry in order to secure a place on the podium as Africa’s leading space-faring nation. Q Catherine Webster is the Communications Officer, SANSA Space Science.

❚❚❚❙❙❙❘❘❘ Planetary science

The first evidence of a comet strike on Earth

The first ever evidence of a comet entering Earth’s atmosphere and exploding, raining down a shock wave of fire which obliterated every life form in its path, has been discovered by a team of South African scientists and international collaborators.

An artist’s rendition of the comet exploding in Earth’s atmosphere above Egypt. Image: Terry Bakker


ar above what is now the Libyan Desert, an extreme event took place 25.5 million years ago. The evidence for this event? A small, very unusual stone, called ‘Hypatia’ found in the area of southwest Egypt. The event? A comet entering the Earth’s atmopshere and exploding. The discovery has not only provided the first definitive proof of a comet striking Earth, millions of years ago, but it could also help us to unlock, in the future, the secrets of the formation of our solar system. ‘Comets always visit our skies – they’re these dirty snowballs of ice mixed with dust – but never before in history has material from a comet ever been found on Earth,’ says Professor David Block of Wits University. The comet entered Earth’s atmosphere above Egypt about 28 million years ago. As it entered the atmosphere, it exploded, heating up the sand beneath it to a temperature of about 2 000 °C, and resulting in the formation of a huge amount of yellow silica glass which lies scattered over a 6 000 km2 area in the Sahara. A magnificent specimen of the glass, polished by ancient jewellers, is found in Tutankhamun’s brooch with its striking yellow-brown scarab. The research, which will be published in Earth and Planetary Science Letters, was conducted by a collaboration of geoscientists, physicists  and astronomers including Block, lead author Professor Jan Kramers of the University of Johannesburg, Dr Marco Andreoli of the South African Nuclear Energy Corporation, and Chris Harris of the

Tutankhamun’s brooch.

University of Cape Town. At the centre of the attention of this team was a mysterious black pebble found years earlier by an Egyptian geologist in the area of the silica glass. After conducting highly sophisticated chemical analyses on this pebble, the authors came to the inescapable conclusion that it represented the very first known hand specimen of a comet nucleus, rather than simply an unusual type of meteorite. Kramers describes this as a moment of career-defining elation. ‘It’s a typical scientific euphoria when you eliminate all other options and come to the realisation of what it must be,’ he said. The impact of the explosion also produced microscopic diamonds. ‘Diamonds are produced from carbonbearing material. Normally they form deep in the earth, where the pressure is high, but you can also generate very high pressure with shock. Part of the comet

impacted and the shock of the impact produced the diamonds,’ says Kramers. The team have named the diamondbearing pebble ‘Hypatia’ in honour of the first well-known female mathematician, astronomer and philosopher, Hypatia of Alexandria. Comet material is very elusive. Comet fragments have not been found on Earth before except as microscopic sized dust particles in the upper atmosphere and some carbon-rich dust in the Antarctic ice. Space agencies have spent billions of dollars to secure the smallest amounts of pristine comet matter. ‘NASA and ESA (European Space Agency) spend billions of dollars collecting a few micrograms of comet material and bringing it back to Earth, and now we’ve got a radical new approach of studying this material, without spending billions of dollars collecting it,’ says Kramers. The study of Hypatia has grown into an international collaborative research programme, coordinated by Andreoli, which involves a growing number of scientists drawn from a variety of disciplines. Dr Mario di Martino of Turin's Astrophysical Observatory has led several expeditions to the desert glass area. ‘Comets contain the very secrets to unlocking the formation of our solar system and this discovery gives us an unprecedented opportunity to study comet material first hand,’ says Block. Q Issued by: Kanina Foss, Senior Communications Officer, University of the Witwatersrand and Herman Esterhuizen, Media Relations Coordinator, University of Johannesburg. 9| 4 2013


Peter Higgs. Image: nobelprize.org

The Nobel Prize for PHYSICS On 8 October 2013 the Royal Swedish Academy of Sciences awarded the Nobel Prize for Physics for 2013 to François Englert, Université Libre de Bruxelles, Brussels, Belgium and Peter W Higgs,University of Edinburgh, UK.


he prize was awarded for ‘the theoretical discovery of a mechanism that contributes to our understanding of the origin of mass of subatomic particles, and which recently was confirmed through the discovery of the predicted fundamental particle, by the ATLAS and CMS experiments at CERN’s Large Hadron Collider’. François Englert and Peter W. Higgs were jointly awarded the Nobel Prize for Physics 2013 for the theory of how particles acquire mass. In 1964, they proposed the theory independently of each other (Englert together with his now deceased colleague Robert Brout). Almost half a century later, on Wednesday 4 July 2012, they were in the audience at the European Laboratory for Particle Physics, CERN, Geneva, Switzerland, when their ideas were confirmed by the discovery of a François Englert. Image: nobelprize.org so-called Higgs particle. 32

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The Standard Model The awarded theory is a central part of the Standard Model of particle physics that describes how the world is constructed. According to the Standard Model, everything, from flowers and people to stars and planets, consists of just a few building blocks – matter particles. These particles are governed by forces mediated by force particles that make sure everything works as it should. These matter particles are the particles that make up atoms – neutrons and protons. Neutrons and protons in turn are made up of smaller particles called quarks. According to the Standard Model only electrons and quarks are indivisible. The atomic nucleus consists of two kinds of quarks – up quarks and down quarks. So, three elementary particles are needed for all matter to exist – electrons, up quarks and down quarks. But in the 1950s and 1960s, new particles were found, both in cosmic radiation and at the newly constructed accelerators. This meant that the Standard Model had to include these new particles as well. Matter particles are not the only things that make up the universe – there are also force particles for each of nature’s four forces – gravitation, electromagnetism, the weak force and the strong force. Gravitation and electromagnetism

