Quest 5(4) by Academy of Science of South Africa

SCIENCE SCIENCE FOR FOR SOUTH SOUTH AFRICA AFRICA

High p er forma nce comput ing: fro m b o ne count er s t o Blue Ge ne

ISSN 1729-830X ISSN 1729-830X

VOLUME 5 • NUMBER 4 • 2009 VOLUME 3 • NUMBER 2 • 2007 R29.95 R20

The hi st or y of co mput ing

Q ua nt um informat ion t ec hnology Space sc ie nce a nd a st rono my

A C AACDAEDMEYM YO FO FS C I EI ENNCCEE OOFF SS O U TT HH AAFFRRI C I CA A SC OU

Cover stories

The Centre for High Performance Computing. Happy Sithole The future of computing in South Africa 5

High performance computing: How did we arrive here? From abacus to Blue Gene – how have computers developed?

Green computing at the CHPC Green computing was an integral part of the planning of the Centre for High Performance Computing in Cape Town.

Graphic visualisation Graphic visualisation is used across the sciences, from physics to biology.

Contents VOLUME 5 • NUMBER 4 • 2009

32 12

Local action against climate change.

Quantum information technology: a novel approach to information transfer From Schrödinger’s cat to information transfer: the applications of quantum mechanics.

350.org

Space science and astronomy: The role of high performance computing

Letting the dead speak: The role of DNA analysis DNA analysis plays an important role in forensic science.

High performance computing takes South African astronomy to the cutting edge of science. 41

Changes in our coastal environment A newly rated NRF young scientist shares her love of science.

Features

42 16

Modelling HIV: The science behind treatment and prevention Understanding how the virus evolved and mutates is crucial to developing drugs and a vaccine.

KELT-south: The little telescope with big ambitions Rudi Kuhn The search for extrasolar planets continues.

Mathematical stastistics flourishes in Africa How a young African statistician is helping to control malaria.

Freshwater biodiversity in Africa The IUCN Pan-African Freshwater Biodiversity Assessment – what it means for the continent.

Where are we going with HIV vaccines? Lynn Morris and colleagues

Regulars Fact file

The search for a vaccine to prevent HIV has not been without its difficulties, but there is light at the end of the tunnel. 22

Vaccine research makes progress: The South African AIDS Vaccine Initiative

Careers Biotechnology

Book reviews

Conflicting reports about an HIV vaccine trial

Diarise SciFest Africa 2010

Results of a recent HIV vaccine trial in Thailand send out contradictory messages.

Diary of events

Building the future of computing and science in South Africa

CSIR news

The Centre for High Performance Computing is trying to bridge the digital divide.

Science news

ASSAf news

James Blighnaught and Leandri van der Elst

Subscription form

Climate change may have grave consequences for agriculture in South Africa

Back page science • Mathematical puzzle

Patricia Southwood New vaccine trials have started in South Africa. 26

HIV and AIDS: 2009 – p.18 • What is DNA? – p.38

Climate change and agriculture

Quest 5(4) 2009 1

SCIENCE SCIENCE FOR FOR SOUTH SOUTH AFRICA AFRICA

ISSN 1729-830X ISSN 1729-830X

High p er forma nce co mput ing: fro m b one count er s t o Blue Ge ne

VOLUME 5 • NUMBER 4 • 2009 VOLUME 3 • NUMBER 2 • 2007 R29.95 R20

The hi st or y of co mput ing

Q ua nt um informat ion t ec hnology Space sc ie nce a nd a st rono my

A C AACDAEDMEYM YO FO FS C I EI ENNCCEE OOFF SS O U TT HH AAFFRRI C I CA A SC OU

High performance computing.

Images: CSIR

SCIENCE FOR SOUTH AFRICA

ISSN 1729-830X

Editor Dr. Bridget Farham Editorial Board Roseanne Diab (University of KwaZulu-Natal) (Chair) Michael Cherry (South African Journal of Science) Phil Charles (SAAO) Anusuya Chinsamy-Turan (University of Cape Town) George Ellis (University of Cape Town) Jonathan Jansen (University of Free State) Penny Vinjevold (Western Cape Department of Education) Correspondence and The Editor enquiries PO Box 663, Noordhoek 7979 Tel.: (021) 789 2331 Fax: (021) 789 2233 e-mail: ugqirha@iafrica.com (For more information visit www.questsciencemagazine.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 Patrick Nemushungwa and back issues Tel.: (012) 349 6624 e-mail: Patrick@assaf.org.za Copyright © 2009 Academy of Science of South Africa

From bone counters to Blue Gene C

omputers have been part of my life for at least three decades. When I started my PhD studies in the late 1970s I was using a main frame computer, which was situated on the main university campus in Aberdeen, Scotland, some 24 kilometres from the university field station, where I worked. In those days I had to translate my data into 0 and 1 format, transcribe it onto a coding sheet and take the coding sheet into Aberdeen (and I didn’t have my own car). The coding sheet then sat in a queue until it was typed onto punch cards by women who sat there all day, five days a week, doing nothing but type up punch cards. These cards were then fed into the main frame overnight in batches and I either spent whole days (or nights) at the computer centre on the main campus, or I used a primitive modem from the field station to access my data. It was clumsy and the operating systems were, frankly, beyond me. My programming skills were almost non-existent and using a computer was something of a trial, unless you were what is now called a ‘geek’. How things have changed! My cell phone has more computing power than the main frame I was using to analyse my PhD data. The iMac that I am using at the moment would have been beyond comprehension a couple of decades ago. What is truly astonishing is the speed with which computing power has developed. And now we have high performance computing and the Blue Gene – the stuff of the science fiction stories of my childhood. With the advent of the desktop computer and – dare I say it – the kind of operating system that Microsoft developed, computers are within the reach of anyone. My 80-year-old mother uses one with ease! This increased accessibility and increased power of computing has brought with it enormous advances in all the sciences, from physics to biology. And now we are looking at developing quantum computers, which will take us even further into the future. However, we musn’t forget the digital divide – something that is just about as important as any of the other inequalities that unfortunately characterise the modern world. Indeed the digital divide is part of what drives that inequality. Easy access to information is something that those of us who live in the developed parts of the world – even in a developing country – take completely for granted. You want to know something, you ‘Google’ it. As you read through this issue of QUEST, take a bit of time to think about those who do not have such access – and think about what you can do to help to lessen this divide.

Bridget Farham Editor – QUEST: Science for South Africa Join QUEST’s knowledge-sharing activities

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2 Quest 5(4) 2009

Write letters for our regular Letters column – e-mail or fax your letter to The Editor. (Write QUEST LETTER in the subject line.) ■ Ask science and technology (S&T) questions for specialist members of the Academy of Science to answer in our regular Questions and Answers column – e-mail or fax your questions to The Editor. (Write QUEST QUESTION in the subject line.) ■ Inform readers in our regular Diary of Events column about science and technology events that you may be organising. (Write QUEST DIARY clearly on your e-mail or fax and provide full and accurate details.) ■ Contribute if you are a specialist with research to report. Ask the Editor for a copy of QUEST’s Call for Contributions (or find it at www.questsciencemagazine.co.za), and make arrangements to tell us your story. To contact the Editor, send an e-mail to: ugqirha@iafrica.com or fax your communication to (021) 789 2233. Please give your full name and contact details.

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The Centre for High Performance Computing

The Centre for High Performance Computing in Cape Town. Image: CSIR

Happy Sithole, Director of the Centre for High Performance Computing, takes us into the future of computing in South Africa.

Dr Happy Sithole, Director, Centre for High Performance Computing. Image: CSIR

These are widely used by many people around the globe, and have been accepted as popular tools. It is thus natural that when something works well, more of its services are required. In this case, the demands

on computers to do more work faster and more accurately are no surprise. The execution of more challenging tasks, which we previously would have never dreamt possible, became feasible through the use of computers.

â&#x2013;˛ â&#x2013;˛

nformation and communication technologies are instrumental in reducing many manual routines in our everyday lives, ranging from documenting our history to automating some simple routines.

Image: CSIR

Quest 5(4) 2009 3

Research Coordinator, Jeff Chen, with students learning the open-source program Ubuntu at the Centre for High Performance Computing. Image: CSIR

Image: CSIR

Computing has grown to a point where its use has been perfected to the extent that most engineering designs and scientific discoveries are dependent on using computers in some way or another. As a third pillar of scientific investigation, scientific and engineering computing complements well the traditional experimental and pen-andpaper investigations. Before the late 1970s scientific computing was done mainly on specialised computer systems, affectionately referred to as main frames and, later on, supercomputers. These were manufacturer-specific, as their operating systems could not be exported from one manufacturer to another. IRIX was a Silicon Graphics operating system, and would not perform similar instructions to those performed by SOLARIS from SUN Microsystems or AIX from International Business Machines (IBM). Hence the supercomputers were expensive as each product had little competition. This also stifled collaboration among researchers, as applications running on a specific machine had to be recompiled when moving them to other machines.

4 Quest 5(4) 2009

In the early 1990s, advances in networks and availability of opensource software, such as Linux, created a new design of computer architecture referred to as clusters. This was literally a cluster of desktops performing parallel instructions and sharing information through Ethernet networks. Further speeding-up of the networks and more cores on a processor made these clusters much faster than the supercomputers of the past, and these were now referred to as high performance computers. This advance is evident; a laptop running two central processing units (CPU) per processor, known as duocore, is faster than the number 500 supercomputer in 1995. Apart from the speed, this development reduced the barrier for entry into supercomputers, and allowed more utilisation and collaboration, as applications and operating systems are based on opensource software. Many countries adopted these supercomputers as tools to increase their scientific knowledge and to support the competitiveness of their industries. Currently more applications in motor and aircraft manufacturing, nuclear energy and weapons, film industry and drug research, are driving the emergence of most high performance computers in the world. This can be obtained in TOP500 list of supercomputers. South Africa is no exception, as these challenges are also on our doorstep. We need to look at mitigating global warming, designing new drugs, perfecting our designs and creating

new knowledge faster. In a nutshell, we need to improve the competitiveness of our industries and improve the quality of life of South Africans. Hence, high performance computing has been adopted as an enabler for scientific and engineering competition. The Centre for High Performance Computing, since it officially started its operations in 2007, has aimed at enabling research, development and innovation, by providing world-class high performance computing facilities for South African citizens. The centre is also looking at building highly skilled personnel for both academia and industry. A wide variety of research, ranging from climate, materials, medical and space science, has been carried out at the facility, and we are looking at growing this use beyond the usual applications. We need to spead the use of high performance computing to human dynamics and financial modelling, and to accommodate other social sciences. The main objective will be on the type of scientific computing that will be aligned with key national initiatives, specifically aimed at improving the quality of lives of South Africans. We are looking forward for more outputs from the users of this facility, and creating more good news from South Africa. We are aware of the challenges posed by low bandwidth and lack of skills and would like to assure the community that a holistic cyber-infrastructure encompassing highspeed networks and large data storage will ensure easy access and entry to high performance computing. â&#x2013;

High performance computing: How did we arrive here?

The modern world of powerful desk-top computers and high performance computing seems a long way from early calculating tools such as the abacus. QUEST finds out how modern computing has developed.

n this age of desktop computing, game stations and cell phones that have great processing power, we sometimes forget that the concept of computing is really about the representation of numbers. However, ‘numbers’ is an abstract concept – and as such – the development of a science of numbers has been intimately tied with the development of societies through the ages. For example, one of the earliest computational devices was a tally stick, used to record ‘how many’ items. Tally sticks were first found in deposits from the Upper Palaeolithic Era by archaelogists; the tally counter was notches carved on animal bones.

Early computers We think of a computer as a box full of electrical circuits. But in fact a computer is any physical object that can calculate or compute. The earliest known tool for computation was the abacus. This was thought to have been invented in Babylon, around 2400 BC. The earliest abacus was thought to have been lines drawn in sand with pebbles representing the beads. This was essentially the earliest computer. Around 2600 BC, the Chinese developed the south pointing chariot, which was a chariot that worked using a complex system of gears connected to a pointing figure. By carefully selecting the wheel size and the gear ratio the figure always pointed in the same direction, so the chariot acted as a non-magnetic compass vehicle. The differential gear system used in the chariot was later used in analogue computers. The earliest known analogue computer is the Antykithera mechanism. This is a mechanical device, also working with gears, which was developed to calculate astronomical positions and which has been dated to around 100 BC. A reconstruction of a south-pointing chariot. Image: Wikimedia commons

A school abacus used in the early 20th century.

The Ishango Bone One of the best known examples of a tally stick is the Ishango Bone. This is a bone tool that is dated to the Palaeolithic Era and is formed from the fibula of a baboon with a sharp piece of quartz fixed to one end. It has a series of tally marks carved in three columns along the length of the bone. It was found in what was then the Belgian Congo in 1960, in an area that is now on the border between modern-day Uganda and Congo.

The Ishango Bone.

Image: Wikimedia images

Euclid’s algorithm for finding the greatest common divisor of two numbers Euclid was a Greek mathematician who lived around 300 BC. The greatest common divisor (GCD) of two numbers is also called the greatest common factor (GCF) or the highest common factor (HCF). The GCD of two numbers is the largest number that divides both of them without leaving a remainder. Euclid’s algorithm is based on the principle that the greatest common divisor of two numbers does not change if the smaller number is subtracted from the larger number.

A 24-by-60 rectangle is covered with ten 12-by-12 square tiles, where 12 is the GCD of 24 and 60. More generally, an a-by-b rectangle can be covered with square tiles of sidelength c only if c is a common divisor of a and b.

▲ ▲

Numbers Before plunging into a history of computing it is important to understand where the concept of numbers came from. Early societies used numbers for counting, for example a number of coins. All known languages have the words for at least ‘one’ and ‘two’. As the understanding of numbers advanced mathematical computations such as addition, subtraction, division and multiplication were developed, as were concepts such as the square root. Eventually, these operations were formalised and even proved. By the Middle Ages (roughly the 5th century through to the end of the 16th century) what is called the positional Hindu-Arabic numeral system had reached Europe. This is a number system that was developed in the 9th century by Hindu and Indian mathematicians. It was then adopted by Persian and Arabic mathematicians, after which time it spread to the Western world. The system is based on ten (originally nine) different glyphs or symbols. The

symbols can be divided into three main families: the Indian numerals, used in India, the Eastern Arabic numerals used in Egypt and the Middle East and the West Arabic numerals, used in the Maghreb and in Europe. It was the introduction of this number system that allowed the systematic computation of numbers. Once mathematicians could put a representation of numbers on paper this allowed them to also calculate mathematical expressions and to produce tables of common functions such as square roots and logarithms.

Zero The concept of the ‘number’ zero (0) developed later than the concept of positive numbers, that is numbers greater than 0 (+1, +2 and so on). It is both a number and the numerical digit that is used to represent it (zero) as a number. The concept of zero is central to mathematics as the additive identity of any whole number (interger). This is expressed mathematically as: 0 + a = a for any number a

Quest 5(4) 2009 5

A Persian astrolabe from 1208. Image: Wikimedia commons

Part of Babbage’s difference engine, assembled after his death by Babbage’s son, using parts found in his laboratory. Image: Wikimedia commons

A fragment of the Antikythera mechanism. Image: Wikimedia commons

thought of as the first programmable analogue computer. However, none of these devices were really computers in the modern sense of the word. A computer, in modern times, is a device that manipulates data according to a set of instructions.

A modern model of Babbage’s analytical engine, built in 1992, found in the Science Museum in London. Image: Wikimedia commons

An analogue computer is a type of computer that uses physical phenomena such as electrical, mechanical or hydraulic quantities to model a particular problem that needs to be solved. In contrast, a digital computer represents variable quantities in increments, as their numerical values change.

Mechanical analogue computers appeared again 1 000 years later in the medieval Islamic world and were developed by Muslim astronomers, such as equatorium of Arzachel. Another example was the astrolabe, initially developed by Abu Rayhan al-Biruni. Muslim mathematicians also developed the science of cryptography, which is the study of ways of hiding information. The modern example that most people think of is ciphers that are used to relay information so that the information cannot be interpreted by anyone who does not have a key to the cipher. The Muslim world was also the source of programmable machines, such as an automatic flute player, humanoid robots and castle clock, which is

6 Quest 5(4) 2009

The foundations of modern computing Charles Babbage, born in 1791, is often thought of as the father of computing. He was the Lucasian Professor of Mathematics at Cambridge University from 1828 to 1839, a post that was held by Isaac Newton. Babbage was interested in finding a way of calculating mathematical tables mechanically, so removing human error. He first discussed the principles of what he called a ‘calculating engine’ in a letter to Sir Humphry Davey in 1822. Babbage’s machines were called difference engines. The first difference engine was put together to calculate values of polynomial functions. There were similar calculators available at the time, but Babbage’s was the first to calculate a series of values automatically. The first difference engine was composed of around 25 000 parts, weighed 13 600 kg, and stood 2.4 m high. But, the engine was never completed, in spite of plenty of funding for the project. Babbage later designed an improved version, difference engine No. 2, which was not constructed until 1989-1991, using Babbage’s plans and 19th century manufacturing tolerances. It performed its first calculation at the London Science Museum, returning results to 31 digits, far more than the average modern pocket calculator. Babbage abandoned the difference engine in favour of the analytical engine, which was essentially the first mechanical general purpose computer. Babbage first described this computer in 1837, but continued to work on the design until his death in 1871. For various reasons, the analytical engine was also never completed.

Alan Turing: The code breaker Alan Turing has been called one of the 100 most important people of the 20th century. He was originally a mathematician and became a codebreaker (cryptographer) and computer scientist. His name is linked with a theoretical device that manipulates symbols that are contained on a strip of tape. This was described in 1936 by Alan Turing and can be used to explain how the central processing unit (CPU) inside a computer works. A Turing machine is a thought experiment, which is a proposal to test a theory, which represents a computer. During the Second World War, Turing worked in the British government’s code breaking centre at Bletchley Park. He devised a number of techniques for breaking German ciphers, including an electromechanical machine called the bombe, which could find the settings for the Enigma machine. After the war, Turing worked at the National Physics Laboratory in Britain, where he designed one of the first stored-program computers, the ACE or automatic computing engine. Computers for everyone The familiar desk-top machines of today started to develop in the 1960s with the ‘small’ third-generation computers that were possible using transistor and core memory technology. They were ‘small’ compared to a mainframe computer, that usually took up a whole room. A typical mini-computer took up one or of a few cabinets the size of a large refrigerator. The first was launched in 1964 and cost upwards of $16 000! From the mid-1980s into the 1990s, the mini-computer was replaced by the micro-computer. These machines were able to develop because the cost of the microprocessing hardware dropped sufficiently. It was at this stage that networking developed – several micro-computers linked together for a variety of functions, including faster processing power.

An artist’s representation of a Turing machine. Image: Wikimedia commons

The Sun Microsystems hybrid supercomputer. Image: CSIR

The Enigma machine The birth of supercomputing What is now called high performance computing was first called supercomputing. A supercomputer is essentially a very, very fast computer, speed being particularly important in calculations. They were introduced in the 1960s, designed mainly by Seymour Cray at Control Data Corporation (CDC). These led the market into the 1970s, when Cray formed his own company, Cray Research. Early supercomputers were very fast scalar processors. A scalar processor calculates one data item at a time. By the early 1970s, however, these machines were using vector processors – capable of performing mathematical operations on multiple data elements at the same time. During the early to mid-1980s, machines with several vector processors working in parallel became the standard. However, in the late 1980s and 1990s, attention was turned towards massive parallel processing systems, in which many calculations are carried out simultaneously. Large problems can often be divided into smaller ones, which are then solved in parallel. These parallel systems contained thousands of ordinary CPUs, some of which were custom-designed. Most modern supercomputers are highly-tuned computer clusters using off-the-shelf processors combined with fast interconnectors that have been designed for a specific task. High performance computing High performance computing uses supercomputers and computer clusters to solve advanced computational problems. Any computer that approaches teraflop speed is regarded as a high performance computer.