This is an artist’s concept of the Universe expansion, where space (including hypothetical non-observable portions of the Universe) is represented at each time by the circular sections. Note on the left the dramatic expansion (not to scale) occurring in the inflationary epoch, and at the centre the expansion acceleration. Image: Wikimedia Commons

are easy to see – they attract or repel. The strong force acts on quarks and holds proton and neutrons together in the nucleus. The weak force is what causes radioactive decay – needed for the nuclear process in the Sun, for example. But although the Standard Model unites the fundamental building blocks of nature and three of the four forces that we know about, we still don’t know how these forces actually work. For example, how does the Moon feel the Earth’s gravity or a piece of metal feel the magnet? Invisible fields The entire Standard Model also rests on the existence of a special kind of particle – the Higgs particle. This particle originates from an invisible field that fills up all space. Even when the universe seems empty this field is there. Without it, we would not exist, because particles acquire mass from contact with the field. The Standard Model is a quantum field theory in which fields and particles are the essential building blocks of the Universe. In quantum physics, everything is seen as a collection of vibrations in quantum fields. These vibrations are carried through the field in small packages, quanta, which appear to us as particles. Two kinds of fields exist: matter fields with matter particles, and force fields with force particles — the mediators of forces. The Higgs particle, too, is a vibration of its field — often referred to as the Higgs field. Without this field the Standard Model would collapse like a house of cards, because quantum field theory brings infinities that have to be reined in and symmetries that cannot be seen. It was not until François Englert with Robert Brout, and

Peter Higgs, and later on several others, showed that the Higgs field can break the symmetry of the Standard Model without destroying the theory that the model got accepted. This is because the Standard Model would only work if particles did not have mass. As for the electromagnetic force, with its massless photons as mediators, there was no problem. The weak force, however, is mediated by three massive particles – two electrically charged W particles and one Z particle. They did not sit well with the light-footed photon. How could the electroweak force, which unifies electromagnetic and weak forces, come about? The Standard Model was threatened. This is where Englert, Brout and Higgs entered the stage with the ingenious mechanism for particles to acquire mass that managed to rescue the Standard Model. The Higgs field The Higgs field is not like other fields in physics. All other fields vary in strength and become zero at their lowest energy level. Not the Higgs field. Even if space were to be emptied completely, it would still be filled by a ghost-like field that refuses to shut down: the Higgs field. We do not notice it; the Higgs field is like air to us, like water to fish. But without it we would not exist, because particles acquire mass only in contact with the Higgs field. Particles that do not pay attention to the Higgs field do not acquire mass, those that interact weakly become light, and those that interact intensely become heavy. For example, electrons, which acquire mass from the field, play a crucial role in the creation and holding together of atoms and molecules. 9| 4 2013


A possible discovery in the ATLAS detector shows tracks of four muons (red) that have been created by the decay of the short-lived Higgs particle. Image: CERN, http://cds.cern.ch/record/1459496

A Higgs particle can have been created and almost instantly decayed into two photons. Their tracks (green) are visible here in the CMS detector. Image: CERN, http://cds.cern.ch/record/1459459

If the Higgs field suddenly disappeared, all matter would collapse as the suddenly massless electrons dispersed at the speed of light. So what makes the Higgs field so special? It breaks the intrinsic symmetry of the world. Nature is full of symmetry – faces are regularly shaped, flowers and snowflakes exhibit various kinds of geometric symmetries. Physics unveils other kinds of symmetries that describe our world, on a deeper level. One such, relatively simple, symmetry stipulates that it does not matter for the results if a laboratory experiment is carried out in Stockholm or in Paris. Neither does it matter at what time the experiment is carried out. Einstein’s special theory of relativity deals with symmetries in space and time, and has become a model for many other theories, such as the Standard Model of particle physics. The equations of the Standard Model are symmetric; in the same way that a ball looks the same from whatever angle you look at it, the equations of the Standard Model remain unchanged even if the perspective that defines them is changed. 34

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The Big Bang Our universe was probably symmetrical at birth. At the time of the Big Bang, all particles were massless and all forces were united in a single force. But this original order no longer exists – we can no longer see its symmetry. Something happened just 10-11 seconds after the Big Bang – the Higgs field lost its original equilibrium. How? It all started symmetrically. Think of a ball in the middle of a round bowl – at its lowest energy state. If you push the ball it starts rolling but still returns to its lowest point. But if you put a hump in the middle of the bowl, the position in the middle will still be symmetrical but it is now unstable. The ball rolls downhill in any direction – and once the ball has rolled down, its position away from the centre hides the symmetry. This is how the Higgs field broke its symmetry and found a stable energy level in a vacuum away from the symmetrical zero position. This spontaneous symmetry breaking is also called the Higgs field’s phase transition – like when water freezes to ice – water changes phase. To make this change transition, four particles were needed, but only one, the Higgs particle, survived. The other three particles were consumed by weak force mediators, two electrically charged W particles and one Z particle – which is how they got their mass. This is the way that the symmetry of the electroweak force in the Standard Model was saved – the symmetry between the three heavy particles of the weak force and the massless photon of the electromagnetic force remains – but you cannot see it. Extreme machines Without the development of the particle collider, the Large Hadron Collider (LHC) at CERN, Higgs and Englert would probably not have seen their theory confirmed in their lifetimes. For a long time two laboratories, Fermilab outside Chicago, USA and CERN on the French-Swiss border, were trying to discover the Higgs particle. Fermilab’s Tevatron accelerator was closed down a few years ago, leaving CERN as the only place where the hunt could continue. CERN was established in 1954, in an attempt to reconstruct European research, as well as relations between European countries, after the Second World War. Its membership currently comprises 20 states, and about 100 nations from all over the world collaborate on the projects. CERN’s grandest achievement, the particle collider LHC is probably the largest and the most complex machine ever constructed by humans. Two research groups of some 3 000 scientists chase particles with huge detectors — ATLAS and CMS. The detectors are located 100 metres below ground and can observe 40 million particle collisions per second. This is how often the particles can collide when injected in opposite directions into the circular LHC tunnel, 27 kilometres long. Protons are injected into the LHC every ten hours, one ray in each direction. A hundred thousand billion protons are lumped together and compressed into an ultra-thin ray — not entirely an easy endeavour since protons with their positive electrical charge rather aim to repel one another. They move at 99.99999 per cent of the speed of light and collide with an energy of approximately 4 TeV each and 8 TeV combined (one teraelectronvolt = a thousand billion electronvolts). One TeV may not be that much energy, it