High performance computing in South Africa In October 2008, the Blue Gene for Africa (BG4A) initiative was launched at the Centre for High Performance Computing in Cape Town. This was a milestone in South Africa’s expanding cyber-infrastructure. The donation of the supercomputer by IBM (NYSE: IBM) followed an extensive series of meetings in 2007 on economic development opportunities in Africa convened by IBM as part of its Global Innovation Outlook. IBM has held eight Global Innovation Outlook (GIO) events for Africa in countries including Kenya, Senegal, Beijing, the US and France. The donation is part of a US$ 120 million investment in subSaharan Africa announced by IBM in December 2007. The Blue Gene®/P system is capable of 14 trillion individual calculations per second, and is five times more powerful than the fastest research computer currently on the African continent, the Blue Gene/L in Egypt. This donation has given impetus to the Blue Gene for Africa initiative, which has three interlinking thrusts: infrastructure; promoting collaborative science (through flagships) with a major impact on the African continent; and human capital development (HCD) — building of highend computing capacity in Africa. Then in September 2009, the Centre for High Performance Computing (CHPC) launched phase 2 of its operations. The latest addition to its facilities is the Sun Microsystems hybrid supercomputer. The Centre for High Performance Computing is involved in many research projects around South Africa, some of which will be featured in this edition of QUEST. ■

More about Blue Gene computers Blue Gene is a computer architecture project that is designed to produce several supercomputers. These computers are designed to reach operating speeds in the petaFLOPS (PFLOPS) range. The current range of Blue Gene computers reach speeds of nearly 500 teraFLOPS. The Blue Gene computer in this article has the processing power of 2 300 laptops.

The Enigma machine was one of a family of cipher machines, made up of electro-mechanical rotors, that were used to encrypt secret messages. The first such machine was developed by a the German engineer Arthur Scherbius at the end of World War 1.

The plugboard, keyboard, lamps, and finger-wheels of the rotors emerging from the inner lid of a three-rotor German military Enigma machine. Image: Wikimedia commons

FLOPS In computing, FLOPS stands for Floating Points Operations Per Second. This is a measure of the computer’s performance. The higher the number of FLOPS, the faster the computer. Computer performance Name

FLOPS

yottaFLOPS

1024

zettaFLOPS

1021

exaFLOPS

1018

petaFLOPS

1015

teraFLOPS

1012

gigaFLOPS

109

megaFLOPS

106

kiloFLOPS

103

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Green computing Green computing was central to the planning and construction of the new computing facilities at the CSIRâ&#x20AC;&#x2122;s Centre for High Performance Computing in Cape Town.

The one megawatt diesel generator at the CHPC. Image: CSIR

A dual-core processor. Image: Wikimedia commons

C Image: CSIR

Dr Khomotso Kganyago.

Pipes filled with chilled water form part of the new cooling infrastructure. Image: CSI

8 Quest 5(4) 2009

Image: CSIR

A multi-core processor is a processing system made up of two or more independent cores. These are usually integrated into a single integrated circuit die (a small block of semi-conducting material with a circuit on it). A dualcore processor contains two cores and a quad-core processor contains four cores.

omputers use power and they generate heat. Anyone who has used a laptop for any length of time will know that. And a laptop contains only a single dual-core processor. The high performance computers in the Centre for High Performance Computing (CHPC) in Cape Town, in constrast, are huge. The latest computer to be installed at the CHPC is the Sun SPARC Enterprise M9000 server with SPARC64 VII quad-core processors (64) and a cluster of four Sun Blade 6048 modular systems. The CHPC has taken mitigation of the energy demands of this system seriously. Not only do these computers require power for their operation, but the heat that they generate needs to be dissipated through a cooling system, which itself requires power. The newer Sun Blade 6048 chassis accommodates Sun cooling door modules. Each blade within the architecture of the new system has 16 dualcore processors and generates a considerable amount of heat, as more processors are now located in a small space. A quad-core processor puts out about the same amount of energy as

at the CHPC Right and right below: The Sun Cooling Door system fits in the rear of the updated Sun Blade 6048 chassis. It has the highest cooling efficiency and capacity in a 100% passive design that does not need additional fans or electrical power to function. Image: CSIR Below: The recently installed chilled water infrastructure.

a clothes iron at full heat, so power consumption both for operation and for cooling is a serious potential limiting factor to the future growth of high performance computing. The Sun hybrid architecture provides an estimated 27 teraFLOPS of peak computing power. Hence the need for green computing interventions in the planning and construction of the new computing and research facility. Green computing A team from the CHPC, led by Dr Khomotso Kganyago, visited the National Centre for Supercomputing Applications in Illinois, USA to get ideas. The result was the CHPCâ&#x20AC;&#x2122;s stateof-the-art data centre. Phase II of the renovation of the CHPC site started in September 2008. There is a new sub-station to accommodate the increased demand of one megawatt of power along with a sophisticated automated mechanism to ensure completely uninterrupted power. This consists of a one megawatt diesel generator coupled with two 500 kilowatt uninterruptible power supply (UPS) units. Along with this is a highly economical cooling system in the server

Image: CSIR

room. Conventional air conditioning is used to cool the ambient temperature. However, the machine itself will be cooled using water, a far more effective system. Both the racks that store the blades and the central processing units are water-cooled with pipes that run through the machine. The new Sun cooling door systems, which have only been installed in six sites around the world, offer six times more efficient rack cooling than standard data centre cooling systems. This significantly reduces energy consumption and increases effective computer density by up to 70% against more conventional cooling systems. The chilled water reticulation system inside the high-powered computer is isolated from the main chilled-water supply network to minimise the total volume of water that could potentially enter the computer room if there was a mechanical breakdown. The total volume of water in the internal system is small enough for it to drain completely through a floor drain system with minimal damage and interruption to computing time. â&#x2013; This article is based on Green computing at the CHPC: The right thing to do. By Biffy van Rooyen, CSIR.

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A scientific visualisation of what happens when two fluids are mixed.

A scientific visualisation of flow in a fluid. Image: Wikimedia commons

Image: Wikimedia commons

Graphic visualisation The Centre for High Performance Computing is involved in several different types of graphic visualisation. QUEST looked at what they are doing.

An example of visualisation to show how a car deforms in an asymmetrical crash using finite element analysis. Image: Wikimedia commons

Visualisations of different types of molecular structures. Image: CHPC

H An image of different types of glass, produced by rendering techniques. Image: Wikimedia commons

An example of the kind of data that can be visualised using ClimView. Image: CHPC

igh performance computers have many uses. Between 75 and 80% of their time is used in numerical simulations. One of the many ways in which numerical simulations can be useful is in graphic visualisation techniques. The Centre for High Performance Computing (CHPC) has set up an Interactive Visualisation Technologies Laboratory. This unit offers researchers the opportunity to use scientific visualisation in the analysis of their data. Scientific visualisation is the interactive display and analysis of data in such a way that the visualisation helps the researcher to understand and gain more insight into the data. Visualisation: Computer graphics Before going any further it is worth understanding something about the background to computer graphics.

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Essentially, visualisation is any technique that is used to create images, diagrams or animations to convey a message. But it is not only since the advent of computers that humans have used visualisation. Cave paintings, Eygptian hieroglyphs, the geometry of the ancient Greeks and Leonardo da Vinciâ&#x20AC;&#x2122;s revolutionary technical drawings are just some examples. Visualisation today is an everexpanding technique that is used in science, education, engineering in product visualisation, interactive multimedia, medicine and so on. Finite element analysis is a mathematical technique that is used to find the approximate solutions of partial differential equations as well as integral equations. It is a good technique to use to solve partial differential equations over complex domains or surfaces of objects, such as cars.

A virtual reality parachute trainer in use. Image: Wikimedia commons

Today, much of this visualisation is carried out using computer graphic techniques. Applications of visualisation There are many applications of visualisation. The CHPC concentrates on scientific visualisation, virtual reality and digital multimedia. Scientific visualisation

Scientific visualisation is used across many areas of science and is used for the visualisation of three-dimensional (3D) phenomena such as architecture, weather data, medical and biological images and so on. In this type of visualisation the images need to be relatively realistic and show surfaces, volumes and sources of light and also often need to have a time component. An example would be the use of rendering techniques to produce images. Rendering techniques generate an image from a model using computer programs. A model is a description of three-dimensional objects in strictly defined language or data structure. The model would contain geometry, viewpoint, texture, lighting and shading information. The CHPC is currently involved in projects that require molecular visualisation. This consists of providing visual images of the systems of the atoms and molecules that chemists or microbiologists, for example, need to analyse. Another scientific visualisation project that the CHPC is involved in is the development of an application that can be used to visualise climatology data. The application is called ClimView. These two images show examples of how the CHPC can collaborate with research into astrophysics and medical imaging. Virtual reality

Virtual reality is a technology that is used to allow someone to

interact with a computer-simulated environment. The interactive environment can be a simulation of a real or imaginary world. Most virtual reality environments are visual, but some include sensory elements such as touch and sound. An application for interacting with molecular data via hand gestures was developed at the CHPC in collaboration with the University of Cape Town. Sensors are placed on the hands of a user and are tracked by an infrared camera (from the Nintendo Wii). Different hand movements allow for operations such rotating, scaling and grabbing molecules. A computer simulation, also called a computer model or computational model, is a computer program or network of computers that simulate an abstract model of a particular system. Computer simulations can be programs that run for a few minutes to network-based groups of computers that run for hours, to ongoing simulations that run for days.

Image: CHPC

The CHPC virtual reality system.Image: CHPC

Digital multimedia

In this context, digital multimedia relates to an application that can combine text, graphics, full-motion video and sound into an integrated package. The CHPC is currently in the process of working with local animation companies to assist them with reducing their production time, which includes rendering time, and are also investigating stereoscopic rendering techniques. Scientific visualisation is an emerging science that aims to develop fundamental ideas that lead to general tools for real applications. The same techniques are used across many different scientific fields â&#x20AC;&#x201C; a truly multidisciplinary approach. â&#x2013;

Investigating stereoscopic rendering techniques. Image: CHPC

Quest 5(4) 2009 11

Quantum information technology: a novel approach to information transfer

Professor Francesco Petruccione.

Information is physical and this means that the laws of quantum mechanics can be used to process and transmit this information in ways that are not possible with existing systems. QUEST asked Francesco Petruccione how this works.

uantum physics arose in the 1920s. Ever since then the discipline has attracted discussion about its meaning and how to interpret its theories correctly. What is quantum physics? Quantum physics or quantum mechanics is a set of principles that describe physical reality at the level of atoms, molecules and the even smaller subatomic particles that make up atoms. The essential feature of quantum mechanics is that it is a mathematical system that explains that matter and radiation can behave like waves and particles at the same time. Quantum mechanics also says that a wave function is the most complete description of any system; the wave function is simply a number that varies between time and place. For most people, quantum mechanics means the famous thought experiment, Schrödinger’s cat. Erwin Schrödinger was an Austrian physicist who devised this thought experiment to interpret quantum mechanics in 1935. Schrödinger wrote: ‘One can even set up quite ridiculous cases. A cat is penned up in a steel chamber, along with

the following device (which must be secured against direct interference by the cat): in a Geiger counter, there is a tiny bit of radioactive substance, so small that perhaps in the course of the hour, one of the atoms decays, but also, with equal probability, perhaps none; if it happens, the counter tube discharges, and through a relay releases a hammer that shatters a small flask of hydrocyanic acid. If one has left this entire system to itself for an hour, one would say that the cat still lives if meanwhile no atom has decayed. The wave function of the entire system would express this by having in it the living and dead cat (pardon the expression) mixed or smeared out in equal parts.’ Essentially, what Schrödinger is saying that location and velocity cannot exist for any body at the same time. This is called the Heisenberg uncertainty principle. Quantum mechanics is essential to the understanding of the behaviour of systems at atomic level and smaller. However, the uses of quantum mechanics are not confined to physics.

Schrödinger’s cat: A cat, along with a flask containing a poison, is placed in a sealed box shielded against loss of information to the system. If an internal Geiger counter detects radiation, the flask is shattered, releasing the poison

that kills the cat. The usual interpretation of quantum mechanics implies that, after a while, the cat is simultaneously alive and dead. Yet, when we look in the box, we see the cat either alive or dead, not a mixture of alive and dead.

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field of quantum information technology was born. Quantum information technology has been gaining tremendous momentum in the research arena over the past decade and its potential impact on the future was realised in South Africa when the Quantum Research Group at the University of KwaZulu-Natal (UKZN) received a substantial amount of funding from the Innovation Fund to set up a Centre for Quantum Technologies and to develop a quantum key distribution system. One of the ultimate goals of quantum technology is to produce a fully self-sustained quantum computer. This research group relies on the high performance computing capabilities offered by the CHPC in Cape Town to carry out the complex simulations required to develop a quantum computer locally. The group uses what are called Monte Carlo techniques for this simulation. Monte Carlo methods are a type of computational algorithm that rely on repeated random sampling to produce their results. An algorithm is a method for solving a problem that uses a finite sequence of instructions.

A diagram showing how qubits can exist in many more states than classical binary bits.

The field of quantum information technology is a good example of classical physics and potential applications working together. ■

Even biological systems, such as smell receptors and protein structures can be better understood in the light of quantum theory.

Professor Francesco Petruccione is in the Department of Physics at the University of KwaZulu-Natal. He has a special interest in quantum mechanics and quantum information technology.

Quantum computers A novel and promising use of quantum mechanics is the development of quantum computers. This has come about because scientists now realise that information is not independent of the physical laws that are used to store and process that information. Modern computers do, in fact, use quantum mechanics in their operation, but the information is still encoded classically. A classical computer has a memory that is made up of bits, where each bit represents either one or zero. Any physical representation of a bit needs a system with two well-defined states, for example a switch where off represents ‘0’ and on represents ‘1’. A bit can also be represented by, for example, a certain voltage level in a logical circuit, a pit in a compact disc, a pulse of light in a glass fibre or the magnetisation on a magnetic tape. In classical systems it is desirable to have the two states separated by a large energy barrier so that the value of the bit cannot change spontaneously. The new approach treats information itself as a quantum concept. Two-state systems are also used to encode information in quantum systems and it is traditional to call the two quantum states |0> and |1>. The really novel feature of quantum information technology is that a quantum system can be in a superposition of different states. That means that the quantum bit can be in both the |0> state and the |1> state at the same time. A pair of qubits can be in any quantum superposition of four states, and three qubits can be in any superposition of eight states. Quantum computers can perform certain tasks, such as solving mathematical problems, to be performed far more efficiently than classical computers can. This has enormous potential, for example in encrypting information. Quantum information technology As scientists started to understand quantum mechanics better and to develop the concept of a quantum computer, so the

Space science & astronomy: the role of high performance computing This Chandra X-ray Observatory image shows the central region of the supernova remnant Cassiopeia A (Cas A for short), the remains of a massive star that exploded in our galaxy. Evidence for a thin carbon atmosphere on a neutron star at the centre of Cas A has been found. Besides resolving a ten-year-old mystery about the nature of this object, this result provides a vivid demonstration of the extreme nature of neutron stars. An artist’s impression of the carbon-cloaked neutron star is also shown. Colour code: red=low-energy X-rays; green=medium-energy X-rays; blue=high-energy X-rays. Image: X-ray: NASA/CXC/Southampton/W. Ho et al.; Illustration: NASA/CXC/M.Weiss

Two cutting-edge research projects in space science and astronomy are currently using the Centre for High Performance Computing in Cape Town. QUEST talks to Daniel Moeketsi about these projects.

he Centre for High Performance Computing (CHPC) is the largest computational science laboratory in southern Africa and provides a unique platform for high performance computing in various fields, including space science and astronomy. Cosmic rays One of the CHPC’s flagship projects is led by Professor Marius Potgieter and his team from North-West University. The team is studying cosmic rays. These are high-energy, charged

particles from outer space that enter the Earth’s atmosphere. The term ray is actually slightly misleading because these highly energetic, charged particles arrive individually and not in the form of rays or beams of particles. The rays have a variety of different energies because they come from a variety of different sources; some from the Sun and some from as yet unkown events that are occuring in the distant reaches of the universe. An example of a cosmic ray source is the supernova

The heliosphere The heliosphere is a ‘bubble’ in space that is blown into the interstellar medium by the solar wind.

Dr Daniel Moeketsi. Image: CSIR

14 Quest 5(4) 2009

The solar system, in logarithmic scale, showing the outer extent of the heliosphere, the Oort cloud and Alpha Centauri. Image: PD-USGOV-NASA

Above: A model of the heliosphere in one area of the solar system. Image: Adapted from Ferreira et al. 2007 Left: Simulated distribution of dark matter in the universe using GADGET software on the CPHC cluster. Image: Catherine Cress

remnant Cassiopeia, shown here. Space physicists are concentrating on the origin of these rays. The way that these rays move through space and into our atmosphere is also of interest. When cosmic rays reach the Earth they collide with molecules, mainly nitrogen and oxygen, producing an air shower. An air shower is a wide (many kilometres) cascade of ionised particles and electromagnetic radiation produced in the atmosphere when a cosmic ray from outer space enters the atmosphere.

These cosmic rays can be harmful to life, but fortunately the Earth’s magnetic shield deflects most of these. The cosmic rays travel through outer space and through the interstellar medium, which is the gas and dust that exists between the star systems within a galaxy. This interstellar medium surrounds our solar system. Within this, the solar wind creates the heliosphere. The solar wind is a stream of charged particles that come from the upper atmosphere of the Sun. This wind consists mainly of the atomic particles, electrons and protons. It varies in temperature and speed over time. The particles escape the sun’s gravity because they have extremely high energies. The solar wind also creates a magnetic field as it travels, which can also deflect cosmic rays from the Earth’s atmosphere. The local interstellar conditions through which the heliosphere moves can change dramatically over thousands of years. These very longterm changes in our interstellar and heliospheric environment are called space climate. Space climate has probably played a significant role in previous and present climate changes, so it is an important topic of research. So where does high performance

computing come in? Once we have a good body of knowledge about any physical system we can start putting together models of these systems to gain more knowledge about how they work. So this team’s research focuses on the computational modelling of heliospace physics, interstellar physics and astrophysics using state-of-theart numerical models that require enormous amounts of computer time and processing power. An example is shown in the figure above right, which shows a computational model of the heliosphere in one area of the solar system. The research is aimed at showing where and how cosmic rays are transported from the time of their creation in the galaxy up to their arrival on Earth. These numerical simulations are used to test different leading theories and to explain and understand recent observations and measurements from, for example the Voyager spacecraft and large telescopes such as those used the the High Energy Stereoscopic System (HESS) collaboration in Namibia. The results will be used to understand the influence of cosmic rays, space weather and space climate on the Earth’s environment, long-duration missions to Mars and working environments on the Moon and Mars. Modelling the cosmos A research collaboration of Dr Kavian Moodley (University of KwaZulu-Natal), Professor Bruce Bassett (University of Cape Town and South African Astronomical Observatory (SAAO)) and Dr Catherine Cress (University of the Western Cape) focuses on computational astronomy and cosmology. Cosmology is the study of the structure and evolution of the universe and its physical constituents. The field lies at the interface of astronomy and particle physics.

Particle physics is a branch of physics that studies the elementary constituents of matter and radiation.

In the past decade cosmology has benefited enormously from a wealth of observational data from cuttingedge experiments and telescopes. See ‘Dark energy and cosmology since 1995’ by Bruce Bennet and Renée Hlozek in QUEST 5(1) 2009. The current model of the expanding universe has thrown up various curved balls in the form of dark energy and dark matter, the origin and evolution of galaxies and galaxy clusters and how exactly these cosmic structures originated. The research collaboration is using high-precision data from new national and international astronomical facilities such as SAAO, the Acatama Cosmology Telescope and the South African Meerkat radio telescope. Analysing and interpreting these data in a way that can help to understand theoretical models requires significant computational power and the team is using existing cosmological software and newly developed computational-intensive algorithms for this. The figure above left shows the distribution of dark matter in the universe, simulated on the CPHC cluster using GADGET software. The future of space science in South Africa With the establishment of the CPHC it has become possible to embark on ambitious projects that need high performance computing in order to process and analyse the numerical data that are generated by local astronomy research groupings. This article is based on an article by Dr Daniel Moeketsi in ScienceScope, published by the CSIR. ■ Daniel Moeketsi is a researcher at the CHPC. He has a particular interest in space weather.

Quest 5(4) 2009 15

Modelling HIV: The science behind treatment and prevention One of the biggest problems with treating HIV and developing an effective vaccine is the virus’ rapid mutation rate. QUEST spoke to Darren Martin about one of the ways in which local scientists are tackling this problem.

he human immunodeficiency virus (HIV) has produced one of the worst pandemics that the world has seen. The last update of global HIV figures, produced by UNAIDS, showed that an estimated 33 million people were living with HIV by the end of 2007. In the same year, there were 2.7 million new cases of HIV and 2 million AIDS-related deaths. HIV can be treated. Antiretroviral drugs allow people with the virus to control its spread through the body and to live a normal life. But these drugs do not cure the disease. They simply prevent progression to AIDS, which is inevitable in most people infected by HIV if they are not given treatment.

However, these drugs are not without their problems. Like most drugs, they can have severe side-effects and what may be worse, people taking the drugs can become resistant to them – or rather, the HI virus can become resistant to the drugs. Most authorities around the world agree that what is really needed is a vaccine that can prevent HIV in the same way that vaccines prevent measles and polio. But finding an HIV vaccine is proving particularly difficult. The key to both the problem of resistance to antiretrovirals and to the difficulties in finding an effective vaccine against HIV is the ability of the virus to mutate. Mutation is a change in the genetic code of an organism or a virus. In the case of HIV, which is a virus, these changes in genetic code can make the virus resistant to antiretroviral drugs.

Why does HIV mutate so easily? Part of the key to understanding why it is that HIV mutates so easily lies in understanding the life cycle of the virus. HIV is a retrovirus and its genetic material is composed of ribonucleic acid (RNA). A diagram of the HI virus.

Drug resistance is the reduction in the effectiveness of a drug. The pathogen against which the drug is directed is either no longer killed by the drug, or is no longer killed in sufficient numbers to prevent illness. In any pool of pathogens there will be a certain number that have a natural resistance to the drug that is being used. HIV has a particularly high rate of mutation – and a person living with HIV may have many viruses that are already resistant to anti-HIV drugs circulating in their body. If only one drug is given to treat the HIV then all viruses except the one with resistance to that drug will be suppressed. The one with resistance will grow to be the predominant virus. This is why HIV treatment includes at least three antiretrovirals – so that at least two drugs will be active against any virus at any one time.

16 Quest 5(4) 2009

The life cycle of HIV can be divided into a number of stages. HIV enters the blood, where it binds to a type of white blood cell called CD4. This binding can occur because there are proteins called receptors scattered accross the surface of CD4 cells that bind to protein molecules on the surface of HIV particles. Once a virus particle has successfully attached to a receptor molecule, the surface of the CD4 cell and the surface of the virus particle fuse, much like two soap bubbles. This is possible because the membranes of HIV particles and CD4 cells are made predominantly out of

Binding to receptor and co-receptors

Image: US National Institutes of Health

What is resistance?

RNA is an important biological molecule that is similar to DNA (see page 38 in this issue). It is different from DNA in that there is a single, not a double, strand of RNA in a cell, the RNA molecules contain ribose and not deoxyribose and RNA has the base uracil rather than thymine, which is present in DNA. RNA is vital to protein synthesis. However, other functions of RNA include regulation of gene expression within cells. RNA is present in the genomes of most viruses.

HIV in plasma

Fusion and virus entry

Uncoating

Reverse transcription

Viral DNA integrated into CD4 nucleus

Transcription and translation

Assembly Maturation Budding A diagram of the HIV life cycle.

need to processed, requires high performance computing. Scientists from the National Bio-informatics Network (NBN) and the University of Cape Town are using a system called a continuous time Markov process to model HIV evolution. A mathematical model uses equations (usually visualised as line graphs) to describe a system in great depth. For example, given a person on antiretriiviral treatment, a good model would allow us to accurately predict how quickly the patient would progress to AIDS or how rapidly the virus will develop resistance to specific drugs. An electron-micrograph of an HI virus budding off a cell. Image: PD-USGov-

the same fatty material. During fusion the virus genetic material and its protective protein coating is delivered into the cytoplasm of the CD4 cell. This is where an enzyme called reverse transcriptase comes in. An enzyme is a biological catalyst – a chemical substance that helps a chemical reaction to occur and which is not itself changed during the reaction. By helping to bring molecules together in the right orientations and at the right concentrations enzymes can allow chemical reactions to occur at room or body temperatures under normal atmospheric pressures that would normally require much higher temperatures and/or pressures.

▲ ▲

Reverse transcriptase catalyses a reaction called reverse transcription, which is an essential step in the conversion of viral RNA into viral DNA. Once formed, viral DNA is integrated into the nucleus of the CD4 cell. It is this process of reverse transcription that is the key to HIV’s high mutation rate. The conversion of RNA into DNA is inherently errorprone; somewhere along the genome an error will occur every two to three replication cycles. HIV mutates fast and easily. Two other important factors that translate the virus’ high ‘basal’ mutation rate into a rapid evolution rate is the enormous speed at which HIV reproduces and the large numbers of HIV genomes within infected individuals. Essentially, HIV harnesses the human body’s immune system to reproduce itself. As it does this, it slowly weakens the immune system until a point where it is no longer able to protect the body from the swarms

of normally harmless environmental bacteria and viruses, a point that defines the onset of full-blown AIDS. It is this mutational process and its consequences that are the reason that HIV can be enormously variable and can respond rapidly to any changes in its environment. Such changes include both continuously adapting immune responses in infected people and exposure of viruses to antiretroviral drugs (see Quest 4(4) 2008; page 9 for a full description of how antiretroviral drugs work). This super-evolvability seriously undermines efforts to develop effective HIV vaccines. It also means that, over the long term, HIV will probably become resistant to all the drugs that we throw at it. HIV evolution If we can better understand the underlying process of HIV evolution, we will be in a better position to monitor drug treatment, develop new drugs and develop vaccines that will either prevent HIV infections or prevent the progression of HIV infection to AIDS. This is where the use of high performance computing techniques come in. We now have the tools to collect large quantities of information both about how HIV behaves within infected people and how its genome sequence changes over time. By combining these data from many different infected patients, scientists will be able to work out the key themes in HIV evolution that could be exploited either to produce better drugs or vaccines or to help doctors choose the specific combinations of different drugs that they prescribe and when they prescribe them. Modelling a system like this one, in which large amounts of data

A Markov process, named after a Russian mathematician, is a type of mathematical model that can usefully be applied to describe the evolution of viruses such as HIV. Such models are extremely powerful because they allow us to reconstruct the unseen evolutionary history of HIV in unprecedented detail. Like a CSI detective, these Markov processes run through all the available evidence (virus sampling locations, dates, genetic sequences, patient immune profiles and more), weigh up all the ways in which events leading to the ‘crime’ might have occurred and, finally, pinpoint the most likely ‘culprits’. Unlike in CSI New York/ Miami/Las Vegas, however, in the analyses that are being performed at the Centre for High Performance Computing, there are usually thousands of pieces of evidence (hundreds of HIV and host gene sequences), and literally millions upon millions of possible ways in which this evidence could be pieced together to finger the true perpetrators, the handful of genetic changes that make HIV so hard to defeat. Despite this, and because of the massive computing power at their disposal, the modelling efforts of the NBN bio-informaticians have paid off very nicely. Sets of HIV mutations that time and again seem to be responsible for overcoming the immune systems of different patients have been identified. More useful from the perspective of defeating HIV, however, has been the identification among these mutations of unprecendented numbers of ‘toggling’ mutations. These indecisive mutations flip backwards and forwards between mutant and non-mutant states. Like a suspect that continually changes his or her story, these ambivalent mutations loudly betray their guilt. Toggling

Quest 5(4) 2009 17

is particularly important because it indicates that human immune systems can sometimes hit HIV where it hurts; the virus dithers between the mutant and non-mutant states because both alternatives are bad. Although toggling mutations are relatively rare within individual natural infections, it may be possible to design vaccines that specifically force toggling on a wide scale, both within and between different infections.

Fact File Q

While it is unlikely that such vaccines would protect people from actually becoming infected by HIV, on both the individual and population scales such a vaccine might result in the irreversible weakening of the virus – perhaps to a point where it is no longer lethal. The way forward In the final edition of QUEST in 2008 (QUEST 4(4)) I wrote that vaccine trials in South Africa had stopped for the time being. This, and other clinical research,

however, has progressed to such an extent that new vaccine trials have once again started in South Africa, as you will see later in this section. ■ Darren Martin is a senior research scientist at the University of Cape Town studying the evolutionary advantages of parasexual reproduction in viruses. Cathal Seoighe is the Stokes Professor of Bio-informatics at the National University of Ireland studying the mathematical modelling of virus evolution.

HIV & AIDS: 2009 T

he latest figures on HIV and AIDS in South Africa from UNAIDS – the Joint United Nations Programme on HIV/ AIDS for South Africa in 2008 show: ■ Number of people living with HIV: 5 700 000 (4 900 000 – 6 600 000) ■ Adults aged 15 – 49 prevalence rate: 18.1% (15.4% – 20.9%) ■ Adults aged 15 and up living with HIV: 5 400 000 (4 700 000 – 6 200 000) ■ Women aged 15 and up living with HIV: 3 200 000 (2 800 000 – 3 700 000) ■ Children aged 0 – 14 living with HIV: 280 000 (230 000 – 320 000) ■ Deaths due to AIDS: 350 000 (270 000 – 420 000) ■ Orphans due to AIDS aged 0 – 17: 1 400 000 (1 100 000 – 1 800 000) Prevalence of a disease is the total number of cases of the disease in a particular population. The incidence of a disease is the number of newly diagnosed cases of the disease during a specific time period.

There appears to be a decline in HIV prevalence among people below the age of 20; in 2006 prevalence in this age group was 15.9% and in 2008 the prevalence is 13.7%. There is significant variation in HIV prevalence by province, ranging from 39.1% in KwaZulu-Natal to 15.1% in the Western Cape. Inter-district HIV prevalence variation in the country is between 46% and 5.3%.

Universal access to treatment Antiretrovirals are drugs that can prevent the progression of HIV to AIDS (see QUEST 4(4) 2008). South Africa has a policy of providing universal access to these drugs to everyone who is infected with HIV. South Africa currently has one of the largest universal access programmes in the world, which reaches over 500 000 people. This graph shows the progress that is being made towards universal access in South Africa based on 2005 and 2007 reports from UN General Assembly (UNGASS), with projections for 2010. Image: Progress to Universal Access Fact Sheet 2008

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Why do we need universal access? ■ 7 400 people become infected with HIV every day. ■ Nearly 4 million people are currently

receiving treatment, while 9.7 people are still in need. ■ For every two people put on treatment, five more become infected. ■ With universal access, approximately 6.7 million people would receive lifesaving antiretroviral treatment, 2.6 million new infections could be averted and 1.3 million lives saved.* * Based on the country-defined targets for 2010, it is estimated that an investment of US$25.1 billion (US$18.9 billion – US$30.5 billion) will be required for the global AIDS response in low- and middle-income countries. With the achievement of country-defined targets for HIV-related services, in 2010, approximately 6.7 million individuals would be receiving antiretroviral treatment.

How will we achieve universal access? UNAIDS has identified nine priority areas for its support to countries to achieve their universal access targets. These areas will contribute directly to the achievement of universal access and will simultaneously enable advancement to the Millennium Development Goals. ■ Reducing sexual transmission of HIV ■ Preventing mothers from dying and babies from becoming infected with HIV ■ Ensuring that people living with HIV receive treatment ■ Preventing people living with HIV from dying of tuberculosis ■ Protecting drug users from becoming infected with HIV ■ Removing punitive laws, policies, practices, stigma and discrimination that block effective responses to AIDS ■ Empowering young people to protect themselves from HIV ■ Stopping violence against women and girls ■ Enhancing social protection for people affected by HIV

Where are we going with HIV vaccines? HIV scientists in South Africa are at the forefront of research into HIV vaccines. Lynn Morris and her colleagues explain what is happening in the ongoing search for a vaccine against HIV.

A history of vaccination Vaccination is one of science’s greatest success stories. Smallpox was eradicated by vaccination, using vaccinia, a virus that is related to smallpox. There is hope that polio will soon be eradicated in the same way. There are successful vaccines against measles, hepatitis A and B and many other viral infections. In these cases we have a pretty good idea about how the vaccines work. But HIV is different. In most viral infections, the body can clear the virus from the body. In HIV however, there is no spontaneous clearance of HIV from the body. Once the virus is established, the person is infected for life. Furthermore, we do not know the type of immune response that we need to stimulate to either provide protection against HIV or to control the levels of the virus in the body – called viraemia. Having said that, the body does mount an immune response against

HIV that lasts for many years. However, HIV’s remarkable ability to mutate allows it to evade and break down these defenses, eventually causing complete immune collapse. This also leads to a highly variable virus – another obstacle to developing a single vaccine that can cope with such enormous diversity. How do vaccines work? Most vaccines work by mimicking what happens when you catch an infection naturally. The cells in the body that are responsible for fighting off the infection, B- and T-cells, retain a memory of the disease. B-cells produce antibodies that fight the infection and the T-cells kill any cells that have become infected with the virus. If the infection returns, the body mounts a rapid response and prevents the infection from taking hold.

▲ ▲

n article in QUEST 4(4) 2008 carried the unfortunate news that the testing of an HIV vaccine in two clinical trials (STEP and Phambili trials, the latter being conducted in South Africa) was prematurely halted. Lynn Morris and her co-workers, writing in the South African Journal of Science earlier this year (2009), say that the disappointing results from these trials ‘caused the scientific community to pause and wonder “What went wrong?” and, even worse, “Is a vaccine against HIV possible?”’ What went wrong is to some extent being answered by a full analysis of the trials that were stopped. However, attempting to answer the second question has allowed HIV scientists to re-think their current approach to vaccine development. There has been a call for a ‘back-to-basics’ approach that requires a better understanding of both the virus and the human immune response to HIV.

Smallpox was eradicated by global vaccination. Image: Public Health Image Library (PHIL), USA

An antibody is a protein that is produced in response to invasion by a pathogenic organism, such as a virus or a bacterium. Antibodies are used by the immune system both to detect and to respond to infection. An antigen is the substance that causes the production of antibodies and which can cause an immune response.

Each antibody binds to a specific antigen – like a lock and a key.

A child receiving an oral polio vaccine.

Image: US Federal Government

Quest 5(4) 2009 19

How do vaccine trials work? Vaccine trials follow the same phases as all clinical trials. In the beginning, basic research takes place in the laboratory. Then the vaccine is tested for safety in animal studies before human trials are started.

A scientist at work in HIV vaccine development. Image: US Military HIV Research

Human clinical trials are divided into phases. A phase 1 trial is the first instance where an experimental HIV vaccine is given to people. Such a trial usually enrolls about 20 to 100 HIV-negative volunteers. A phase 1 trial is all about safety, looking for any side-effects. This is done by comparing the vaccine with a control or placebo (an inactive substance, such as normal saline). A phase 1 trial can also provide initial data on the dose and administration schedule (the time between vaccinations) that achieve the optimal immune response. All these trials are randomised and double-blinded. This means that neither the volunteer nor their doctor know whether they are getting an active vaccine or a placebo. Once phase 1 trials show the experimental HIV vaccine to be safe, it can advance into phase 2 trials for further safety testing. Phase 2 trials enroll up to several hundred people. These trials still focus on safety, but researchers gather more in-depth information about the human immune response and further data on the most effective dose and administration schedule. A phase 2 trial can last two to three years.

Volunteers at Cape Town’s Emavundleni Centre. Image: Allen Jefthas, MRC

The most promising experimental vaccines then move into phase 3 trials. These trials enroll thousands of HIV-negative volunteers. Phase 3 trials are designed to answer the question of whether or not a vaccine is effective in preventing HIV infection. phase 3 data indicating a vaccine’s safety and effectiveness in large numbers of people are required for a vaccine to be approved by a country’s drug approval process. A phase 3 trial can take three to five years to complete. Experimental vaccines used in all phases of testing are not produced from live virus or from HIV-infected human cells. Volunteers cannot get HIV infection or AIDS by receiving an experimental vaccine.

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A vaccine to a specific virus or bacterium is made up of a weakened or killed strain of the same organism, which stimulates the B cells into producing neutralising antibodies that bind to the virus and prevent it from infecting new cells. At the same time the T-cells, which are called cytotoxic T-cells (CTLs), kill any cells that have become infected with the virus. One of the problems with developing an HIV vaccine is that it has not been possible to stimulate a broad immune response similar to the one illustrated above. In fact, a broad neutralising antibody response to HIV has rarely been demonstrated even in people infected with the virus. Many of the early HIV vaccine trials concentrated on trying to stimulate T-cell responses, because it is this response that seem to be able to control virus replication in the early stages of HIV infection. Both the STEP and Phambili trials that were stopped were testing the Merk Adenovirus 5 (Ad 5) vaccine that was designed to stimulate T-cell production. This did in fact happen in people given the vaccine, but unfortunately the production of these T-cells did not control HIV replication in people who became infected during the trial. This has led scientists to question whether the T-cell response itself does in fact show immune protection in an infected person or whether the Merk Ad 5 vaccine failed to stimulate the right kind of T-cells. Laboratory research on monkeys, however, does suggest that T-cell responses can control HIV replication, so the basic approach remains sound. What have we learned from the HIV vaccine efficacy trials? There is no doubt that there have been major setbacks in the HIV vaccine field in recent years. But a lot has been learnt during the trials. For example, the Vaxgen trial looking at the efficacy of recombinant gp120, the major viral envelope protein that was reported in 2003 has provided conclusive evidence about a crucial aspect of HIV science in the form of what does not stimulate the production of protective antibodies against the virus. The STEP trial has provided information about the non-protective properties of the T-cell response to HIV, although the exact nature of the protective properties of the T-cell response is still not known and will require more research. We also need to understand more about the vector components of vaccines and design

Outreach staff surround Dr Surita Roux at the Emavundleni Centre in Cape Town. Image: Allen Jefthas, MRC

better vectors. The most recent vaccine trial to have been published is RV144, which was carried out in Thailand. RV144 tested a prime boost vaccine strategy that combined two vaccines based on strains (subtypes) of HIV that circulate in Thailand. The first, or ‘prime’ vaccine, known as ALVAC HIV, was developed by sanofi pasteur and the booster vaccine, AIDSVAX B/E, was originally developed by VaxGen and is now licensed to Global Solutions for Infectious Diseases. This proof of concept study, which began in 2003, was designed to evaluate the vaccine strategy’s ability to prevent HIV infection, as well as its ability to reduce the amount of HIV in the blood of those who became infected after they enrolled in the study. There is further information about this trial in another article (page 26) in this edition of QUEST. Where to from here? A proof-of-concept study is a trial that is designed to show clinical efficacy with a small number of strictly selected participants.