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more or less equals that of a flying mosquito, but when the energy is packed into a single proton, and you get 500 trillion such protons rushing around the accelerator, the energy of the ray equals that of a train at full speed. In 2015 the energy will be almost double in the LHC. Particle experiments Particle experiments appear to be quite crude – particles are smashed together at enormous velocities and somehow particle physicists are supposed to work out how the particles are constructed. The search is particularly difficult, however, as the physicists are looking for entirely new particles that are created from the energy released in the collisions. Mass is a type of energy – E = mc2 according to Einstein’s theory. This equation makes it possible for even massless particles to create something new when they collide – two photons collide and create an electron and its antiparticle, the positron. Two gluons collide and produce a Higgs particle – if the energy is high enough. The protons are like small bags filled with particles — quarks, antiquarks and gluons. The majority of them pass one another without much ado; on average, each time two particle swarms collide only 20 head-on collisions occur. Less than one collision in a billion might be worth following through. This may not sound much, but each such collision results in a sparkling explosion of about a thousand particles. At 125 GeV, the Higgs particle turned out to be over a 100 times heavier than a proton and this is one of the reasons why it was so difficult to produce. However, the experiment is far from finished. The scientists at CERN hope to bring further ground-breaking discoveries in the years to come. Even though it is a great achievement to have found the Higgs particle — the missing piece in the Standard Model puzzle — the Standard Model is not the final piece in the cosmic puzzle. One of the reasons for this is that the Standard Model treats certain particles, neutrinos, as being virtually massless, whereas recent studies show that they actually do have mass. Another reason is that the model only describes visible matter, which only accounts for one fifth of all matter in the universe. The rest is dark matter of an unknown kind. It is not immediately apparent to us, but can be observed by its gravitational pull that keeps galaxies together and prevents them from being torn apart. In all other respects, dark matter avoids getting involved with visible matter. However, the Higgs particle is special – maybe it could manage to establish contact with the dark matter. Scientists hope to be able to catch a glimpse of dark matter as they continue the chase of unknown particles in the LHC in the coming decades. The laureats François Englert is Belgian, born in 1932 in Etterbeek, Belgium. He received a PhD in 1959 from Université Libre de Bruxelles, Brussels, Belgium. He is Professor Emeritus at Université Libre de Bruxelles. www.ulb.ac.be/sciences/physth/people_FEnglert.html

Peter W Higgs is British, born in 1929 in Newcastle upon Tyne, UK. He received a PhD in 1954 from King’s College, University of London, UK. He is Professor Emeritus at the University of Edinburgh, UK. www.ph.ed.ac.uk/higgs/ Material for this article courtesy of nobelprize.org. Q

The galloping dung beetle. Image: Wits University

Galloping dung beetles could be counting their steps back home By Kanina Foss A species of dung beetle in the Western Cape has given up its ability to fly and instead gallops across the sand in a behaviour which researchers suspect evolved as a way to navigate back and forth from home. ‘This species of Pachysoma grabs bits of poo and gallops forward with it. That is really odd. Most insects walk with a tripod gait. They plant three legs in a triangle, while swinging the other three legs forward. It’s an incredibly stable way of walking because you’ve always got three legs on the ground. For an insect to abandon the tripod gait and use its legs together in pairs like a galloping horse is really radical. The big question is: why are they doing it?’ says Professor Marcus Byrne of Wits University. Pachysoma is also different to most dung beetles in that it collects dry dung and hoards it in a nest which it provisions with repeated foraging trips, instead of rolling one, wet, dung ball in a straight line away from competitors at the dung pile, never to return. A team of scientists including Byrne and colleagues from Lund University in Sweden think the species might have changed the way it walks because it needs to be able to find its way back and forth from its nest. ‘For most dung beetles, it’s always a one way trip – grab the poo, run away and never go back. The very marked pacing of Pachysoma’s gallop might be giving it a better signal in terms of estimating the return distance from the food to its nest. When it gallops, it slips less in the soft sand,’ says Byrne. Ants have been shown to count their steps as a way to navigate back and forth from home, and bees have been proven to use the optical flow of scenery across their retinas to measure how far they’ve travelled to forage from the hive. The team thinks the Pachysoma dung beetles are doing both. ‘Bees use optic flow as a measure of how fast and how far they’ve flown. Dung beetles have two eyes on each side of their head, one on top and one on the bottom, looking at the sand and we think Pachysoma might be registering optic flow with its bottom eye over the sand,’ says Byrne. But Pachysoma has not only changed the way it moves across land, it has also lost its ability to fly. ‘There are 800 species of dung beetle in South Africa and most of them fly. To fly makes sense because poo is a very ephemeral resource. It’s only useful for a few days and it’s very patchy – you don’t know where you’re going to find the next dropping. That’s why Pachysoma is so weird. Why would anyone give up flying?’ says Byrne. The team suspects that Pachysoma has sealed its wing cases to conserve moisture in the arid West Coast environment. ‘Breathing causes massive water loss. We think they’ve closed the elytra case to create a breathing chamber which keeps moisture inside,’ says Byrne. The unique behaviour of this galloping, flightless species has allowed it to dominate a niche market among dung collectors of the Western Cape. Kanina Foss is a Senior Communications Officer at Wits Univerisity.

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The Nobel Prize for CHEMISTRY On 9 October 2013 the Royal Swedish Academy of Sciences awarded the Nobel Prize for Chemistry to Martin Karplus, Michael Levitt and Arieh Warshel ‘for the development of multiscale models for complex chemical systems’.

Arieh Warshel. Image: nobelprize.org

The chemical equation for photosynthesis in plants.

An overview of the process of photsynthesis.


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Michael Levitt.

Martin Karplus.

Image: nobelprize.org

Image: nobelprize.org


hemists used to create models of molecules using plastic balls and sticks. Today, the modelling is carried out using computers. In the 1970s, Martin Karplus, Michael Levitt and Arieh Warshel laid the foundation for the powerful programs that are used to understand and predict chemical processes. Computer models mirroring real life have become crucial for most advances made in chemistry today. Chemical reactions occur at lightning speed. In a fraction of a millisecond, electrons jump from one atomic level to the other. Classical chemistry has a hard time keeping up. It is virtually impossible to experimentally map every little step in a chemical process. Aided by the methods that lead to the award of the Nobel Prize for Chemistry, scientists can use computers to unveil chemical processes, such as a catalyst’s purification of exhaust fumes or the photosynthesis in green leaves. A thought experiment Imagine that you would like to create artificial photosynthesis. Photosynthesis is probably the most important chemical reaction on the planet – the reason that life exists at all. Photosynthesising green leaves produce oxygen by converting light energy from the Sun into chemical energy that can be used for fuel. Carbohydrates, such as sugars, are made from carbon dioxide and water. From the diagram you can see that during photosynthesis, water molecules are split, oxygen is created and hydrogen is released. This hydrogen could be used to fuel vehicles. Mimicking the process of photosynthesis could produce more