At the time of writing the article in the South African Journal of Science, new South African vaccine trials were planned. These have now started – and will be discussed in the next article. This shows conclusively that despite these setbacks there is still optimism among scientists that we can find a vaccine against HIV. Although the results of some vaccine trials have been disappointing so far, history tells us that the best way to curb viral epidemics is through vaccination, so the search continues. ■ Lynn Morris is in the National Institute for Communicable Diseases, Johannesburg. Carolyn Williamson is in the Division of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town. Koleka Mlisana is at the Centre for the AIDS Programme of Research in South Africa (CAPRISA) at the University of KwaZulu-Natal. Glenda Gray is in the Perinatal HIV Research Unit, University of the Witwatersrand.

South African AIDS Vaccine Initiative The South African AIDS Vaccine Initiative (SAAVI) is a lead programme of the South African Medical Research Council (MRC), and collaborates with regional and international partners to find an affordable, effective, and relevant HIV vaccine for southern Africa. Established by Government in 1999, SAAVI has supported the research of scientists, ethicists, and socio-behavioural researchers at academic institutions across South Africa. Funding from the Initiative contributes towards several world class assets. These include four fully developed and two developing trial sites in six provinces, a GLP-compliant laboratory of the HIV Vaccine Research Group at the University of Cape Town, and a non-human primate colony at the MRC Animal Facility at Delft, Western Cape. SAAVIâ&#x20AC;&#x2122;s dedicated Community Involvement Programme, Masikhulisane, also raises awareness, educates, and promotes human rights regarding HIV vaccine research and development. SAAVI has been funded by: the National Department of Health, the Department of Science and Technology, Eskom, the European Union, Transnet, and the Impala Platinum Community Development Trust. SAAVI needs approximately R65 million per year to continue with this national initiative. To meet this amount, SAAVI currently requires additional funding of R45 million per year to add to the grant received from the National Department of Health. SAAVI would welcome any contributions towards this goal. For more information on SAAVI, please visit:

www.saavi.org.za or call

080 VACCINE

Quest 5(4) 2009 21

Vaccine research makes progress: South African AIDS Vaccine Initiative Patricia Southwood of the South African AIDS Vaccine Initiative tells QUEST about the new HIV vaccine trials in South Africa. Vaccine trial volunteers at the Emavundleni Centre. Image: Allen Jefthas, MRC

Professor Tony Mbewu, president of the Medical Research Council (MRC), at the launch of the vaccine trials. Image: Tony Erasmus, MRC

Elise Levendal, the Interim Director, SAAVI. Image: Tony Erasmus, MRC

Minister of Science and Technology, Naledi Pandor, enjoys the launch of the HIV vaccine trials. Image: Tony Erasmus, MRC

22 Quest 5(4) 2009

arlier this year, South Africa made headlines with the launch of a phase 1 HIV vaccine clinical trial to test the safety and immune response to the first two South African developed HIV vaccines. The two vaccines, SAAVI DNA-C2 and SAAVI MVA, were developed by researchers at the University of Cape Town (UCT) with funding from the South African AIDS Vaccine Initiative (SAAVI) and the United States (US) National Institutes of Allergy and Infectious Diseases (NIAID). Both vaccines are based on strain C of HIV, the most common strain in sub-Saharan Africa. The vaccines do not contain any whole or live parts of HIV and cannot cause HIV infection. The DNA vaccine will be given at the first few visits to prime or create an initial immune response, followed by several doses of the MVA vaccine at subsequent visits to boost or strengthen the immune response. The vaccines are preventative HIV vaccines and will be tested in healthy, HIVnegative adults, who are at low risk of HIV infection. The highest possible standard of HIV prevention including risk-reduction counselling and HIV prevention methods will be provided. Currently all 48 trial participants needed for this trial have been

enrolled and have begun their clinic visits. There are 18 participants at each South African site including one site in Soweto, and another in Crossroads, Cape Town. There are also 12 trial participants at sites in the United States. Not everyone in the study will get the vaccines. Some people will get a placebo, which is sterile salt water that does not contain the vaccine. Neither the trial site staff nor the participants will know who gets the vaccine or placebo until the end of the trial. Researchers will then compare the results from people who got the placebo with the results from people who got the study vaccines. Results from the trial are expected in about a year to 18 months. SAAVI is a lead programme of the South African Medical Research Council (MRC). The NIAID is part of the US National Institutes of Health (NIH), an agency of the US Department of Health and Human Services (DHHS). Trial sites in this SAAVI 102/HVTN 073 clinical trial are part of the HIV Vaccine Trials Network (HVTN) who will run the clinical trial. SAAVI will contribute to the development of the infrastructure to conduct the clinical trial at the two HVTN trial sites in South Africa. The HVTN is supported through a cooperative agreement with the NIAID.

The Emavundleni Centre in Cape Town, one of the HIV vaccine trial sites. Image: Allen Jefthas, MRC

Questions and answers SAAVI 102/HVTN 073 HIV vaccine clinical trial

A phase 1 placebo-controlled clinical trial to evaluate the safety and immunogenicity of SAAVI DNA-C2 vaccine boosted by SAAVI MVA-C vaccine in HIV-uninfected healthy vaccinia-naïve adult participants in South Africa and the US. 1. What is the SAAVI 102/HVTN 073 trial?

SAAVI 102/HVTN 073 is the name of a phase 1 placebo-controlled clinical trial to test the safety and immune response of two experimental (study) HIV vaccines. These vaccines do not

contain any live or whole HIV cells. For more information on the vaccines, see Question 4. The study vaccines cannot cause HIV infection. Not everyone in this study will get the study vaccines. Some people will get a placebo, which is sterile salt water that does not contain the vaccine. Researchers will compare the results from people who got the placebo with results from people who got the study vaccines. Whether a trial participant receives the study vaccines or the placebo will be decided randomly. Neither the study staff nor the participants will know who gets the vaccine or placebo. 2. Who is conducting this clinical trial?

This trial is sponsored by the Division of AIDS (DAIDS), within the National Institute of Allergy and Infectious Diseases (NIAID) at the National Institutes of Health (NIH), an agency of the US Department of Health and Human Services (DHHS). The HIV Vaccine Trials Network (HVTN) will run the trial. The HVTN is an academically based research organisation of scientists, educators and community members committed to eliminating the spread of HIV in the world by finding a safe and effective vaccine. The Network is supported through a cooperative agreement with the NIAID, part of the NIH. To learn more about the HVTN, please visit www. hvtn.org. In South Africa the trial will be conducted by researchers and staff at two HVTN designated trial sites, one at the Emavundleni Centre in Crossroads, Cape Town and one at the Perinatal HIV Research Unit (PHRU),

3. What is a vaccine, and what is a vaccine clinical trial?

A vaccine is given to people to prevent infection or fight disease. Currently there is no vaccine against HIV that works. In order to find an effective HIV vaccine, researchers need to test study vaccines that seem most likely to help the body fight HIV. A vaccine clinical trial is a way to test a study vaccine to see if it is safe to give to people. It is also a way to measure the immune response caused by the study vaccine. If early trials show that the study vaccine is safe and the immune response is good, researchers may test for efficacy – whether the study vaccines work to prevent HIV infection or to slow disease progression to AIDS – in later trials. ▲ ▲

How do you test an HIV vaccine? Each potential vaccine is tested in various stages taking a number of years. These stages include initial laboratory work, followed by testing the vaccine in animals and then in human clinical trials. All clinical trials must be approved by the relevant authorities before they can begin. In South Africa, these authorities include the Medicines Control Council (MCC), the relevant research ethics committees (RECs) and other necessary bodies. In addition, the safety and rights of trial participants are protected by volunteers going through a process called informed consent. Here trained counsellors give volunteers information about HIV vaccine trials, the reasons for the trial, possible risks and benefits, and trial procedures. Volunteers are then given time to think about whether they want to join the trial, and those who wish to enrol are asked to sign an informed consent form. Even once participants enrol, they may still leave the trial at any time.

based at the Chris Hani Baragwanath Hospital, Soweto. The South African MRC is a statutory organisation established by an Act of Parliament in 1969. Its mission is to improve the nation’s health and quality of life through promoting and conducting relevant and responsive health research. SAAVI was established by the South African government and Eskom in 1999 to coordinate the research and development of an affordable, effctive and locally relevant HIV vaccine for southern Africa. SAAVI is a lead programme of the South African MRC. The MRC as represented by SAAVI has agreed to cooperate with the NIAID as represented by DAIDS in the conduct of the SAAVI 102/HVTN 073 clinical trial. As part of this cooperation, SAAVI will contribute towards the development of the infrastructure to conduct the clinical trial at the two designated HVTN clinical trial sites located in South Africa.

Key messages about HIV vaccines ■ Just like the vaccine that stopped smallpox, an HIV vaccine is one of our best hopes to control the HIV epidemic. However, a successful HIV vaccine would not cure HIV and should be part of a comprehensive HIV prevention, treatment and care strategy. ■ There is no successful vaccine yet but South Africa is involved in a number of clinical trials as part of a global effort to develop a safe and affordable HIV vaccine that works. ■ A successful HIV vaccine will be safe and will prevent HIV infection, or if infection occurs, will slow down the time that it takes for a person to get AIDS. ■ The vaccine will teach the body’s immune system (our defence system against germs) to recognise and to fight HIV if exposed to the virus at a later time. ■ HIV vaccines cannot infect you with HIV because they do not contain any whole or live HIV. ■ Testing an HIV vaccine takes a long time to ensure that it is safe and that it works – most vaccines in public use today took at least 10 to 20 years to develop, test and license for public use.

Quest 5(4) 2009 23

4. What kind of experimental vaccines, or ‘study vaccines’, are being tested in the SAAVI 102/HVTN 073 clinical trial?

There are two experimental vaccines that are being tested. They are called SAAVI DNA-C2 and SAAVI MVA-C. From here on, we will call them the DNA vaccine and the MVA vaccine, or the ‘study vaccines’. The study vaccines were developed for SAAVI by scientists at the University of Cape Town (UCT), South Africa, through joint funding from SAAVI and the NIAID. To try to get the best protection, the vaccines were designed to represent the HI viruses circulating in South Africa, namely HIV subtype C. The DNA vaccine was constructed in South Africa using a main component (plasmid backbone) provided by the Dale and Betty Bumpers Vaccine Research Centre (VRC) of the NIAID and was manufactured in the USA. The MVA vaccine was designed by the team at UCT and constructed and manufactured in the USA. The study vaccines will be tested in a prime-boost approach. This means that the DNA vaccine will be given to prime the immune response followed by the MVA vaccine to boost or enhance the immune response. Both study vaccines will be injected intramuscularly. The DNA vaccine SAAVI DNA-C2 is made out of DNA, which is a natural substance found in all living things, including people and viruses. DNA tells cells to make proteins. In this study, the DNA vaccine will tell the body to make a small amount of some proteins that are found in HIV. The body’s immune system may recognise these proteins and prepare itself to fight HIV. This is called an immune response. The DNA vaccine is similar to natural DNA, but it was made in a laboratory. A person cannot become infected with HIV or AIDS from the DNA vaccine or from these proteins. The MVA vaccine SAAVI MVA-C2 was made from a virus called Modified Vaccinia Ankara (MVA) virus. It is similar to the smallpox vaccine that has been used worldwide. The MVA virus in the vaccine has been changed so that it cannot grow in humans or spread to other people. Like the DNA vaccine, the MVA vaccine will tell the body to make small amounts of some proteins that are found in HIV. These proteins may cause the body to have an immune response. A person cannot become infected with HIV or AIDS from the MVA vaccine or from these proteins. 5. Are these study vaccines safe?

Based on the data from animal studies, and the use of similar

24 Quest 5(4) 2009

vaccines in humans, scientists believe that these study vaccines are safe for use in human trials. But there is always the possibility that there could be problems no one expected. That is why these study vaccines, like any new drugs or vaccines, need to be tested in people in a clinical setting. Each participant’s health and safety will be watched closely throughout the trial.

different design. It is very important that participants avoid exposure to HIV during the study. The trial site staff will give trial participants comprehensive risk reduction counselling to help them learn how to reduce behaviour that puts them at risk of getting HIV.

6. Can these study vaccines cause HIV infection?

Study vaccines are designed to mimic (look like) the structures of HIV. By doing this, the study vaccines may cause a response from a person’s immune system. During this response, the immune system may learn to recognise HIV without being exposed to HIV. If a person who received the study vaccines is later exposed to HIV, hopefully the immune system will be prepared to respond. However, it is not yet known if these study vaccines will prevent HIV infection or slow disease progression to AIDS. If the results from this phase 1 clinical trial are promising, more clinical trials need to be conducted to see if the study vaccines work. So, it is important to remember that being given the study vaccines does not mean a trial participant is protected from HIV infection. This is explained to participants and they are counselled on how to avoid behaviour that will put them at risk of HIV infection.

It is impossible to get HIV infection or AIDS from these study vaccines. They are not made from live HIV, killed HIV, or HIV-infected cells. HIV study vaccines are designed to lower the chance of someone becoming HIV- infected if that person is exposed to HIV. We do not know if the study vaccines tested in this trial will decrease, increase, or not change a trial participant’s chance of becoming infected if he or she is exposed to HIV. There is a chance that these study vaccines could increase a trial participant’s risk of becoming infected if he or she is exposed to HIV. A previous study called the STEP Study, which was conducted in the USA, tested an HIV study vaccine that contained a weakened common cold virus called adenovirus type 5 (Ad5). In a subset of participants from this study who were previously infected with Ad5 and who were uncircumcised, there was a higher number of HIV infections in those who received the vaccine than those who received the placebo. The people who became infected with HIV in the STEP Study did not get HIV from the study vaccine. They became infected with HIV from another infected person. There was also a South African trial of the Ad5 study vaccine called the Phambili study. It was stopped following the above results from the STEP study. The group of trial participants from Phambili who had been infected with Ad5 before entering the study and who received the study vaccine did not have more HIV infections than the group who had been infected with Ad5 before entering the study and who got the placebo. One reason could be that fewer trial participants were vaccinated in the Phambili trial compared to those who were vaccinated in the STEP Study. Researchers are still looking at the STEP study results to try to learn more and to understand the relationship between vaccination, circumcision and prior infection with Ad5. The study vaccines used in this trial are not like the vaccine used in the STEP study as they have a completely

7. How could the study vaccines help prevent HIV and/or AIDS?

8. Why is this trial being done?

This is a phase 1 trial, meaning its main purpose is to test if the study vaccines are safe to give to people and how the immune system responds to the vaccines. The study vaccines have already been tested in the laboratory and in animals. 9. Who is eligible to participate in SAAVI 102/HVTN 073?

Each participant must meet certain criteria to be eligible (to qualify) to participate in the trial. Participants must be healthy adults who are between 18 and 45 years old and HIV-negative (free of HIV infection). Participants also must not have received the smallpox vaccine in the past. They must be at low risk of getting HIV infection. Potential participants are asked about their medical history and are given a physical examination. They then have blood and urine samples taken for routine testing. They are also asked about their sexual activity and alcohol or drug use. People who want to join the trial and were born female will be given a pregnancy test. Those who are pregnant or breastfeeding are not eligible to join. Anyone in the trial who was born female and who is

capable of getting pregnant must agree to use effective birth control starting at least 21 days before the first injection of the clinical trial and continuing until the last clinic visit. 10. When and where is this trial being conducted?

SAAVI 102/HVTN 073 is an international trial and will be done in two countries: the US and South Africa. The trial is being conducted at two sites in South Africa, one in Cape Town and one in Soweto, and at three sites in Boston, MA, in the US. The trial began enrolling participants in the US arm in late 2008 and early 2009 and has 12 participants enrolled. South Africa began enrolling participants in mid 2009. 11. How will the safety and rights of trial participants be protected?

The HVTN and SAAVI work hard to protect the safety and rights of the trial participants. Before they join the trial, volunteers will be given information about HIV vaccine trials, the reasons for the trial, possible risks and benefits, and about trial procedures. The clinic staff will allow plenty of time to talk with volunteers, answer their questions, and to give information to them in writing. After the trial has been fully explained, volunteers are asked to sign an informed consent form. They sign this form before being screened for eligibility and before enrolling. The informed consent form helps confirm that trial participants have made an informed decision about joining the trial. Volunteers will have plenty of time to think about whether they want to join the trial. They may decide not to enrol. If they do enrol, they may still leave the trial at any time without losing the benefits of their standard medical care. During the trial, the clinic staff will monitor trial participants to make sure the study vaccines are not causing them problems. Participants will be given any new information that could affect whether they want to stay in the study. Participants will be reminded often that being in a vaccine trial does not mean they are protected from HIV. They will be counselled at every clinic visit on ways to avoid becoming infected with HIV. (This counselling will include, for example, talking about correct condom use.) It is important for participants to understand that any new study vaccine may have both medical and nonmedical risks. Community Advisory Boards or Groups (CAB/Gs) are also a mechanism to ensure that any human

rights issues and other concerns raised by the community are addressed. 12. Could either study vaccine cause a ‘false-positive’ or ‘vaccine-induced positive’ test result on an HIV antibody test?

Some study vaccines may make a trial participant test positive on an HIV antibody test, even if the participant is not infected with HIV. One way study vaccines can create an immune response is by causing the body to make antibodies. Common HIV tests look for antibodies against HIV. This means that after a participant gets a study HIV vaccine, a standard HIV test may say the person has HIV, even if that isn’t the case. This result is called a ‘false-positive’ or ‘vaccine-induced positive’ result. Each site involved in the SAAVI 102/ HVTN 073 trial will use other HIV tests that can detect whether a person is really infected with HIV. These tests can be used to determine if a positive HIV test result is a vaccine-induced positive result or due to true HIV infection. There are no health problems associated with a false-positive HIV test result that are caused by a study HIV vaccine. However, someone who gets that type of test result may be treated unfairly by others. People with a positive HIV test result, even a vaccine-induced positive result, are not allowed to donate blood. They may also have problems getting insurance, travelling to other countries, or with their relationships with friends and family. The trial site staff can help with such problems. 13. How long will it take to find out if this combination of study vaccines works?

It could take several years to find out if this combination of study vaccines helps the immune system to protect against or control HIV infection. Within the next year, results from the SAAVI 102/HVTN 073 phase 1 trial will help researchers determine whether they should proceed with further clinical trials on these vaccines. The results from the phase 1 study will show whether the study vaccines are safe and immunogenic (they cause an immune response). If results from this phase are promising, phase 2 and 3 clinical trials may be conducted in bigger numbers of people. Phase 2 trials test for vaccine safety, immune response and the best way to give the study vaccine/s. Phase 3 clinical trials continue to test for safety and to see if the study vaccine/s is effective – whether it protects against HIV infection or if it slows disease progression to AIDS. Often there is a phase 2b trial – it produces further safety

and efficacy data to give an idea of whether the vaccine/s is effective. The outcomes of a phase 2b study help to guide future research. Participants who receive the study vaccines in SAAVI 102/HVTN 073 will not be eligible for any future clinical trials on these products. 14. Who reviewed, approved and monitors this trial?

In the US, the study vaccines are considered ‘investigational’, meaning that the US Food and Drug Administration (FDA) only allows them to be used in research. These study vaccines have been made according to FDA guidelines and the clinical trial protocol was reviewed by the FDA, who allowed the protocol to move forward through the usual review process. The Protocol Team (the people who designed the trial) also carefully reviewed the information about the study vaccine before deciding to begin the trial. Similarly, the study vaccines have been approved for use in research in a phase 1 clinical trial in South Africa by the South African Medicines Control Council (MCC). The Institutional Review Boards (IRBs) or Independent Ethics Committees (IECs) or Research Ethics Committees (RECs) at each participating research centre have also reviewed and approved the clinical trial protocol (trial plan). RECs are also involved in reviewing changes to the clinical protocol from an ethics and human rights point of view. Ethical concerns about the trial can also be directed to these bodies to be addressed. The local Institutional Biosafety Committees (IBCs) have also reviewed and approved the clinical trial protocol. Community members, for example, by way of Community Advisory Boards or Groups (CAB/Gs) are involved throughout the trial to ensure that the research is acceptable to the community. CAB/Gs are therefore one mechanism to ensure that any human rights issues and other concerns raised by the community are addressed. ■ For more information About the NIAID/DAIDS: www.niaid.nih.gov About the HVTN: www.hvtn.org About the MRC: www.mrc.ac.za About SAAVI: www.saavi.org.za About UCT’s IIDMM: www.iidmm.uct.ac.za About PHRU: www.hivsa.com About DTHC: www.desmondtutuhivcentre. org.za SAAVI Info-Line: 080 822 2463

Quest 5(4) 2009 25

Conflicting reports about an HIV vaccine trial You may have seen reports in the press recently that an HIV vaccine trial in Thailand showed that the vaccine reduced the risk of becoming infected with HIV by 31%. And then you may have seen other reports suggesting that these results are pure chance.

n 24 September 2009, the final results of an HIV vaccine trail were announced by the US Army Surgeon General. He reported that the prime-boost combination that made up the RV144 phase 3 trial reduced the rate of HIV infection by 31.2% compared with placebo. This was indeed exciting news – the first HIV vaccine candidate to successfully reduce the risk of HIV infection in humans. So what is happening? Was the vaccine effective or are the results due purely to chance? Let’s start by looking at the trial itself. The trial in question was the RV144 phase 3 trial, which was carried out in Thailand by the US Military HIV Research Program in partnership with the Thai ministry of

A scientist collating data in the RV144 trial. Image: US Military HIV Research Program

A volunteer in the RV144 trial receiving the vaccine.Image: US Military HIV Research Program

26 Quest 5(4) 2009

health. The trial enrolled 16 000 Thai men and women who volunteered to participate. RV144 tested a prime-boost strategy. This is a combination of two vaccines, one after the other, designed to create a stronger immune response. This is called a prime-boost strategy. The trial began in 2003 and looked at whether the vaccine could prevent infection in the first place and, in those who became infected after they had enrolled in the study, if the vaccine could reduce the amount of HI virus circulating in their blood. The 16 000 trial participants were aged between 18 and 30. Half received the prime-boost vaccine and half received a placebo. The volunteers received vaccines over the course of six months and were then followed for three years, during which time they had regular HIV tests and were counselled about remaining HIV-negative. Where the problems lie The questions that have been asked about the results of this trial hinge on how the results were analysed and the question of statistical significance. Statistical significance is a mathematical technique that is used to calculate whether results of any experiment are meaningful or if they are due to chance. At the end of any clinical trial, participants are put into three categories. These are: ■ Intention-to-Treat (ITT): this group includes everyone in the study, even if they are later found to be unsuitable for other reasons. In this case, the ITT group included seven subjects who were actually HIVpositive before the study began. This arm of the trial showed vaccine efficacy of 26.4%. ■ Modified Intention-to-Treat (mITT): excludes certain subjects who are later found not to meet eligibility requirements for a study, but includes everyone else, even if they did not receive the full trial treatment. In this case, the mITT group is everyone in the clinical trial except the seven HIV-positive subjects. Some people in the mITT group did not receive all six injections of the HIV vaccine. This

arm of the trial showed vaccine efficacy of 31.2%. ■ Per-Protocol (PP): this group includes only the subjects who completed the trial and received the full treatment or dosage. For study RV144, this is everyone who received all six injections on time. This is the smallest group, with the fewest number of people. This arm of the trial showed vaccine efficacy of 26.2%. It was only the results for the mITT group (31.2%) that meet the usual scientific standards of statistical significance. This means that if researchers look only at the PP group – the subjects who received every vaccine injection on schedule – they cannot rule out the possibility that the results were due to chance, rather than to actual protection by the vaccine. There were also questions asked about the way in which the results were publicised; only the statistically significant result from the mITT group was provided to the media. Defending the results The US Army Surgeon General, Colonel Nelson Michael, who was the main investigator in the trial, defended the way that the trial results were publicised. He argued that the main reason for the trial was ‘proof of concept’, that is, to show that two ‘unlikely’ vaccine combinations can have any effect at all. He says that the trial was not meant to provide a vaccine that gave complete immunity against HIV or to suggest a way in which a vaccine could be administered. Other HIV scientists, while not exactly defending the approach to releasing results to the media, see the trial as an important breakthrough in HIV vaccine research. Deborah Jack, chief executive of the National AIDS Trust in the United Kingdom, called the Thai trial ‘a milestone in the search for a vaccine against HIV’. Jack also highlighted the potential for this study to lead to a more successful vaccine. ‘These results are an incredible opportunity for scientists to discover new clues about HIV and learn how an HIV vaccine could work in practice.’ ■

Building the future of computing and science in South Africa Few youngsters from disadvantaged backgrounds have access to computers at school or at home, leaving them with a serious disadvantage later in their careers. QUEST spoke to Daniel Moeketsi about how the Centre for High Performance Computing is hoping to turn this situation around.

or many of us reading this magazine, a computer has been part of our daily lives for many years. This is, however, not the case for many youngsters from previously disadvantaged areas of South Africa. And without the skills that daily use of a computer brings, these young men and women find themselves at a serious disadvantage when they carry on to university or technical colleges, regardless of the scientific discipline they have chosen. There is also the issue of attracting young talent into computing as a field of specialisation. The Centre for High Performance Computing (CHPC) has set out to provide outreach programmes to teach computer hardware and software to fill some of these gaps. Reaching out The outreach programme is a joint initiative between the Computer Olympiad, the Western Cape Department of Education (WCDoE) and the CHPC. The aim of the CHPC programme is to raise awareness of and interest in high performance computing across all disciplines. It is managed by Daniel Moekestsi, who is a research scientist at the CHPC, who describes this as a pilot programme that is taking place over five years. Phase 1 of the outreach programme was launched in November 2008. This involved a basic introduction to computers, using machines dontated by the Western Cape Department of Education. Valentino van de Heyde, Daniel’s honours student at the University of the Western Cape and Eric Mbele of the CHPC put together a course to teach students what they call the ‘nuts and bolts’ of computer hardware. This includes learning how to put a computer together from scratch, installing Ubuntu Linux, working with Linux and OpenOffice, and an introduction to Python programming. The course took place every Saturday for about ten weeks. This series of seven lectures finished in March this year (2009), after which Phase 2 started. Phase 2 teaches students the complexities of operating systems Python is a general-purpose, high-level programming language, with particularly clear syntax.

and introduces the students to high performance computing. The first group of ten students from the Western Cape graduated from the Basic Hardware and Software Course in May 2009. Each student received a certificate, signed by Professor Colin Wright, head of research at the CHPC, and the computer that they had each built to keep for their own use. The CHPC now has 50 computers available and is busy selecting students for the next phase of the programme, who will start in December this year and January 2010. All students are given an apptitude test from the Computer Olympiad to check that they have the potential skills that are required for the courses. These apptitude tests consists of tests of basic mathematics, logic and reasoning, the ability to manipulate information and to identify structures. At the end of January 2010, it is hoped that 25 students will enter the advanced scientific programme. These students will also have the opportunity to enter the second round of the Computer Olympiad. Further outreach The CHPC education and outreach programme intends to train at least 20 learners a year in the next three years and plans to engage stakeholders such as the South African Agency for Science and Technology Advancement, and science centres across the country to roll-out the project at national level. The hardware and software programmes are not the only form of community outreach that the CHPC offers. During National Science Week in 2009, 220 students visited the CHPC to see what high performance computing is all about. The CHPC also encourages university students and intersted members of the public to arrange to see the facilities of the CHPC to learn what the centre has to offer. Computing is no longer an isolated entity. There is now not a science that does not require the use of computers, so students from disadvantaged backgrounds often struggle when they reach work or higher education because they lack computer experience. The CHPC is hoping to be able to help to bridge that gap and to expand its outreach programme nationally. ■

Students taking part in the basic hardware and software courses offered in the outreach programme. Image: CHPC/CSIR

CHPC acting technical manager Dorah Thobye and Dr Daniel Moeketsi award a certificate for the basic computer hardware and software course to a learner from Crystile Secondary School, in Hanover Park. Image: CHPC/CSIR

The Computer Olympiad The Computer Society of South Africa (CSSA) Computer Olympiad is one of the oldest and largest competitions of its kind in the world. The competition is open to all full time students in South Africa. Each potential entrant completes a first round paper and, once into the comptetition, carries on to the second and third rounds depending on his or her results. The aims of the Olympiad are to: ■ Identify, encourage and reward programming aptitude ■ Promote and encourage computer studies ■ Create an awareness of the potential uses of computers For more information see http://www.olympiad. org.za/

Quest 5(4) 2009 27

Climate change and agriculture James Blignaut and Leandri van der Elst discuss the consequences of climate change for one of South Africa’s most important sectors, agriculture.

ural South Africa, and indeed much of the rest of Africa, is dependent almost entirely on agriculture to survive. Those in urban areas are also dependent on what the land produces, meaning that agriculture is equally important for all South Africans. Although agriculture provides only 3% of our GDP, the nature of the sector is such that any problems will have a relatively large effect on our daily lives. The relative contribution of agriculture to life, livelihoods and the general psychology (or social capital) of the country or nation cannot be overemphasised. The pillars of economic development include food, water and energy. Without the security of these three, people cannot develop and become self-sufficient and independent. And if people on the grassroots level cannot become (or remain) self-sufficient and productive, the economic core of the country is threatened. This reinforces the strategic and relative importance of agriculture since food and water security go hand-in-hand with most, if not all, other economic development needs. The agriculture sector is therefore vital for the maintenance of political stability through successful land management and reform. The nature of agriculture Agriculture in South Africa, as in so many other parts of Africa, is made up of an informal (largely noncommercial) and formal (commercial) component. Informal agriculture includes the subsistence farmers who produce goods (e.g. crops or cattle) to sustain themselves and their families, and sometimes the immediate community. This is smallscale production and even if there is a surplus of goods, there are often no accessible markets available. Ideally, government would like to integrate these farmers into the formal agriculture sector. There are essentially three divisions

within the formal agricultural sector: field crops, horticulture and animal production. These farmers produce agricultural products on a large scale and trade these on the open market. These two sectors appear to be unrelated, with little conncection between them. However, the reality of climate change will affect both and each sector needs to find strategies to deal with this overarching phenomenon. Climate change Over the past three decades the world’s climate, including that of Africa, has changed. This is a reality. A reality that is taking place fast. We can see climate change all around us in the increase in the frequency and intensity of extreme events such as droughts and floods. And the emphasis is on rapid. Climates around the world have been changing ever since the beginning of time, but the rate and intensity of the change we’re experiencing now is beyond anything we know of in the past. Why is this? The climate of a continent, a country or a region is never stable; there are always changes in response to the fact that any system seeks what is called a steady state. However, this steady state never arrives because there are always other factors that work on the system on a continuous basis. These factors are called drivers. The main driver responsible for the current rapid change is global atmospheric levels of carbon dioxide (CO2). While CO2 is a non-toxic, composite gas that occurs naturally in the atmosphere, its concentration is of particular concern. CO2 levels fluctuated at levels between 270 – 290 parts per million up to 1800, but then started to increase dramatically. Levels of CO2 are now approaching 400 parts per million and are set to rise to beyond 450 parts per million by 2030 – 2050 (See Figure 1). This increase in CO2 is caused mainly by the combustion of fossil fuels, leading to the formation of a

Left (above): A diagram showing how the greenhouse effect works. Left (middle): The ice cap on Tanzania’s Mount Kilimanjaro is slowly melting. Figure 1: Changes in global temperature and CO2-concentration levels.

Image: NASA

Image: IPCC Forth Assessment

report, 2007. Figs 1.1 and 2.3 http://www.ipcc.ch/publications_and_data/publications_ipcc_fourth_assessment_report_synthesis_report.htm

28 Quest 5(4) 2009

Q Climate change

in South Africa

with currently unknown organisms, that are likely to threaten crop yields and human health. So you can see that climate change not only has an impact on agriculture, but that it is likely to have a considerable impact on farmers because of their dependence on the climate. The occurrence, timing, frequency and intensity of climatic events, for example rainfall, as well as the distribution of these events within a season of growth, have definite impacts on agricultural production. And these effects will be felt in both the formal and informal agricultural sectors. Water – the main ingredient Much can and should be done to reduce CO2 levels nationally, for example by encouraging the development of renewable energy sources and the industry that can arise around these. However, it is the farmer, his family and the rest of us who will fell the impact of climate change at the local level. Farmers can do plenty to try to reduce their own CO2 emissions, such as moving to a no-tilling system of crop management. However, farmers are going to have to find innovative ways to adapt to a changing climate. In the past it was possible for commercial farmers to rely on ample surface

Top: Rainwater harvesting in practice near Thaba Nchu. Image: James Blignaught

Above: Water restoration in progress on an ostrich farm near Oudtshoorn. Image: Sue Milton

and ground water resources and, through irrigation, buffer themselves against the effect of changing climatic conditions. With climate change, water availability will be under increasing pressure and water will eventually become a luxury as the demand for water, especially in urban areas and by the manufacturing sector is rising and the supply becoming more erratic.

▲ ▲

gas layer around the outer edges of the atmosphere that allows the rays of the sun to enter the atmosphere, but which prevents the reflected heat to escape. This is refered to as the ‘greenhouse effect’ and leads to a build up of heat within the atmosphere. This build up of heat causes changes in climatic patterns and processes, such as the melting of icebergs, glaciers (e.g. on the top of Mount Kilimanjaro), and increased rates of evaporation and transpiration of water, which has serious consequences for farming. Climate change in Africa While Africa is the continent with the lowest CO2-emission levels and rates, it is arguably one of the most vulnerable to changes in climate. There are various reasons for this: ■ Africa’s generally low levels of income ■ Africa’s, by and large, hot and relatively arid climate ■ Agriculture is one of Africa’s main forms of livelihood and income ■ The increase in the frequency and intensity of extreme climatic events, which will almost certainly reduce, on average, crop and animal production. These changes are likely to vary from year to year and from region to region. These changes are also likely to have a major impact on the production, access and distribution of food ■ Varying climatic conditions will probably also change the rainfall regimes and have an impact on water security ■ Africa does not have the resources to import large amounts of food, and/or to invest in climate adaptation programmes ■ Africa still has to develop its energy sector (implying, most probably, more CO2 emissions) to allow economic development, and ■ Africa has neither the expertise nor the financial and other resources to map and monitor the distribution and spread, and to combat invasive alien organisms (e.g. exotic plants) but also pests and diseases that are likely to become more widespread on a warmer climate, such as cholera and malaria. Climate change may also lead to worse pest infestations, possibly

No-tilling is the word used for a system of farming in which crops are planted without ploughing or using herbicides to control weeds, which results in less soil erosion and lower losses of soil nutrients.

Quest 5(4) 2009 29

Above: Water use by sector in the year 2000.

Image: SSA (STATISTICS

SOUTH AFRICA) (2006) Water Resource Accounts for South Africa: 1995 & 2000. Statistics South Africa,Pretoria, South Africa.

Right: Community-based farming in Lesotho.

Image: A Basson

It will become vital to introduce methods that conserve water and that use water efficiently. This has an impact on the meat producers as well as the crop farmers, because the animals are dependent on grazing material that requires rain for its production. Most commercially farmed animals are are housed in feedlots that demand significant quantities of water daily, either from a surface or ground water source. While commercial farmers can still consider capital-intensive alternatives such as improved irrigation systems, this is not possible for subsistance farmers or, often, for the newly emerging commercial farming sector who are hampered by lack of capital and knowledge. Rainwater harvesting and conservation must be improved and along with this, changes in farming practice that improve yield but that are less water intensive are needed. These include the use of organic and non-harmful fertilisers and an increase in the biodiversity of the farming ecosystem, which will make it more able to absorb changes in its environment. But is the climate changing? Recent research has shown that eight of the nine provinces experienced considerable temperature increases during the last three decades. Only Mpumalanga province has become marginally cooler. The same research showed that the annual rainfall in South Africa was declining. Only the Western Cape has shown consistent annual rainfall. So, on the whole, South Africa has become hotter and drier since the early 1970s. Historic changes in the pattern

30 Quest 5(4) 2009

and amount of rainfall, as well as changes in minimum and maximum temperature ranges, cause changes in agriculture production in South Africa. For example, changes in rainfall affect field crops, as these are most likely to be adversely affected by sudden or gradual changes in climatic conditions. And because agriculture influences other sectors, changes in the climate also result in changes in other sectors and ultimately in the economy. How is water used by South African agriculture? The Department of Water Affairs and Forestry (2004) estimates that in 2000, South Africa had a total reliable surface water supply of 13 226 million m3 while, in the same year, South Africa used 13 041 million m3. This leaves a surplus of only 186 million m3, or 1.4% of the total reliable surface water supply for that year. Furthermore, 12 of the countryâ&#x20AC;&#x2122;s 19 water catchments reported water deficits, which were only partially balanced by an intricate system of inter-basin water transfer schemes. This means that the surplus, and/or the unallocated balance of a vital natural resource is approaching zero; clearly identifiable thresholds of critical scarcity. This implies that the economic value of unutilised water is very high, far exceeding that of the prevailing bulk water tariff. If the demand for water demand grows â&#x20AC;&#x201C; which it surely will â&#x20AC;&#x201C; by more than 1.4%, the amount of water used in some, often water-intensive, sectors must be reduced. Eventually, water rationing will become essential. A shortage of water has negative implications for economic development. There are other water

supply options, but these are limited and often very costly. These include importing more water from Lesotho (which is already occurring to some extent), the intensive use of ground water and return flow, desalination, the development of more dams and even importing water from the distant Congo River. The implementation of any of these options would have a significant effect on the tariff paid for water, making drinking water less accessible to those who are most in need. Other options include water augmentation through the restoration of natural capital, and rain water harvesting, options that tend to be cheaper than those mentioned earlier, but they do have a limited capacity given the significant demand. Surface water use Agricultural practice that make use of irrigation, consumes approximately 60% of the available surface water and is by far the largest single surface water user. In total, agriculture in general consumes about 65% of the total available surface water (SSA 2006). The use of surface water for irrigation has increased steadily from 7 630 million m3 in 1995 to 7 921 million m3 in 2000, an increase of 291 million m3, or 4%. Ground water use Surface water use is increasing rapidly and there is no indication of a decline in use in any sector. The use of groundwater is also increasing rapidly. It was estimated that at the end of 2001 ground water use was almost half of the amount of surface water used. About 41% of the potential ground water was in use in 2000 (SSA 2006). This allows some further development but this source of water is also dwindling fast.