The site of drug binding to a receptor. Image: www.schrodinger.com

efficient solar panels. Understanding the molecular process and being able to harness it could help you to solve some of the problems of global warming and climate change – a good reason to get excited about your experiments. How is this related to the work done by the Nobel chemistry laureates? Scientists are able to go into the Internet and search for three-dimensional images of the proteins that are used in photosynthesis. These images are freely accessible in large Internet databases. Using a computer you can do what you like to the images. You can see giant protein molecules made up of tens of thousands of atoms. In the middle of all these atoms is a small region called the reaction centre – where the water molecules are split. And what is really important – only a few atoms are directly involved in this reaction. Important atoms are four manganese ions, one calcium ion and several oxygen atoms. The image clearly shows how atoms and ions are positioned in relation to each other – but it says nothing about what these atoms and ions do. Somehow, electrons must be taken out of the water and there are four protons to deal with. How does this happen? This is where Karplus, Levitt and Warshel’s work comes in. Traditional chemistry cannot map the details of this process because most of these things happen in a fraction of a millisecond – nothing you can do in a test tube. Your computer image also isn’t a lot of help because it shows proteins at rest. When sunlight hits the green leaves, these proteins are filled with energy and the entire atomic structure is changed, so to understand the chemical reaction you need to know what this energetic state looks like. Modelling software There are already computer programs that allow you to calculate various possible reaction pathways – called simulation or modelling. This allows you to get an idea of the role of specific atoms at different stages of the chemical reaction. From this you can then carry out real experiments to show whether or not your model is correct. Each of these processes – experiment leading to simulation over and over again – can give you new clues and lead to further experiments and simulations. Theoretical chemistry now

relies heavily on computers. The work of Karplus, Levitt and Warshel is groundbreaking in that they managed to make Newton’s classical physics work side-by-side with the fundamentally different quantum physics. Previously, chemists had to choose to use one or the other. The strength of classical physics is that calculations are simple and can be used to model really large molecules. Its weakness is that it offers no way to simulate chemical reactions. For that, chemists had to use quantum physics. But such calculations required enormous computing power and could therefore only be carried out for small molecules. This year’s Nobel laureates in chemistry took the best from both worlds and devised methods that use both classical and quantum physics. For instance, in simulations of how a drug couples to its target protein in the body, the computer performs quantum theoretical calculations on those atoms in the target protein that interact with the drug. The rest of the large protein is simulated using less demanding classical physics. Today the computer is just as important a tool for chemists as the test tube. Simulations are so realistic that they predict the outcome of traditional experiments. The Nobel laureates Martin Karplus, was born in 1930 in Vienna, Austria. He received a PhD in 1953 from the California Institute of Technology, CA, USA. He is Professeur Conventionné, Université de Strasbourg, France and Theodore William Richards Professor of Chemistry, Emeritus, Harvard University, Cambridge, MA, USA. Michael Levitt was born in 1947 in Pretoria, South Africa. He received a PhD in 1971 from the University of Cambridge, UK. He is the Robert W and Vivian K Cahill Professor in Cancer Research, Stanford University School of Medicine, Stanford, CA, USA. Arieh Warshel was born in 1940 in Kibbutz Sde-Nahum, Israel. He received a PhD in 1969 from Weizmann Institute of Science, Rehovot, Israel. He is Distinguished Professor, University of Southern California, Los Angeles, CA, USA. Q 9| 4 2013


The Nobel Prize for MEDICINE On 7 October 2013 the Royal Swedish Academy of Sciences awarded the Nobel Prize for Medicine for 2013 to James E Rothman, Randy W Schekman and Thomas C Südhof for their discoveries of machinery regulating vesicle traffic, a major transport system in our cells.

Randy Schekman. Image: nobelprize.org

James Rothman. Image: nobelprize.org


his year’s Nobel Prize for Medicine honoured three scientists who have solved the mystery of how cells organise their transport systems. Each cell is a factory that produces and exports molecules. For instance, insulin is manufactured and released into the blood and signalling molecules called neurotransmitters are sent from one nerve cell to another. These molecules are transported around the cell in small packages called vesicles. The three Nobel laureates have discovered the molecular principles that govern how this cargo is delivered to the right place at the right time in the cell. Randy Schekman discovered a set of genes that were required for vesicle traffic. James Rothman unravelled protein machinery that allows vesicles to fuse with their targets to permit transfer of cargo. Thomas Südhof revealed how signals instruct vesicles to

Each cell in the body has a complex organisation where specific cellular functions are separated into different compartments called organelles. Molecules produced in the cell are packaged in vesicles and transported with special and temporal precision to the correct locations within and outside the cell. Image: nobelprize.org


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Thomas Südhof. Image: nobelprize.org

release their cargo with precision. Through their discoveries, Rothman, Schekman and Südhof have revealed the exquisitely precise control system for the transport and delivery of cellular cargo. Disturbances in this system have deleterious effects and contribute to conditions such as neurological diseases, diabetes, and immunological disorders. How cargo is transported in the cell In a large and busy port, systems are required to ensure that the correct cargo is shipped to the correct destination at the right time. The cell, with its different compartments called organelles, faces a similar problem: cells produce molecules such as hormones, neurotransmitters, cytokines and enzymes that have to be delivered to other places inside the cell, or exported out of the cell, at exactly the right moment. Timing and location are everything. Miniature bubble-like vesicles, surrounded by membranes, shuttle the cargo between organelles or fuse with the outer membrane of the cell and release their cargo to the outside. This is of major importance, as it triggers nerve activation in the case of transmitter substances, or controls metabolism in the case of hormones. How do these vesicles know where and when to deliver their cargo? Traffic congestion reveals genetic controllers Randy Schekman was fascinated by how the cell organises its transport system and in the 1970s decided to study its genetic basis by using yeast as a model system. In a genetic screen, he identified yeast cells with defective transport machinery, giving rise to a situation resembling a poorly planned public transport system. Vesicles piled up in certain parts of the cell. He found that the cause of this congestion was genetic and went on to identify the mutated genes. Schekman identified three classes of genes that control

Schekman discovered genes encoding proteins that are key regulators of vesicle traffic. Comparing normal with genetically mutated yeast cells in which vesicle traffic was disturbed, he identified genes that control transport to different compartments and to the cell surface. Image: nobelprize.org

Rothman discovered that a protein complex enables vesicles to fuse with their target membranes. Proteins on the vesicle bind to specific complementary proteins on the target membrane, ensuring that the vesicle fuses at the right location and that cargo molecules are delivered to the correct destination. Image: nobelprize.org

different facets of the cell´s transport system, thereby providing new insights into the tightly regulated machinery that mediates vesicle transport in the cell. Docking with precision James Rothman was also intrigued by the nature of the cell´s transport system. When studying vesicle transport in mammalian cells in the 1980s and 1990s, Rothman discovered that a protein complex enables vesicles to dock and fuse with their target membranes. In the fusion process, proteins on the vesicles and target membranes bind to each other like the two sides of a zipper. The fact that there are many such proteins and that they bind only in specific combinations ensures that cargo is delivered to a precise location. The same principle operates inside the cell and when a vesicle binds to the cell´s outer membrane to release its contents. It turned out that some of the genes Schekman had discovered in yeast coded for proteins corresponding to those Rothman identified in mammals, revealing an ancient evolutionary origin of the transport system. Collectively, they mapped critical components of the cell´s transport machinery. Timing is everything Thomas Südhof was interested in how nerve cells communicate with one another in the brain. The signalling molecules, neurotransmitters, are released from vesicles that fuse with the outer membrane of nerve cells by using the machinery discovered by Rothman and Schekman. But these vesicles are only allowed to release their contents when the nerve cell signals to its neighbours. How can this release be controlled in such a precise manner? Calcium ions were known to be involved in this process and in the 1990s, Südhof searched for calcium-sensitive proteins in nerve cells. He identified molecular machinery that responds to an influx of calcium ions and directs neighbour proteins rapidly to bind vesicles to the outer membrane of the nerve cell. The zipper opens up and signal substances are released. Südhof´s discovery explained how temporal precision is achieved and how vesicles´ contents can be released on command. Vesicle transport gives insight into disease processes The three Nobel laureates have discovered a fundamental process in cell physiology. These discoveries have had a major impact on our understanding of how cargo is delivered with timing and precision within and outside the cell. Vesicle transport and fusion operate, with the same general principles, in organisms as different as yeast and humans. The system is critical for a variety of physiological processes in which vesicle fusion must be controlled, ranging from signalling in the brain

Südhof studied how signals are transmitted from one nerve cell to another in the brain, and how calcium (Ca2+) controls this process. He identified the molecular machinery that senses calcium ions and converts this information to vesicle fusion, thereby explaining how temporal precision is achieved and how vesicles can be released on command. Image: nobelprize.org

to release of hormones and immune cytokines. Defective vesicle transport occurs in a variety of diseases including a number of neurological and immunological disorders, as well as in diabetes. Without this wonderfully precise organisation, the cell would lapse into chaos. The laureates James E Rothman was born in 1950 in Haverhill, Massachusetts, USA. He received his PhD from Harvard Medical School in 1976, was a postdoctoral fellow at Massachusetts Institute of Technology, and moved in 1978 to Stanford University in California, where he started his research on the vesicles of the cell. Rothman has also worked at Princeton University, Memorial Sloan-Kettering Cancer Institute and Columbia University. In 2008, he joined the faculty of Yale University in New Haven, Connecticut, USA, where he is currently Professor and Chairman in the Department of Cell Biology. Randy W Schekman was born in 1948 in St Paul, Minnesota, USA, studied at the University of California in Los Angeles and at Stanford University, where he obtained his PhD in 1974 under the supervision of Arthur Kornberg (Nobel Prize 1959) and in the same department that Rothman joined a few years later. In 1976, Schekman joined the faculty of the University of California at Berkeley, where he is currently Professor in the Department of Molecular and Cell Biology. Schekman is also an investigator at Howard Hughes Medical Institute. Thomas C Südhof was born in 1955 in Göttingen, Germany. He studied at the Georg-August-Universität in Göttingen, where he received an MD in 1982 and a doctorate in neurochemistry the same year. In 1983, he moved to the University of Texas Southwestern Medical Center in Dallas, Texas, USA, as a postdoctoral fellow with Michael Brown and Joseph Goldstein (who shared the 1985 Nobel Prize in Physiology or Medicine). Südhof became an investigator of Howard Hughes Medical Institute in 1991 and was appointed Professor of Molecular and Cellular Physiology at Stanford University in 2008. Q 9| 4 2013



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❚❚❚❙❙❙❘❘❘ News Prestigious gold award for NMMU scientist A second Nelson Mandela Metropolitan University (NMMU) scientist has been honoured nationally for exceptional services to the advancement of science. Professor Maarten de Wit has been awarded the prestigious S2A3 Gold Medal by the Southern Africa Association for the Advancement of Science, following in the footsteps of the likes of the late palaeoanthropologist Prof Phillip Tobias, and NMMU’s own Prof Richard Cowling, a botanist who received the award in 2009. The earth stewardship scientist was recognised for his contribution both locally and internationally to this growing transdisciplinary field of science. Prof. De Wit is an NRF (National Research Foundation) A-rated researcher and has been working to define the transdisciplinary field of research in geology and mineralogy into a new discipline termed Earth Stewardship Science. He plans to launch the world’s first courses in Earth Stewardship Science from NMMU. The concept of Earth Stewardship Science was birthed in Prof De Wit’s Africa Earth Observatory Network (AEON), which he founded at the University of Cape Town 10 years ago, giving rise to hubs at universities across the country. 'This institute was set up by 18 scientists in different disciplines, from the humanities

Professor Maarten de Wit.

to hard physics. Our aim was to solve the planet’s future and emerging problems – this can only be done as a team.' Prof De Wit said the Eastern Cape presented a unique 'laboratory' for Earth Stewardship Science, with a range of problems to solve, including those affecting the coastline and wetlands, as well as poverty and rural development. Prof De Wit, who was born in Holland

and schooled in Ireland, completed his PhD in Geosciences at Cambridge University. From there, he spent four years at Columbia University in New York, conducting most of his field work in Chile, trying to understand the origin of the Andes and how this mountain range connected with Antarctica. Inquiries: maarten.dewit@nmmu.ac.za