Q Climate change

This crop is the result of conservation farming in Lesotho.Image: A Basson

Water – the limiting factor By now it should be clear that water is one of the main resources limiting economic investment and development. There are very real constraints on water supply, which cannot continue to grow at current rates. What makes the increase in water demand worse is the decline in the water availability because of changes in the climate. There has to be some form of intervention, and fast. Water plays a significant role in the predominantly horticulture production areas, such as the Western Cape, where viticulture plays a major role. Horticulture, like animal production, makes extensive use of irrigation that temporarily offsets any sudden decline in rainfall. In contrast, dryland agriculture, especially field crops, does not have this option and is therefore much more vulnerable to changes in climatic conditions (rainfall) than horticulture and animal production. Field crop production is likely to be most affected by any adverse changes – sudden or gradual – in climatic conditions. There is a remarkable correlation between rainfall and crop production, whether summer (e.g. maize) or winter crop (e.g. wheat). This means that if the temperature continues to rise and rainfall continues to decline, as it has during the past four decades, the three major maize and wheat production areas of South Africa are likely to markedly reduce crop production. Gross farm income (gross revenue or turnover) over the last four decades has, however, increased. But this steady growth has been countered by a rapid rise in production costs in all

provinces, leading to a declining net income (revenue minus cost). Climate change does not always mean a decline in gross income; more often a decline in net income is mainly the result of an increase in input costs. However, without irrigation growth in gross income might be considerably reduced. And on top of this the costs of expansion and intensification of production are rising much faster than the value of what farmers are producing. Where to next? South Africa, on average, has been hotter and drier during the last 10 years than during the 1970s. If this represents future climatic trends this has major implications for South African agriculture. There is very little scope for the expansion of irrigation, given the limited supply of surface and ground water and the pressing socio-economic needs of a rapidly urbanising population. This implies that farmers are likely to rely increasingly on water-saving techniques that may drive their costs up even further. And this is in a sector that has a small net income margin and which is already facing rapid cost rises. This is likely to make it increasingly difficult for emerging farmers to enter the sector, despite the official national policy to help them. What’s more, these factors will have a significant impact on overall food security. Given trends of declining rainfall and increasing average temperature, both field crop production and horticulture are extremely vulnerable, especially rain-fed field crops. Such

a decline is also likely to lead to a decline in net income in the most productive provinces. Only 1.4% of South Africa’s water yield is currently available for the poor, most of whom currently have no access to potable piped water. These 15 million people, who comprise 35% of the population (SSA 2002), are obliged to find and physically carry water to their homes and their livestock, on a daily basis. This is clearly not an acceptable situation. Finally, we need to recognise that we are living in a rapidly changing world. Ecological systems, including agrosystems, were always subject to influences from extreme events and global forcing factors, such as new markets or the collapse of old ones. In today’s interconnected world, with massively accelerating climate changes, ‘business as usual’ is no longer good enough. We must take stock of the current trends and adapt our ways of thinking, acting, farming and managing vital resources, such as water. ■ James Blignaut is a lecturer at the Department of Economics, University of Pretoria, ASSET Research (www. assetresearch.org.za) and Jabenzi (www. jabenzi.co.za), email: james@jabenzi.co.za Leandri van der Elst is a research assistant at ASSET Research (www.assetresearch.org.za), email: leandri@unboxed.co.za

REFERENCES Blignaut JN, Ueckermann L, Aronson J. Agriculture production’s sensitivity to changes in climate in South Africa. South African Journal of Science. 2009a; 105: 61-68. Blignaut JN, Van Heerden JN. The impact of water scarcity on economic development initiatives. WaterSA. 2009b; 35: 415-420. Botha FS. A proposed method to implement a groundwater resource information project (GRIP) in rural communities, South Africa. 2005. M.Sc. thesis, University of the Free State, Bloemfontein. DWAF (Department of Water Affairs and Forestry). National Water Resource Strategy. 2004. Pretoria: Department of Water Affairs and Forestry. SSA (Statistics South Africa). South African Statistics 2002. 2002. Pretoria: SSA. SSA (Statistics South Africa). Water Resource Accounts for South Africa: 1995 & 2000. 2006. Pretoria: SSA. Vegter JR. Groundwater Development in South Africa and an introduction to the Hydrogeology of the Groundwater Regions. 2001.Water Research Commission (WRC) document TT 134/00. Pretoria: WRC.

Quest 5(4) 2009 31

Image: Warren Johnson

Local action against climate change

Saturday 24 October was the International Day of Climate Change. QUEST editor, Bridget Farham, was at the event on her local beach.

Noordhoek beach, Cape Town, one of the areas that will disappear if we do not take enough action against rising sea levels. Image: Warren Johnson

Why 350? Scientists say that 350 parts per million (ppm) carbon dioxide (CO2) in the atmosphere is the safe limit for humanity. Accelerating arctic warming and other early climate impacts have led scientists to conclude that we are already above the safe zone at our current 390 ppm, and that unless we are able to rapidly return to 350 ppm this century, we risk reaching tipping points and irreversible impacts such as the melting of the Greenland ice sheet and major methane releases from increased permafrost melt.

32 Quest 5(4) 2009

live at 10 metres above sea level – about a kilometre from one of the most spectacular beaches in the world. On Saturday 24 October 2009 people in 181 countries came together for the most widespread day of environmental action in the Earth’s history. At over 5 200 events around the world, people gathered to call for action on the climate crisis. At 12 noon on the 24 October, several hundred people gathered on Noordhoek beach to form the number 350 on the sand and to sign a petition to President Jacob Zuma to urge our government to take global climate change seriously. The event was organised by the

Wildlife and Environment Society of South Africa (WESSA) – see www.wesa.org.za for more information on their activities. Similar events took place elsewhere in Cape Town and in the rest of South Africa. The idea was to form the figure 350 on the sand – something that was being done by millions of people around the world on the same day. Photographs of this global event, along with information on climate change, can be seen on www.350.org. From 7–8 December 2009 leading scientists and policy makers from around the world will gather in Copenhagen, Denmark at a meeting that is being

Image: Warren Johnson

billed as the meeting that ‘will determine the future of humanity’. Delegates at this week-long conference have the challenge of working out ways of preventing humanity from exceeding the 250 000 megatonnes of carbon that is the maximum amount that we can put into the atmosphere if we are not to critically change our climate. If we keep going at current rates that ration will have been used up in the next 20 years. Some people think that we are already starting to see the effects of climate change. Indeed, as I write this, Cape Town is in the midst of unseasonally heavy rain and low temperatures. The rain is causing widespread flooding, which meterologists think may be due to high sea temperatures. Other parts of South Africa are dealing with drought; Gauteng had unseasonal cool, rainy days last summer, and so it goes on. Are these strange weather patterns related to global climate change? At the moment, no-one can say for sure, but these types of anomalies may become more and more common as we relentlessly pump carbon into the atmosphere. Initiatives such as 350.org are vital community responses to an issue that affects every one of us. Keep an eye on the web site for more action highlights. ■

Right: Hundreds of local Capetonians decided to show their support for mitigation of climate change. Image: Bridget Farham Below: People flocked to the beach to participate, each being allocated a position in the number 350. Image: Bridget Farham

Letting the dead speak: DNA analysis is not only about catching the criminals. As QUEST found out from scientists at the University of the Western Cape, DNA can help to right the injustices of the past. Older forensic technologies: Blood types and fingerprints There are older technologies that still play an important part in helping to identify individuals who may have been at a crime scene. Conventional blood typing is one of the most reliable methods. After the discovery of the ABO blood typing groups, scientists found that the differences among the ABO groups between people could be used to determine who might be the donor of a blood stain at a crime scene. Conventional blood typing can be used to reduce the number of possible donors to a crime scene to a minimum; in other words to reduce the number of possible suspects. Forensic DNA typing is trying to do the same thing. However, the advantage of DNA is that each person has a unique DNA profile, whereas there are only a few blood groups which all of the population share. When coupled with the fact that DNA is much more stable in the environment than is blood, DNA typing is much more powerful than conventional blood typing of evidence material. Most people are familiar with dermatoglyphic fingerprints obtained from the fingers which, like DNA, are unique to each individual. However, these are often less helpful to the police because they are not always left behind at a crime scene as evidence. It was at the end of the 1900s that people realised that each personâ&#x20AC;&#x2122;s fingerprints were individual and, like all aspects of a person, were genetically determined. The minute variations in fingerprints result from a combination of genetic and nongenetic events during embryonic development; thus even two identical twins can be distinguished by their fingerprints. However, fingerprints can only be found at a crime scene if a person touches a suitable surface with bare fingers. But DNA can be extracted from hair, skin cells, blood, fragments of bone, teeth or any body fluids left at a crime scene.

cross the world, there are areas that suffer under ruthless governments. Opponents of these regimes are often abducted, murdered and buried in unmarked graves. Analysis of the DNA found in the remains of these bodies can play an important role in identifying the victims. There are, sadly, many examples of where this has been necessary. The former Yugoslavia is probably one of the best examples, with the most thoroughly investigated mass grave sites anywhere in the world. In that country an estimated 40 000 unidentified bodies are believed to have been buried in mass graves. In 1996 the International Commission of Missing Persons (ICMP) was set up to help to identify the remains in these graves. DNA analysis is a key technology in this process of mapping human genocide. Truth and reconciliation The South African Truth and Reconciliation Commission was set up in 1995, chaired by Desmond Tutu. Based in Cape Town, but carrying out hearings around the country, the commission made significant progress in examining the abuses that were committed during the apartheid era in South Africa. However, there were still large numbers of people

Left (from top): A scanning electron micrograph of human blood cells, showing red blood cells, white blood cells and platelets. Image: Wikimedia commons A fingerprint.

Image: Wikimedia commons

OJ Simpson at his murder trial, demonstrating how he wore gloves. Image: Wikimedia commons

34 Quest 5(4) 2009

Archbishop Desmond Tutu. Image: Wikimedia commons

Q Biotechnology

The role of DNA analysis Alec Jeffreys with X-ray film images of DNA profiles.

missing when the commission closed its proceedings, which lead to the establishment of a Missing Persons Task Team (MPTT) within the South African National Prosecuting Authority. This team used evidence generated by the Truth and Reconciliation Commission and their own investigations to identify the most likely burial sites of activists. They also exhumed (dug up) the remains, which needed to be investigated. The University of the Western Cape (UWC) initiated a DNA testing programme to add to the non-DNA evidence that was gathered by the MPTT. Sean Davison, Mongi Benjeddou and Maria Eugenia D’Amato were members of the UWC team. They used innovative techniques in biology, technology and genetics alongside the evidence provided by classical physical anthropology. However, as they point out, DNA analysis can provide an additional source of evidence that is particularly useful when body parts have been separated from one another or victims are buried in mass graves. Dental records are also important, but these need a fully intact skull or jawbone, as well as access to previous dental records. DNA, on the other hand, can be used as long as enough has been preserved in the skeletal remains and as long as reference samples can be obtained either from surviving relatives or from personal items belonging to the victim that contain biological material. This involves forensic DNA analysis.

of the differences in DNA sequence do not show themselves in physical appearance but must be investigated using laboratory techniques. These DNA fragments are called polymorphic because they vary in shape from person to person. Essentially, DNA profiling is the process of separating an individual’s unique, polymorphic fragments from the common ones. The past 30 years have seen rapid advances in the science of molecular biology, which have made it possible to identify these differences and to reveal them as a pattern that can be used to distinguish any two individuals. This pattern can be compared with a unique personal barcode, similar to a supermarket bar code, which is referred to as a ‘DNA profile’. Recently, DNA technology has moved from the laboratory into the courts of law. DNA technology is used essentially to reconstruct events; what happened, where it happened, when it happened and who was involved. It cannot determine why something happened. When science is applied in this way we add the adjective ‘forensic’, which means that the science is applicable in a court of law. Forensic analysis is performed on evidence to assist the court in

establishing physical facts so that crimes can be resolved. The original ‘DNA fingerprint’ looked at many locations in the DNA of a person’s genome at the same time. A person’s genome is made up of all the DNA that he or she posseses, both in the chromosomes (where the DNA is packaged) and in the mitochondria (the parts of a cell that provide energy).

The result is a multi-banded pattern whose complexity suggests a fingerprint, and which is unique to each individual, although identical twins are not different from each other. The term ‘DNA fingerprinting’ was coined, and for the first time geneticists could demonstrate that the DNA in every cell of every person contains a code that is unique to that individual. Nowadays the expression ‘DNA fingerprint’ has been replaced by the more technically correct expression ‘DNA profiling’. DNA typing The fundamental techniques involved in genetic profiling were discovered almost by accident in 1984 by the geneticist Alec Jeffreys of the University of Leicester in Great Britain. He apparently looked at the X-ray film

▲ ▲

Forensic DNA analysis With the exception of identical twins each individual’s DNA is unique. However, approximately 99.5% of the DNA code is the same for all people. Because we all belong to the same species this large chunk of common DNA codes for our species-specific characteristics. For example, we have feet instead of hooves, skin instead of scales, mouths instead of beaks, and so on. It is the other unique 0.5% of DNA that is of interest to forensic scientists. This portion varies greatly between people and shows itself in individual characteristics such as eye colour, hair colour, and blood type. Most

Image: National Institutes of Health

Quest 5(4) 2009 35

The first use of DNA typing Alec Jeffreys’ discovery was put to the test in a landmark case after two teenage girls were murdered in the small town of Narborough, Leicestershire in 1983 and 1986. In 1983, 15-year-old schoolgirl Lynda Mann was found raped and murdered in the Narborough area. Forensic scientists visited the scene, and a semen sample taken from her body was found to belong to a person with a blood type that matched only 10% of the adult male population. Unfortunately, with no other leads or forensic evidence, the murder hunt was eventually wound down. Three years later, Dawn Ashworth, also 15, was found strangled and sexually assaulted in the same area. Police were convinced that the same assailant had committed both murders and recovered semen samples from Dawn’s body that revealed that her attacker had the same blood type as Lynda’s murderer. The prime suspect was a local boy, Richard Buckland, who after questioning revealed previously unreleased details about Dawn Ashworth’s body. Further questioning led to his confession and imprisonment, but he denied any involvement in the murder of Lynda Mann. Convinced that Buckland had committed both crimes, Leicestershire police contacted Alec Jeffreys. Using his technique for creating DNA profiles, Dr Jeffreys compared semen samples from both murders, against a blood sample from Richard Buckland. The tests conclusively proved that both girls were killed by the same man, but not by Buckland, who became the first person in the world to be cleared of murder through the use of DNA profiling. Leicestershire police then decided to undertake the world’s first DNA mass intelligence screen. All adult males in three villages - a total of 5 000 men - were asked to volunteer and provide blood or saliva samples. Blood grouping was performed and DNA profiling carried out on the 10% of men who had the same blood type as the killer. The mass screening work was a painstaking task that took six months to complete, and when they discovered that no profiles matched the profile of the killer, it seemed that all possibilities had been exhausted. However, the investigation took a strange twist when a year later a woman overheard her work colleague bragging that he had given his DNA sample while masquerading as his friend, Colin Pitchfork. Pitchfork had apparently persuaded the man to take the test for him. Pitchfork was subsequently arrested and his DNA profile was found to match with the semen from both murders. He was eventually sentenced to life imprisonment for the two murders in 1988.

Colin Pitchfork. Image: Wikimedia commons

36 Quest 5(4) 2009

A mass grave site in Bosnia. Image: Wilkimedia commons

Scientists working in the UWC Forensics Laboratory. Image: UWC Forensics Laboratory

DNA extraction techniques. Image: UWC Forensics Laboratory

image of a DNA experiment using DNA from one of his technicians and the technician’s family. He noticed that there were both similarities and differences in the family’s DNA. He used this variation in the genetic code as the basis for what was first called DNA fingerprinting and then DNA profiling. Mass graves However, it is important to understand that conventional DNA typing systems do not work in every instance. When remains are quite old or badly degraded, often bone, teeth and hair are the only biological sources left from which to draw a sample. DNA samples that have been highly degraded often fail to produce results with DNA typing systems that use DNA from the nucleus of a cell; however, it is sometimes possible to obtain information using mitochondrial DNA (mtDNA). Most of the human genome is located within the nucleus of each cell. However, there is a small circular genome found in the mitochondria,

the energy-producing organelle in the cytoplasm. Each cell contains several thousand mitochondrial DNA molecules, whereas there are only two copies of nuclear DNA per cell, one from each parent. It is this greater number of mtDNA molecules that allows greater success, relative to nuclear DNA, with biological samples that have been severely damaged. Unlocking the past There are many mass grave sites in South Africa, which contain the remains of victims of human rights abuses under the former apartheid regime; these were revealed at the hearings of the Truth and Reconciliation Commission. Following the exhumation of mass graves of apartheid activists, scientists from the forensic DNA laboratory at UWC became involved in a DNA testing programme to help to identify these remains. In most of these cases the bodies had been destroyed by burning, by using explosives or using acid, resulting in highly degraded DNA. In

An example of the type of human remains that the laboratory uses for DNA analysis. Image: UWC Forensics Laboratory

The Innocence Project DNA testing has been a major factor in changing the criminal justice system. It has provided scientific evidence that our system convicts and sentences innocent people, and that wrongful convictions are not isolated or rare events. In the United States an organisation called the Innocence Project has been set up to assist in the clearing of wrongfully convicted people through the use of DNA testing. This project only handles cases where postconviction DNA testing of evidence can yield conclusive proof of innocence. Since it was founded in 1992 the organisation has successfully cleared 244 people, 17 of whom had been on death row. These innocent people had served an average of 12 years in prison before their release. In all these cases DNA evidence provided irrefutable proof of wrongful conviction, as well as providing DNA profiles of the actual perpetrators of the crimes. The UWC Forensic DNA laboratory is planning to initiate an Innocence Project in South Africa, first by raising awareness and concern about the failings of our criminal justice system. It is a facet of our society that eventually touches every citizen. The prospect of innocents languishing in jail for crimes that they did not commit should be intolerable to every South African, regardless of race or politics.

such instances conventional DNA typing systems usually did not work, but it was possible to recover DNA information using mtDNA. Case 1: The remains of four people buried together This was the first case that the UWC scientists worked on. Four activists were abducted in 1987, tortured and their bodies blown apart with explosives. The non-DNA evidence suggested that their fragmented remains had been buried together in a cemetery north of Pretoria. The MPTT identified four fractured hip bones, which were given to the UWC lab for analysis. mtDNA samples were taken, along with other DNA samples, and compared with samples obtained from relatives of the victims. Two of the missing activists were positively identified using these techniques.