Global first as Wits researchers split pollen Wits researchers have become the first to cut sections through pollen grains and make it possible to view a three-dimensional image of the internal wall. This positions them to determine how the characteristics of the internal wall help to classify plants of particular interest. PhD student Alisoun House has become the international pioneer of this technique with her research on Acanthaceae, a notably eurypalynous (wide range of pollen features), large family of plants whose classification remains contentious. It’s difficult to find features that define Acanthaceae as a family but one of the features that has been used is pollen. Until now, all of the research has been done by looking at the external features of the pollen – what it looks like on the outside. Under the supervision of Professor Kevin Balkwill, House used a focused ion beam-scanning electron microscope (FIB-SEM) to slice through the pollen grains of species belonging to Acanthaceae. She then used an ordinary scanning electron microscope (SEM) to look at the inside walls exposed by the cut. ‘Kevin had the idea that this microscope could be used. People have used it to look at fossilised pollen but it’s the first time it’s been done on fresh pollen from living plants,’ says House. The FIB-SEM is like an ordinary SEM but where the SEM uses a focused beam of electrons to image the surface of a sample in the chamber, the FIB uses a focused beam of ions to cut a section through a sample in a chosen position. Wits has one of only two or three FIB-SEMs in the country. House’s experiments proved that it was possible to use the technique to get a three-dimensional image of the internal wall structure of the pollen grains. ‘We can now see features in the internal wall that we couldn’t see before using older technology which afforded only thin, twodimensional slices,’ says House. She will now investigate whether the images are able to further prove similarities between different plants within the family, making the technique a good taxonomic tool. The hope is that these newly visible features of the internal walls of pollen grains will add to the body of information and enable more accurate classifications.

Whole pollen grain of Justicia flava and a cross-section showing the whole cut surface. Scale bars: 2 µm. Image: Alisoun House

Whole pollen grain of Isoglossa ovata and a cross-section through the whole grain. Scale bars: 3 µm. Image: Alisoun House

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Fluttering by Pocket guide to butterflies of South Africa. By Steve Woodhall. (Cape Town. Struik Nature. 2013.) Another wonderful pocket guide and this time to features of our gardens and country walks that often go unrecognised – butterflies. The introduction provides concise and useful information about butterflies (and moths) who are members of the insect order Lepidoptera – the name taken from the Greek for the tiny scales that make up their wings. Before launching into the descriptions of the butterflies themselves, there is an introduction to the eggs – well illustrated so that you know what these funny things sitting on your garden plants and walls are. As in many southern African field guides, the all-important biomes are outlined and there is also a section on where to find butterflies. The guide describes more than 250 of South Africa’s nearly 700 butterfly species, from the tiniest blues and coppers to the enormous swallowtails and emperors. Each species is illustrated by a colour photograph and has a distribution map within the description. The species’ size is also given to prevent confusion as well as an inset photograph of any common variations in colour. A useful feature is the coded colour bar showing when a particular butterfly is most abundant. An excellent resource for any keen naturalist.

All the trees Field Guide to the Trees of Southern Africa. By Braam van Wyk and Piet van Wyk. (Cape Town. Struik Nature. 2013.) The first edition of this book was published in 1997 and it has remained the most popular field guide for trees of the region. As one of the authors, Braam van Wyk, points out this success is almost certainly due to the way that the book is set out, using an easy-to-undertand group recognition approach. The species are grouped based on leaf and stem features, which makes it accessible to


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the general user as well as to botanists. Only the species that are most likely to be encountered are featured – including all the southern African species would result in an enormous and cumbersome volume. There are around 1 200 native tree species in the region – many of them rarely seen by the average amateur naturalist. This field guide describes 1 000 of the southern African species. Species are arranged in 43 groups based on leaf and stem features, which are also colour coded, with a key to the groups at the beginning of the book. There are two large maps – one of biomes and vegetation types and one of regions and centres of plant biodiversity and endemism, so you can orientate yourself according to the region you are in. The book is illustrated throughout with full-colour photographs of leaf and stem features and the species accounts include distribution maps, which are coded according to whether a species is endemic to southern Africa, native to the region but also found further north in Africa, or a naturalised alien. The book is a bit big to carry on a hike, but is certainly something to have on the shelves or in the car when travelling.

Island birds Chamberlain’s Birds of the Indian Ocean Islands. By Ian Sinclair and Olivier Langrand. (Cape Town. Struik Nature. 2013.) Struik Nature have been producing excellent bird books for many years. This book covers a huge area of the Indian Ocean, dotted with islands and remarkably rich bird life, given that there are generally fewer species on islands than on continents – although there is obviously some movement between these islands and continental Africa. The first edition of this book was completed in 1998. Since then there have been quite significant changes in the avifauna of the islands. Species that were feared extinct, such as the Madagascar Pochard, have been rediscovered. Some rare species, such as the Madagascar Serpent Eagle, the Madagascar Red Owl and the Sakalava Rail have been found in new locations. There are also species new to science, such as the Tsingy Wood Rail, which have been described. The region covered is defined in a map at the start of the book, which also has a quick reference guide on the inside

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front and back pages, and A-Z quick reference to bird groups and the colour coding of the bird groups. In all, 502 species have been fully covered and there is a list of the species that are still under investigation – using genetic techniques to distinguish species from sub-species. The bird families are introduced with the number of species to be found and the page number of their description. There is also a section showing how to locate endemic birds in each island group. Each species described is illustrated by accurate coloured paintings done by Normon Arlott, Hilary Burn, Peter Hayman and Ian Lewington. Over 160 new illustrations have replaced older ones. Distribution maps are included with each species description. A must-have for any birder travelling to the Indian Ocean.

Star gazing 2014 Sky Guide: Africa South: Astronomical Handbook for Southern Africa. Astronomical Society of Southern Africa. (Cape Town. Struik Nature. 2013.) You know the end of the year is close when this little annual handbook is published. This is the indispensible guide to the night skies in southern Africa and all keen astronomers, amateur and otherwise, will have a copy. There are clear instructions on how to use the guide, which is quite technical, but not beyond the reach of anyone interested in the skies above us. The year’s highlights are detailed early, so that you know what to look out for on particular dates. Each month has an almanac, details about the constellations, the planets and the moon, as well as further information on any highlights for that particular time. For the newcomer there is a section on basic observing skills and what to look for when buying a telescope, as well as a listing of observatories and a useful glossary of terms.