The DNA project inquest concluded that his death was a result of suicide. His body was not returned to the family, who spent the next 30 years trying to locate his remains. A possible grave site was finally located as a result of evidence given at the TRC and the remains were exhumed. The UWC team were sent a femur from these remains, which they matched to samples taken from Ngudle’s family. His remains were finally returned to his family for burial in May 2007. Case 3: Ten missing ANC activists This case involved highly degraded samples because of circumstances of the individual’s deaths. Ten ANC activists were trapped by members of the then Northern Transvaal Security Police, one of whom posed as an MK member who was to take the group to Botswana for military training with the ANC. On 26 June 1986, the group was driven in a minibus towards Botswana. Once past Zeerust, the vehicle was ambushed by the security

The collection and retention of DNA profiles for the purpose of criminal intelligence is governed by the Criminal Procedures Act (CPA) of 1997. This act allows the storing of DNA profiles in a National DNA Database (NDDSA) in some situations, but does not allow for a convicted offender database. However, there is a new bill before parliament, the Criminal Law Amendment Bill, which will provide an overall framework for fingerprint and DNA collection and storage, and will allow the South African police to increase arrest and conviction rates. Put simply, the greater the number of DNA profiles on the database, the greater the chance of solving crimes and catching criminals. The new law, when passed, will ensure that every person arrested for an alleged offence, as well as all convicted offenders, will have their DNA profiles loaded onto the database. These profiles will continually be searched against DNA profiles collected from crime scenes, to try and find a ‘match’ between the profiles in order to identify a suspect. Given the number of repeat offenders in South Africa there is a strong possibility that eventually the individuals who commit any crime would previously have been convicted of a similar crime and would already have his or her DNA profile in the national database. Even if a perpetrator is not identified through the DNA database, crimes may be linked to each other if the same DNA profile is found in different crime scenes, thereby aiding an investigation and eventually leading to the identification and conviction of criminals.

▲ ▲

Case 2: Looksmart Ngudle In 1961 Looksmart Ngudle became the Western Cape commander of the African National Congress’s military wing, uMkhonto weSizwe (MK). In 1963, Ngudle was detained, soon after the introduction of the 90day detention law, which allowed the security police and military intelligence greater opportunities to detain and torture people. Abuse was common because the law allowed detainees to be kept in solitary confinement without charge or trial for indefinite periods and without access to lawyers. Ngudle had gone into hiding when the high command of MK was captured just months after the introduction of the 90-day detention law. However, an informer led the police to him and he was arrested on 19 August 1963. Shortly after his arrest he was found hanged in his cell at Pretoria North police station. An

DNA analysis at the UWC Forensics Laboratory. Image: UWC Forensics Laboratory

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forces and the activitsts forced to lie on the ground, where they were injected with an unkown substance that made them unconscious. Their unconscious bodies were then placed in another minibus, which was driven off the road into a tree. The vehicle was set alight with petrol and a limpet mine, which later exploded in the fire, and two AK47s were placed in the vehicle as well. The severely burnt remains were taken to the George Stegman Hospital, after which the remains were sent to the Ga-Rankuwa state mortuary. They were given paupers’ burials on 31 July 1986 in the Winterfeld cemetery. The exact site of the graves became uncertain because the grave markers had been removed. However, a series of graves were later exhumed by the MPTT and the remains sent to UWC for analysis. Because the remains

Fact File Q

were so severely degraded, separate samples were also sent to a laboratory in the USA. The UWC scientists managed to generate full bone and teeth samples for four of the ten skeletons, which were compared with living relatives. With the identification of these four men, it was thought that the remaining skeletons were highly likely to be the other missing ANC activists. Not only crime DNA profiling is generally thought of as a way of apprehending criminals, but, as the UWC research shows, it is also useful for identifying the victims of criminal acts. Without this technology, many people would remain unknown and unclaimed – and their stories of human rights abuses untold. ■ Professor Sean Davison came to South Africa from New Zealand, after obtaining a PhD in molecular biology. He is

currently Professor in the Department of Biotechnology at UWC, where he specialises in research on forensic DNA analysis. Mongi Benjeddou finished his undergraduate studies in Tunisia. He completed his MSc in Greece and finally gained a PhD in the field of molecular virology at the University of the Western Cape in South Africa. He is a Senior Lecturer in the Department of Biotechnology (UWC). His current research interests are the field of human population and forensic genetics. Eugenia D’Amato gained her PhD at the University of Buenos Aires, Argentina, with the forensic research group DNA Fingerprinting Service (Servicio de Huellas Digitales Genéticas). Her current research interest is the development of a system of Y-STR markers with high discriminatory capacity for the South African population. SUGGESTED READING http://www.innocenceproject.org/ http://www.dnaproject.co.za www.pub.ac.za www.saasta.ac.za

What is DNA?

NA stands for deoxyribonucleic acid. It is a nucleic acid that contains the genetic instructions that are used for the development and functioning of all known living organisms and some viruses. The DNA molecule stores information and it is often thought of as a blueprint or a code because it contains the instructions that are needed to put together proteins. The chemical structure of DNA is of two long chains, or polymers, of simple units called nucleotides. These chains form a

double helix, with a backbone of sugars and phosphate groups that are joined by chemical bonds. Each sugar in the backbone is attached to one of four types of molecules called bases. These are adenine, guanine, cytosine and thymine. Adenine always pairs with thymine and guanine always pairs with cytosine. It is the sequence of these base pairs along the backbone of the DNA molecule that encodes information. Within cells, DNA is organised into long structures called chromosomes.

The history of DNA The discovery of the double-helix structure of DNA is a biological detective story. The molecule was first isolated by the Swiss doctor Friedrich Miescher who discovered a microscopic substance in the nucleus of cells. In 1919, Phoebus Levene identified the base, the sugar and the phosphate nucleotide unit. He suggested that DNA consisted of a string of nucleotides that were linked together by the phosphate groups. It was not until 1953 that James Watson and Francis Crick suggested what is now known to be the correct double helical structure of DNA. Their suggested structure, along with experimental evidence to support the structure, was published in the journal Nature. SUGGESTED READING Watson JD. The Double Helix: A Personal Account of the Discovery of DNA. Atheneum, 1980.

DNA forensic techniques

The chemical structure of DNA. Image: Wikimedia commons

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DNA typing for forensics takes advantage of locations within the human genome that do not code for protein. These locations typically involve repetitive DNA sequences that have a variable number of repeat sizes. Because nonprotein-coding DNA is used, DNA databanks that contain DNA typing information do not reveal any information about an individual’s health status or whether the individual has or is a carrier of a genetic disease. The sensitivity of DNA profiling tests has dramatically increased over the last two decades. Forensic scientists can now obtain enough DNA from saliva left on the end of a cigarette to get a DNA profile result. The speed at which results can be obtained

James Watson.

Image: Wikimedia commons

The chromosomes found in a man. The XY chromosomes are the sex chromosomes. has also dramatically improved. This is all due to the discovery of the polymerase chain reaction (PCR), a technique that can amplify large amounts of specific small sequences of DNA from the human genome. It is also due to the advent of various DNA fingerprinting tools. DNA profiling uses a variety of DNA typing systems, including: restriction fragment length polymorphism (RFLP) typing, short tandem repeat (STR) typing, single nucleotide polymorphism (SNP) typing, mitochondrial DNA (mtDNA) analysis, and Y-chromosome typing. The first approach to DNA typing used RFLPs. These are variations within specific regions of genomes that are detected by restriction enzymes. RFLP analysis originated in the 1970s after the discovery of restriction enzymes, or proteins that can cut DNA into smaller molecules based on specific DNA sequence recognition sites. A restriction enzyme recognises and cuts DNA only at a particular sequence of nucleotides. RFPLs contain repeating units that are 20 – 50 base pairs long per repeat and a person can have anywhere from 50 to several hundred repeats. This repeat length is inherited. This DNA typing approach was the one first discovered by Alec Jeffreys and is the principle behind today’s DNA profiling systems. The advantage of using a RFLP-based analysis for DNA profiling is that repeating regions are highly variable from person to person. Therefore, it is highly unlikely that DNA profiles from unrelated individuals would be identical. However, there are also several drawbacks to this technique. Since these regions are large, it is often difficult to clearly separate the fragment using electrophoresis, which is a technique that uses a DNA sample loaded into a gel that migrates towards a positively charged electric field based on size. A larger amount of purified high quality DNA is also required for this technique. Thus, DNA samples extracted from crime scene specimens may be not suitable

in quality for this type of analysis. High purity, in terms of DNA extractions, can be compromised according to the source of the sample. If, for example, the sample is blood and is extracted from clothing, the dye from the cloth might alter the mobility of the extracted DNA in the gel, making the analysis difficult. RFLP analysis has been replaced by short tandem repeat (STR) analysis. STR regions are comprised of two to four base pair repeats that are repeated between five and 15 times. STR analysis is currently the standard approach to forensic DNA profiling. This is mainly because shorter repeat sequences are easier to analyse. STR analysis is faster, less labour intensive, and can be automated. A single reaction can analyse four to six STR regions using very little DNA (only one nanogram is usually sufficient). If only a small amount of DNA is recovered or if it is degraded, it may be possible to use STR analysis, but not RFLP analysis. STR analysis uses the polymerase chain reaction to amplify DNA in the region where the STR is located. After PCR amplification we then use electricity to migrate the DNA fragments in a gel. The short fragments migrate faster than the larger molecules and so separate the DNA fragments. The migration of the PCR products can be compared to control DNA molecules that have a known size. If run together, the size of the unknown STR can be estimated. These separated fragments are recorded as a graph on a computer. The number of repeats is recorded for each DNA region (locus) and this is what we call a profile. We interpret a profile one locus at a time. The polymorphisms displayed at each STR locus are by themselves very common, typically each polymorphism will be shared by around 5 – 20% of individuals. However, when we do DNA profiling between nine and 13 loci are amplified. The more STR regions that are tested in an individual the more discriminating the test becomes.

Francis Crick. Image: Wikimedia commons

Because we look at so many loci at one time each person’s profile looks different. The profile of a person is then stored on a computer database as a list of numbers representing the loci that have been amplified and the number of repeating units at those loci. Forensic analysis can involve matching these numbers against DNA profiles obtained from crime scene evidence. A significant problem in using DNA profiling as evidence in court proceedings is the possibility that a mistake was made in the sample extraction, preparation, or analysis. For this reason, investigators take precautions to reduce human error. Each forensics laboratory must maintain a high level of quality control and quality assurance standards to prevent this from happening. DNA profiling is one of the most powerful tools in crime prevention and detection used in the world today. Forensic applications of DNA profiling are: ■ Identify or exclude a known suspect ■ Link a suspect, victim and crime scene ■ Reconstruct a crime scene ■ Convicted felon DNA databases ■ Paternity testing ■ Missing persons investigations ■ Identification of human remains.

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Careers Q

A career in biotechnology

Left: A dry valley in Antarctica. This is one of the exciting areas that a degree in biotechnology could lead to through the study of organisms in extreme environments. Image: Don Cowan

What is biotechnology The use of living organisms or their products for commercial purposes. What qualifications do you need? To enter an undergraduate biotechnology programme you need a good matric that includes life and physical sciences. You can also enter a postgraduate biotechnology programme if you have a relevant first degree, such as microbiology. Where would this technology be applied? ■ Yeast used in baking bread and brewing wines/beer ■ Breeding of food crops ■ Developing drugs and synthetic hormones ■ Producing transgenic plants (resistant to pests, insects, herbicides) ■ Using genetically altered bacteria to clean up oil spills ■ Food safety Why study biotechnology? To improve the quality of life using molecular genetic techniques. What will you be taught? ■ Microbiology – the study of living organisms of microscopic size, e.g. bacteria, algae, and fungi. Viruses are also included in the study of

microbiology, although they are generally not thought of as living organisms ■ Biochemistry – the study of the chemistry of life (structure, properties and changes of biomatter) ■ Molecular biology – the study of the molecular basis of life, including the biochemistry of molecules such as DNA and RNA The nature of the work Because biotechnology is interdisciplinary, biotechnologists work together with people from different fields such as biology, chemistry, biochemistry, microbiology, molecular biology, immunology, genetics, engineering, food science, agriculture, forensics and so on. Research areas in biotechnology ■ DNA forensics ■ Environmental and industrial biotechnology ■ Fruit-tree genetics ■ Food biotechnology ■ Plant biotechnology ■ Protein structure and function ■ Cancer research ■ Human genetics ■ Proteomics ■ Diabetes Career opportunities Qualified biotechnologists are employed in leading business houses and pharmaceutical companies, police forensic DNA laboratories, chemical industries, bioprocessing industries, industries related to agriculture and pollution control activities of the major industries. Biotechnologists can also join government and corporate-run research and development organisations. ■

Left above: Typical equipment in a biotechnology laboratory.

Image: UWC Biotechnology

Left: A biotechnology student at the University of the Western Cape.

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Image: UWC Biotechnology

Q Women in Science

Changes in our coastal environment A newly rated NRF young scientist shares her love of science.

r Nicola James is an unassuming young woman who quietly got on with making every bit of work she put into her postgraduate studies count. Nikki, as she likes to be called, was recently appointed as an aquatic biologist at the South African Institute for Aquatic Biodiversity (SAIAB) in Grahamstown and has just been awarded her NRF Y1 rating. This rating is awarded to scientists under the age of 35 years who show the potential to become leaders in their field. There is a rigorous selection process. In Nikki’s case this involved referee’s reports being considered by an assessment panel before a decision was reached. Applicants often have to apply a number of times before being awarded a rating. Nikki achieved her rating on her first application. After receiving her MSc with distinction from the University of KwaZulu-Natal, Nikki registered at Rhodes University in Grahamstown for her PhD under the supervision of Professor Alan Whitfield and Dr Paul Cowley. Her field of study is global change in the coastal zone, specifically climate change and its effects on estuaries. In acknowledging her achievement at a special function at SAIAB, Professor Alan Whitfield, himself an NRF A-rated scientist, congratulated Nikki and emphasised that the award carries certain expectations – one

of these is that the rated scientist becomes a leader in his or her field. Climate change is a major challenge for the future and currently there is little, if any, other research in South Africa that focuses specifically on estuaries as indicators of climate change. Nikki is already something of a leader in this field through her contact with researchers around the world who are investigating climate change. Asked what advice she would give young scientists who want to become rated, Nikki referred to the advice she received from her MSc supervisor, Associate Professor Lynnath Beckley – ‘Publish or perish’. From an early stage Nikki published all the papers she could from her MSc and PhD theses in as many of the top scientific journals as possible. This gave the referees a substantial body of published work to refer to in considering her application. SAIAB is immensely proud of its standing in the scientific community. Since its earliest days SAIAB has produced NRF-rated scientists. All its retired scientists were rated at the time of their retirement and two-thirds or 66% of SAIAB’s current, full-time scientists are NRF rated. Three of these are Y-rated young scientists with a bright future ahead of them. There are approximately 150 Y-rated scientists in the natural sciences in South Africa. ■

Top: Nikki at work in the field.

Image: SAIAB

Above: Professor Alan Whitfield congratulates Nikki James on her NRF Y1 rating. Image: SAIAB

Q Science news Parasites may have killed T. rex Holes in the skeleton of the famous skeleton of Tyrannosaurus rex, Sue, which lives in the Field Museum in Chicago, USA may have been caused by tiny parasites, according to new research. The small, smooth holes in the skeleton’s jaw have apparently puzzled scientists for some years. However, a new study suggests that the holes were caused by an infection with the parasite Trichomonas. While dinosaurs became extinct about 65 million years ago, species of Trichomonas are still around.

Trichomonas is a protozoan organism that can cause infection in the teeth and jaws, which could lead to holes in the bone of the jaw as it progressed. Modern-day birds and crocodiles can be infected with the parasite, which was what gave Ewan Wolff, a palaeontologist at the University of Wisconsin-Madison, the idea that this could be the cause of the holes in Sue’s jaw. Scientists saw holes similar to those in Sue’s jaw in an osprey and they knew that the bird had been infected with Trichomonas before it died. Wolff says that the dinosaur could have caught the infection from eating infected tissue or it could have been passed on during a fight with another infected dinosaur.

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This artist’s drawing depicts the pulsar planet system discovered by Aleksander Wolszczan in 1992. Image: NASA/JPL-Caltech/R. Hurt (SSC)

Rudi Kuhn describes the role of KELT-South in the discovery of extrasolar planets.

KELT-South: The little telescope with big ambitions T

An artist’s impression of the extrasolar planet HD 189733 b, now known to contain methane and water. Astronomers used the Hubble Space Telescope to detect methane — the first organic molecule found on an extrasolar planet. Hubble also confirmed the presence of water vapour in the Jupiter-size planet’s atmosphere, a discovery made in 2007 with the help of the Spitzer Space Telescope. They made the finding by studying how light from the host star filters through the planet’s atmosphere. Image: Giovanni Tinetti

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he Sutherland observing site of the South African Astronomical Observatory (SAAO), just outside the town of Sutherland in the Northern Cape, is home to SALT (Southern African Large Telescope), one of the largest telescopes in the world. Recently, a much smaller telescope has also found a home on the observing site and even though it is 250 times smaller than SALT, scientifically it is just as valuable. Where SALT will be looking mainly at the faint and distant universe, KELTSouth will be looking at relatively bright and close stars within our own galaxy to determine if they have planets orbiting around them. A history of extrasolar planets The first announcement of a planet outside our own solar system (called an extrasolar planet or exoplanet) came in 1992 from the studies of the pulsar PSR 1257+12 by two radio astronomers Aleksander Wolszczan and Dale Frail. A pulsar is what is left behind when a large star has come to the end of its life and exploded in what astronomers call a supernova. Astronomers were very

puzzled by this planet because nobody suspected that anything could survive the supernova explosion. The first planet to be discovered orbiting a solar-type star (a star like our own Sun) was one around the star 51 Pegasi. This planet was determined to be about the same size as Jupiter, but it orbited its parent star in only 4.2 days! This planet was very controversial when its discovery was first announced, as astronomers had believed that all other planetary systems would have to be like ours, with small rocky planets close to the parent star and large gas giant planets further out. Here was a system that had the large gas giant planet in the ‘wrong’ position. Theories of how planets formed had to be revised completely and have continued to evolve with the discovery of more and more extrasolar planets. Since that first discovery, only 17 years ago, 403 extrasolar planets have been discovered and the rate of discovery is increasing (for a full list of extrasolar planets with constant updates and a ton of other information, have a look at the Extrasolar Planets Encyclopaedia on the Internet at http://exoplanet.eu/).