Walking with flowers Common Wild Flowers of Table Mountain and Silvermine. By Hugh Clarke, Bruce Mackenzie and Corinne Merry. (Cape Town. Struik Nature. 2013.) I am particularly biased towards liking this book because Table Mountain and Silvermine reserve are on my doorstep and I regularly venture onto their wonderful slopes and plateaus. And

if I am walking, rather than running, this book will now accompany me. This is a particularly rich area of the Cape Floristic Kingdom, with some of the most unspoilt fynbos you could hope to find – astonishing given that it is set among a city of 3.75 million people. Table Mountain was recently voted one of the world’s new seven wonders of nature and is a World Heritage Site. Silvermine is next to Table Mountain in the south and is home to a large number of endemic species – species found nowhere else in the world – like Erica urnaviridis, which only grows on the higher ground of Silvermine East around Muizenberg Peak, or Erica nevillei growing on Noordhoek Peak in Silvermine West. There is a concise section on using the book, followed by descriptions of flower walks on Table Mountain and Silvermine. All is illustrated with beautiful photographs of the area, showing its spectacular outlooks. The flowers are colour coded, each illustrated with excellent photographs and good descriptions. A truly lovely book.

Flowers in Botswana Wild Flowers of Southeast Botswana. By Gwithie Kirby. (Cape Town. Struik Nature. 2013.) This volume covers the flowers that are found commonly in the southeast part of Botswana, bordering South Africa. The proceeds from the sale of the book have been pledged to the Mokolodie Wildlife Foundation, which is headed by Sir Ketumile Masire and was established in 1991 to promote nature conservation and environmental education for the children of Botswana. Again, the book is colour coded – a very easy way to present a guide aimed at the amateur naturalist. There is a brief outline of the different coloured flowers at the start of the book and then each species description is illustrated with large photographs of the 9|4 2013




flowers, with insets of specific characteristics if appropriate. The guide features over 330 of the more common wild flowers found in the region, many of which are also found in the northern parts of South Africa. The cultural significance of the flowers is marked by the inclusion of the Setswana common names and the traditional uses of the plants. Now for a trip to Botswana.

Geological travels Geology off the beaten track – exploring South Africa’s hidden treasures. By Nick Norman. (Cape Town. Struik Nature. 2013.) This book made me want to get into my car and head off to follow the routes so ably described by Nick Norman as he takes you on a wonderful trip around the geology of this fascinating part of the planet. South Africa has exceptionally good areas in which to study geology. If you study our geology you will come away with a real understanding of how our planet has changed over millions of years and evolved into the landscapes of today. There are 13 chapters that each cover a route that is of particular geological interest – complete with maps for each area, showing where you will see particular features. There are also geosites and GPS readings to pinpoint key sites. The diagrams in the book explain geological processes that are hard to describe, such as the crustal architecture of southern Africa and the way in which Algoa Bay has changed over geological time. The photographs are clearly labelled and geological features are highlighted with arrows or dotted lines so tha they are easy to see. There is a glossary of geological terms and a bibliography for those who want to explore further. The book was partially funded by De Beers and is a book that every family should have in their car.

Great gardens Succulent Paradise – twelve great gardens of the world. By Gideon F Smith and Estrela Figueiredo. (Cape Town. Struik Lifestyle. 2013.) This is a beautiful book, with lavish illustrations of twelve succulent gardens, from South Africa, France, Monaco, Italy, Switzerland, the USA and Mexico. What is particularly interesting is how many of the succulent species that are grown around the world originate in South Africa.


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Before moving into the gardens there are sections on exploring the world for succulents, how exotic succulents have ‘gone native’ in countries to which they were introduced, gardening with succulents, using succulents to green cities and how succulents can survive in a changing world. The photographs are superb, both of the individual plants and of the environments in which they are featured. Written by two South Africans, this book will make you look at succulents in a new way.

For the children Curly the Chameleon. By Charles de Villiers, illustrated by Claire Norden. (Cape Town. Struik Nature. 2013.) Curly the chameleon lives in a bush in the garden. He believes that he is a dragon, but a dragon that regards a small fly as a meal. Using rhyming prose, children are taken through Curly’s life, the characteristic features of chameleons, like swivelling eyes, the texture of his skin and how he feeds. Cats are his biggest enemy in an urban environment and Curly is able to escape notice by changing colour to blend in with his surroundings and outwit the cat. But the bird of prey is another matter and curly is taken on a hair-raising fly-past of his garden, finally escaping by wriggling so much that he is dropped, luckily landing safely on a tree branch in the garden. There are pop-out characters from the book for children to use to make up their own stories once they have read the book. Altogether great fun.

❚❚❚❙❙❙❘❘❘ ASSAf News

Young Academy of Science inaugurates new members The South African Young Academy of Science (SAYAS) inaugurated 10 new top young scientists as members at its annual inauguration ceremony on 6 November 2013. SAYAS was launched in 2011 as a mechanism to propel South Africa’s young scientists to fully participate in local and internationally relevant research and development agendas. It provides a national platform where leading young scholars from all disciplines in the country can interact, and also access international networking and career development opportunities.  The new young scientists represented the major universities in the countries and have research interests ranging from gender studies to quantum physics. The inauguration was also an opportunity to launch the report on the Research Experience of Young Scientists in South Africa, which was presented by Alta Schutte of North-West University. The authors of the report were Caradee Wright, Genevieve Langdon, Christine Lochner and Bronwyn Myers. Part of SAYAS’s mandate is to provide a deeper understanding of the needs and challenges of young scientsts in the country. The findings from the report will also act as a baseline for future SAYAS activities. To summarise the main findings of the study: n Most (46%) of postgraduate science students are studying at masters level. n 33% are studying at doctoral level. n Only 9% are studying at postdoctoral level and 12% are at honours level. The bulk of postgraduate science students are from four universities – Stellenbosch, Pretoria, Cape Town and North-West. Of the young scientists surveyed, 43% said that it was their desire for an academic career that had prompted them to do postgraduate studies – the proportion increasing to 58% among those doing a PhD. This potentially highlights a gap in students' knowlege about other possible careers after postgraduate science studies, such as industry, as well as suggesting that students are not aware of the needs

of broader society in terms of the developmental needs of the country. A problem with the report is that, in spite of the best efforts of SAYAS and ASSAf, responses were poorly representative of national enrolment figures in that 65% of respondents were white (national enrolment 19%) and only 20% were from black students

(national enrolment 59%). There was also an over-representation of respondents from the natural sciences – 39% against 11% national enrolment. In future SAYAS plans to conduct similar surveys, which may be specifically tailored to postdoctoral students and also a destination study to find out where our graduates are going.

Editorial committee of The Research Experience of Young Scientists in South Africa report. From left: Alta Schutte, Genevieve Langdon, Bronwyn Myers and Caradee Wright (Absent: Christine Lochner). Image: ASSAf

Jerome Singh (outgoing co-chair of SAYAS), Alex Broadbend (incoming co-chair of SAYAS), Patience Mthunzi (incoming co-chair of SAYAS) and Caradee Wright (outgoing co-chair of SAYAS). Image: ASSAf

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DNA: The code of life The human genome: first in Africa Where do chameleons come from?

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Velvet worms: DNA and conservation The oldest scorpion Short tails key to modern birds Nantechnology in space

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The electromagnetic spectrum: key to understanding our Universe Time machines and the accelerating Universe

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Study Science at WITS UNIVERSIT Y Why choose Wits? The Faculty of Science at the University of the Witwatersrand is internationally recognised for its innovative programmes which cover the Biological, Earth, Mathematical and Physical Sciences. The study of science opens doors to many exciting careers in diverse fields such as medical research, chemistry, computer science, biotechnology, genetic engineering and environmental sciences. The Wits Faculty of Science is one of the leading science faculties in the country and has an excellent track record in both teaching and research. Research strength ensures that staff members keep in touch with the latest developments in their fields. In addition to basic research in various fields, including mathematical modelling, high energy physics, biotechnology, molecular biology and environmental sciences, increasing effort is being devoted to applied research linked to a variety of activities in southern Africa.

The Bachelor of Science (BSc) A BSc degree will introduce you to the basic scientific disciplines. It is a stepping stone rather than an end in itself and many of our students go on to study at postgraduate level.

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Ghost of Jupiter Nebula This ghostly image from NASA’s Spitzer Space Telescope shows the disembodied remains of a dying star, called a planetary nebula. Planetary nebulas are a late stage in a sun-like star’s life, when its outer layers have sloughed off and are lit up by ultraviolet light from the central star. The Ghost of Jupiter, also known as NGC 3242, is located roughly 1 400 light-years away in the constellation Hydra. Spitzer's infrared view shows off the pace: cooler outer halo of the dying star, coloured here in red. Also evident are concentric rings around the object, the result of material being periodically tossed out in the star's final death throes. In this image, infrared light at wavelengths of 3.6 microns is rendered in blue, 4.5 microns in green, and 8.0 microns in red.

light to communicate with cells, but this method has been restricted by its limited ability to pass through tissues. Now HMS researchers at the Wellman Centre for Photomedicine at Massachusetts General Hospital have developed a way to deliver a light signal to specific tissues deep within the body. Harvard Medical School

Institutes of Health, Vanderbilt University mechanical engineer Michael Goldfarb has spent several years developing the leg, which operates with special sensors, an electric motor, a battery and computer technology. The image shows an example of a state-ofthe-art bionic leg. National Science Foundation

One day, we may fill the tank with fungi fuel!

A diagram showing the hydrogel implant at work. Image: Harvard Bio-Optics Lab/Wellman Centre for Photomedicine, Massachusetts General Hospital


Over his 50-year career, Montana State University plant pathologist Gary Strobel has travelled to all seven continents to collect samples of endophytes from remote and sometimes dangerous places. Endophytes are microorganisms – bacteria and fungi – that live within the living tissue of a plant. With support from the National Science Foundation (NSF), Strobel, engineer Brent Peyton and their team at Montana State University have discovered that endophytes have the ability to make diesel-like fuel. One hydrocarbon-producing fungus comes from the Ulmo tree of Patagonia. Another is a citrus fungus from Florida. And, amazingly, it takes the team just a few weeks to create the fuel. Strobel says the long-term goal is to improve the process of using microbes that degrade plant material, especially agricultural waste, to make economically feasible quantities of hydrocarbons. He adds fungi and bacteria hold great potential for breakthroughs in medicine, plastics and green chemistry as well. National Science Foundation

The ghost of Jupiter nebula. Image: NASA/JPL-Caltech/Harvard-Smithsonian CfA

Talking with light

A bionic leg. Image: University of Illinois

Light passing through an optical fibre can either carry in a signal that stimulates the activity of cells embedded in the hydrogel implant or bring back a signal generated by cells responding to something in their environment. As researchers develop new therapies based on making specific cells to do specific things, getting the right message to the right group of cells at the right time remains a major challenge. Some scientists have explored using

Bionic leg makes amputee faster on his feet A shark attack survivor now knows what it feels like to be part bionic man. Craig Hutto, a 23-year-old amputee in the US, has volunteered to play guinea pig, testing a state-of-the-art prosthetic leg with powered knee and ankle joints. With early support from the National Science Foundation (NSF) and continued support from the National

Fungi may one day fuel vehicles. Image: Snežana Trifunovic, via Wikimedia Commons)


A jar contains a special cell that doubles every minute. If the jar is full at 16h00, at what time was it a quarter full?

Answer to Maths Puzzle no. 26: Solution 4 x 2 x 2 x 2 = 32 kg

Win a prize! Send us your answer (fax, e-mail or snail-mail) together with your name and contact details by 15:00 on Friday, 7 February 2014. The first correct entry that we open will be the lucky winner. We’ll send you a cool Truly Scientific calculator! Mark your answer ‘Quest Maths Puzzle no. 27’ and send it to: Quest Maths Puzzle, Living Maths, P.O. Box 195, Bergvliet, 7864, Cape Town, South Africa. Fax: 0866 710 953. E-mail: livmath@iafrica.com. For more on Living Maths, phone (083) 308 3883 and visit www.livingmaths.com.

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TRANSFORM The South African Agency for Science and Technology Advancement (SAASTA) is opening people’s eyes to the wonder of science by listening and communicating; by engaging with them and making them aware of new scientific knowledge; by working together and sharing the excitement of science; and by building a new generation of young scientists. For more information visit www.saasta.ac.za

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