Q Astronomy The KELT-South building just before sunset. The 40-inch telescope can also been seen in the background. Image: Rudi Kuhn

we can conclude that something orbiting the star is making it change its position due to the gravitational pull that an object has on the star. Usually the star will have another star or even a black hole orbiting around it, but sometimes a planet will also make the star change position. Another signature of a planet orbiting a star will show itself when we break up the light into different colours. Just as a rainbow or a prism will break up the light from the Sun into many colours, we can do the same thing to light coming from stars. This process of breaking up the light into colours is called spectroscopy. Each star contains elements in its atmosphere that will absorb light at very specific wavelengths. By measuring the positions of these ‘absorption lines’ accurately and comparing them to known absorption lines in the laboratory, we can tell if these absorption lines are shifting in position. If a periodic shift occurs then we can again conclude that something orbiting the star is making it ‘wobble’ back and forth. This wobble can only be caused by the gravitational pull the orbiting object has on the star. The KELT-South telescope uses another one of these signatures called a ‘transit event’ (explained in detail later) to find extrasolar planets. What is KELT-South? KELT is an acronym for Kilodegree Extremely Little Telescope. The word ‘kilodegree’ refers to the fact that the telescope observes thousands of square degrees in the sky while it is operating, compared to typical modern telescopes which observe ▲ ▲

Detecting extrasolar planets There are a number of techniques that astronomers use to find extrasolar planets and many new techniques are being developed as our ability to monitor stars more closely increases. These methods include the radial velocity (RV) or ‘wobble’ method, the astrometric method, the pulsar timing method, the transit method, gravitational microlensing and direct imaging. Taking a picture of a planet directly is very difficult because the planet is tens of thousands of times fainter than the star it orbits. It is almost like trying to take a picture of a mosquito right next to the headlights of a car that is 20 metres away from you. Nevertheless, astronomers have found ways to block out the light from the star and take pictures of the area surrounding the star, called the circumstellar disk, and in these disks they have found large ‘blobs’ of material that orbit the star in a regular way. These blobs might one day grow large enough to become planets themselves. Most of the methods used to discover extrasolar planets are indirect methods, meaning that the planets themselves are not imaged or photographed. Instead the star that the planet is orbiting is monitored very closely for small changes. Certain types of changes in the light coming from the star (called signatures) will indicate the presence of a planet around that star. One signature is a shift in position of the star. If we can measure the position of a star in the sky very accurately and over a period of days or weeks and we see that the position of that star changes periodically,

Lightcurves obtained using the KELT-North telescope in Arizona that show the short decrease in brightness levels of the star as another object passes in front of the star. These are probably not planets, but these data show the ability of the KELT-North telescope to find extrasolar planets. Image: KELT-North

KELT-South: technical specifications KELT-South is a single telescope housed in its own building in Sutherland. It is not a ‘telescope’ in the modern, commonly thought-of sense, since it does not have an optical tube. It consists of an optical assembly (CCD detector, medium-format camera lens, and filter) mounted on a robotic Paramount ME telescope mount. The mount is manufactured by Software Bisque, located in Golden, Colorado, USA. It is a German Equatorial Mount, and therefore has some peculiarities in normal operations. A dedicated computer is used to control the telescope, camera, observation scheduling, and data archiving system tasks. One goal in assembling KELT-South was to use as many off-the-shelf components and software packages as possible to speed the development. The KELT-South detector is an Apogee Instruments Alta U16 thermoelectrically cooled CCD camera. This camera uses the Kodak KAF-16803 front-side-illuminated CCD with 4096 x 4096 nine micrometer pixels (36.88 x 36.88 mm detector area) and has peak quantum efficiency of roughly 65% at 600 nm. The telescope will operate in a wide-angle survey mode that uses a Mamiya 645 80 mm f/1.9 medium format manual-focus lens with a 42 mm aperture. This lens provides a roughly 23 arcseconds per pixel image scale and a 26 x 26 degree field of view. The camera/lens combination sits on a mount, which points the camera at a desired place in the sky. The camera/lens/mount assembly is what is referred to as ‘the telescope’ in this article.

During a recent visit to Sutherland, the Minister of Science and Technology Ms Naledi Pandor was given a tour of the KELT-South telescope. Rudi explains how the telescope operates. Image: John Richards

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This graphic shows approximately what we would expect to see as the planet begins to cross in front of its parent star and how the light coming from that star will lessen slightly because the planet is blocking a little bit of the light. Studying the details of the light curve — how deep the dip is, how wide, how steep the drop off — reveals subtle clues about the planet. Image: NASA/JPL-Caltech/UDM/GSFC

Artist’s impression of a hot-Jupiter extrasolar planet that is so close to its parent star that the outer atmosphere of the planet is actually boiling away into space. Image: ESA, Alfred VidalMadjar (Institut d’Astrophysique de Paris), CNRS, NASA

A zoomed-in view of a transit lightcurve after data reduction has been done. The solid grey line is the predicted lightcurve obtained by modelling the planet and star interaction, while the black dots are the actual observations. Image: Brown, TM. Published in ApJ paper ‘Transmission Spectra as Diagnostics of Extrasolar Giant Planet Atmospheres’, 2001

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areas tens of thousands of times smaller. KELT-South is a small scientific telescope, commissioned and built by Vanderbilt University in Nashville, Tennessee, USA. It is extremely small compared to most other telescopes. Most modern scientific telescopes have their apertures measured in metres, while the aperture of KELT-South is measured in centimetres. The telescope was based on the design of KELT-North, which was conceived and designed at the Ohio State University Department of Astronomy, Columbus, Ohio, by Dr Joshua Pepper. KELTNorth was deployed in late 2005 in Arizona, and has been operating since then. That telescope has been gathering data for several years, and the science team is looking forward to its first discovered planets. The KELT-South telescope will serve as a counterpart to its northern twin, surveying the southern sky from Sutherland for transiting planets over the next few years. Construction of the KELT-South telescope started in early September 2008 and by midOctober 2008 the telescope had achieved first light. The commissioning phase of the telescope started in November 2008 and was completed in August 2009. During this time there were many changes to the software as well as checks to make sure that the telescope behaved exactly as was expected. Using the results from the commissioning phase, adjustments were made to the telescope in September 2009 and full operation and data gathering started in October 2009. What will KELT-South be used for? The main purpose of KELT-South is to detect transiting extrasolar planets. An extrasolar planet orbits a star other than our Sun, and is therefore not part of our solar system. A small fraction of extrasolar planets orbit their stars so that the plane of their orbit is edge-on from our line of sight. That means that once each time the planet orbits, it eclipses its star, an event we call a transit. When an object passes in front of a star, the light from that star will show a small but measurable decrease in brightness, provided that the object that passed in front of it is large enough. Usually the change in

brightness of the star is around 1% for a Jupiter-sized planet. The planet also needs to be very close to its parent star for the light level to drop by this amount and thus the transit method is biased toward finding very large and hot planets, the so called ‘hot-Jupiters’. With sensitive instruments, we on Earth can see that transit and use it to find out a huge amount about the planets and its star. Because transiting extrasolar planets are so useful for science, we want to find as many as possible. KELT-South is a tool that was built to help astronomers find these special planets. In order to find extrasolar planets, KELT-South takes pictures of large parts of the sky, night after night, over many months and even years. The reason for observing such a large part of the sky at once is because if the telescope had to observe only a few stars at a time to search for extrasolar planets, it would take an extremely long time. So, to increase the efficiency of the KELT-South survey, the telescope monitors large parts of the sky, which sometimes contain up to 200 000 stars. Each image is analysed and a record of the precise brightness of each of those stars in stored in a database. This process is repeated every night and over time a large database of star brightness levels is accumulated. A plot of the brightness levels of a star over time is called the lightcurve of the star. We then examine the lightcurve of each star in the database to see if we can find a time where the light from the star dims by just the right amount for the right amount of time, then returns to its normal brightness. If we’re lucky, some of those cases will be the planet transiting its star, blocking the light and making it appear to get a little dimmer. However, there are a number of other things that can cause a similar dimming of a star, so we have to carefully analyse and re-observe those stars with other telescopes to find out if we’re really seeing a planet in action. How does KELT-South work? The KELT-South telescope is fully robotic. This means that there is nobody present at the telescope when it is operating, unlike most of the other telescopes on the observing plateau in Sutherland. The computer

The KELT-South building with the roof open, ready to start observing the heavens. Image: Rudi Kuhn

The KELT-South telescope in sleep mode during the day time. Image: Rudi Kuhn

This annotated image shows key features of the Fomalhaut system, including the newly discovered planet Fomalhaut b, and the dust ring and circumsteller disk. The light from the central star has been blocked to show the surrounding region. Image: NASA, ESA, and Z. Levay (STScI)

that controls the telescope was programmed so that it is smart enough to make decisions about which parts of the sky to observe and when the best times are to observe them all by itself. The telescope enclosure is also equipped with sensors that will tell the control computer about the weather conditions outside and, based on pre-programmed conditions, the control computer will open the roof and start the observing for that particular night. The telescope will continue to observe parts of the sky as long as the weather stays favourable, and because the full moon is so bright, the telescope will try to avoid areas close to it. Once the night is over the telescope will go into sleep mode and the roof of the building will close to protect the delicate instruments during the daytime. While the telescope is sleeping, the control computer will start to analyse the images taken the previous night. Because the telescope observes such a large part of the sky in a single image, there might be cases when clouds are blocking part of the image. These images are no good for the final data reduction process and the control computer will delete these during the analysis process. Once the analysis of the images is complete, the control computer will compress the data to save hard drive space and copy the data to two external USB drives connected to the machine. A typical night of observing contains roughly 200 images and takes about 9GB of hard drive space. Once these external hard drives are almost full, the control

computer will email astronomers in Cape Town an alert telling them that the hard drives need to be replaced. The hard drives are then sent to Vanderbilt University in Nashville for final analysis. The reduction of the data is done on a pipeline specifically designed for the KELT-South telescope and usually takes between three and four weeks to complete. Future of KELT-South The KELT-South telescope is expected to operate for the next five to seven years, taking images every night. This will enable the entire southern skies to be mapped at least three times and hopefully many new planets will be discovered with this small instrument. We are very pleased with the progress we have made with the telescope and we are very much looking forward to the first data set to come from KELTSouth which we hope will be early in the New Year. Who knows? We might even get a planet for Christmas this year! â&#x2013; Rudi Kuhn is a NASSP MSc student currently working on the search for extrasolar planets. For more information and updates on the KELT-South project visit the wiki site at: http://keltsouth. pbwiki.com/. Above right: Image of the centre of the Milky Way Galaxy taken with the KELTSouth telescope. This was a 15 second exposure and the Galagtic Bulge and dust lanes are clearly visible. Image: KELT-South Right: Image of the Large and Small Magellanic Clouds (our two closest neighbouring galaxies). This was a two minute exposure and shows great detail in the structure of the LMC. Image: KELT-South

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Mathematical statistics flourishes in Africa

All the TWAS young affiliates gathered in Durban.

Lawrence Kazembe has used his skills in mathematics to further our understanding of malaria. QUEST talked to him about his research.

Lawrence Kazembe is a senior lecturer in applied statistics at the University of Malawi.

About the Academy of Sciences for the Developing World (TWAS) TWAS represents the best of science in developing countries. Its main mission is to promote scientific excellence and capacity in the South for science-based sustainable development. TWAS fellows are internationally renowned scientists who are elected by their peers. TWAS currently has 902 members from 90 countries.

46 Quest 5(4) 2009

awrence Kazembe is one of five young scientists from sub-Saharan Africa selected by the Academy of Sciences for the Developing World (TWAS) who was recognised in Durban in October 2009. Lawrence did his undergraduate degree in statistics and economics at the University of Malawi and then received a scholarship to study at the University of the Eastern Mediterranean in Cyprus from 1998 to 2000. His MSc subject was mathematical statistics, using statistical techniques to study environmental pollution in the Swiss Alps. He then applied these same techniques to mapping malaria risk in African countries, which has formed a major part of his research ever since. Lawrence continued his interest in malaria at the University of KwaZuluNatal, where he completed his PhD in 2007. He has also been a consultant for the Ministry of Health in Zambia, where he was involved in identifying core indicators that would help to put together public health policy. He is also working with the Malaria Alert

Centre of the College of Medicine at the University of Malawi. His main research has focused on looking at the statistical relationships between environmental factors and the risk of being infected with malaria. He showed that the main environmental factors associated with malaria risk were altitude, the amount of rainfall and the waterholding capacity of the soil. This was translated into a higher risk of malaria along low-lying lake shore regions, which allows policy makers to target resources at specific areas, something that is important where resources are finite. He is currently working on a project funded by the World Health Organisation and the Special Programme for Research Training in Tropical Diseases, which focuses on predicting malaria risk in flood-altered environments in Malawi. The University of Malawi is currently expanding its statistics programme and Lawrence is responsible for teaching around 30 students and he is hoping to start working with their first intake of postgraduate students in 2010. â&#x2013;

Q Biodiversity

Freshwater biodiversity in Africa The IUCN Pan-African Freshwater Biodiversity Assessment will integrate freshwater biodiversity in the development process throughout Africa.

he International Union for Conservation of Nature and Natural Resources (IUCN) recently made public the findings of a major international project to assess the conservation status of southern African freshwater biodiversity. Funded by the European Commission, the IUCN Southern African Freshwater Biodiversity Assessment is the result of collaboration between the South African Institute for Aquatic Biodiversity (SAIAB), the IUCN-Species Survival Commission and Wetlands International. The IUCN is an international non-governmental organisation that facilitates biodiversity conservation and sustainable development projects around the world. The southern African assessment is part of a broader IUCN Pan-African Freshwater Biodiversity Assessment project, and provides a good example of the value and relevance of natural history collections and their associated information in our rapidly changing world. The overall assessment will enable water resource managers and environmental planners throughout Africa to centralise and integrate information on freshwater biodiversity into plans for infrastructural developments that have an impact on aquatic biodiversity. The two key objectives of the project are: to promote the conservation and sustainable use of freshwater biodiversity in Africa; and to safeguard the livelihoods of millions of people who depend on the goods and services of aquatic ecosystems. The project specifically aims to ensure that environmental planning in Africa is based on reliable and up-to-date information on the status, distribution and ecological requirements of freshwater biodiversity. The information that was collected and collated includes details of species’ taxonomy, geographical distribution and abundance of freshwater fishes, crabs, snails, dragonflies and water plants. Each species was assessed for its current conservation status according to the official IUCN red list category ranging from ‘Critically Endangered’

to ‘Least Concern’. This was a monumental task carried out by a multidisciplinary team of scientists, amounting to no less than a meticulously detailed account of each species in a list of more than a thousand species. SAIAB scientists and collaborating colleagues categorised the 354 freshwater fish species that occur in southern Africa into five categories on the basis of the threat of extinction. The information came mainly from several fish collections, of which the largest and most important were the National Fish Collection housed by SAIAB and the freshwater fish collection of the Albany Museum, also in Grahamstown. More than 50 000 fish specimen records were plotted on maps and validated by scientists with handson field experience of where these species are found and the extent to which they may be threatened. The other aquatic organisms assessed, molluscs, crabs, dragonflies, damselflies and aquatic plants, were similarly gauged by scientists from other organisations both in South Africa and abroad. The completed report, launched in May 2009, states that many freshwater species in southern Africa are at increased risk of extinction from the impacts of development. The study found that species in South Africa are more at risk than those in neighbouring countries. Results from the assessment of the total 1279 freshwater species of plants and animals in southern Africa show that the more developed a country is, the more species are threatened with extinction. Of the 94 species threatened in southern Africa, 78 are found in South Africa, the most developed country in the region. The report highlights three ‘hotspots’ of species diversity.

Top: Examples of distribution maps for illustrated fish species, two of which are widespread and two highly restricted. Red/black dots indicate museum records, green shading indicates overall occurrence inferred from records. Image: SAIAB Above: Denis Tweddle (left), an honorary research associate at SAIAB, has played a major coordinating role in the southern African chapter of the IUCN biodiversity assessment project. Image: SAIAB

These include the Komati and Crocodile River tributaries of the Inkomati system in Mpumalanga and the Mbuluzi river basin, also in Mpumalanga and Swaziland. It further notes that many of southern Africa’s coastal drainages have sites which contain species that only occur in that area. The take-home message for conservationists and developers alike is that it is imperative to take an ecosystems approach to protecting threatened species. River catchments feed freshwater into estuaries and sustain sensitive coastal areas, all of which have to be seen as whole systems. Development and conservation planning must be managed together. This report comes from the South African Institute for Aquatic Biodiversity, a Research Facility of the National Research Foundation (NRF). ■

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Books Q

Alien landings Invaded: The Biological Invasion of South Africa. By Leonie Joubert. (Johannesburg. Wits University Press. 2009) Leonie Joubert is probably South Africa’s best known science writer and she tackles difficult and sometimes controversial subjects with rigour and passion. This book is no exception. An invasive alien species is one that ‘occurs outside of its natural ecosystem, having arrived in a place, an “adopted home, by intentional or unintentional human involvement. Most of all, it’s one that has the potential to “cause harm to the environment, economies or human health.”’ As Joubert says, we are most familiar with invasive alien plants – the pines, wattles, gum trees, hakea and hyacinth that pervade our environment. But it is not only plants that are invasive aliens. Feral pigs and the European yellow jacket wasp each get their own chapter in this book, as does the Argentine (or sugar) ant. Water is a big issue in drought-prone South Africa and the woody invaders wattle, pine, eucalyptus, mesquite and lantana are some of the worst offenders in terms of stealing this precious resource. The invasions take in all our ecosystems: marine invaders along the coast; insects from far off continents; indigenous birds shifting their range, as well as introduced foreigners. The list goes on.

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Joubert sees these invasive aliens as biological pollution – something that did not occur to our European ancestors as they moved around the world trying to make each new country a little more like ‘home’. And with increasing global trade, accidental introductions have become more common as alien species unwittingly hitch a ride between continents. She takes the reader on a journey through the biology of invasion, explaining terms, the National Environmental Management Biodiversity Act (NEMBA) of 2004. The book is filled with colour photographs, mainly by Roger Bosch, and the text is also broken up with explanatory boxes for specific issues and topics where these add to the main story line. There are clear sections, introducing the reader to the concept of invasion and its effects on ecosystems generally, before moving to specific issues, such as the introduction of various bird species, the Triffid weed and its impact on the Nile crocodile and the importance of road and railway verges and power line servitudes as refuges for threatened native species. She also includes a chapter on genetically modified crops and global food security, presenting a balanced approach to this often passionately debated subject. Invaded is an excellent introduction to the whole issue of invasive aliens, but more than that, it takes the reader into the detail of specific invasions and their cost, setting out very clearly exactly why such practices should stop and why every country needs to preserve its native ecosystems for the sake of global biodiversity. Our essential trees Photo Guide to the Trees of Southern Africa. By Braam van Wyk, Piet van Wyk and Ben-Erik van Wyk. (Pretoria. Briza Press. 2008) This field guide is beautifully illustrated with photographs of each tree that is described and includes photographs of the detail of leaf shape as well as the tree’s reproductive structures. This is probaby one of the main strengths of this comprehensive guide to South African trees. But, like any really good field guide, this book contains far more than simply a way of identifying trees. The guide covers Namibia, Botswana, Zimbabwe, Mozambique south of

the Zambezi River, South Africa, Swaziland and Lesotho. It starts with an introduction to the biomes and habitat of trees, explaining that trees in a landscape and the way that they grow often reflect the biome, veld type or habitat to which the tree is adapted. There is then a brief description of southern African biomes and the adaptations that their characteristic trees have. There is a separate section on fruit trees, describing the fruits that are native to southern Africa and pointing out that these are often edible and delicious, forming an important part of the diet of rural people. Trees are an important part of our landscape, not least because we use their wood. An interesting couple of pages describe furniture and craftwork from trees, as well as firewood trees and medicinal and poisonous trees. The relationship between trees and animals is an interesting one, sometimes destructive, but also commensal. In any case, trees are vital to maintaining a healthy ecosystem and it is this that characterises treeanimal interactions. The architecture of trees is important in their identification and this is dealt with thoroughly, with detailed diagrams explaining the complexities of tree growth. A careful explanation of how to identify trees and how to use the various codes in the book should help those unfamiliar with botanical terms. The species accounts are in alphabetical order and include a photograph of the whole tree, its leaves and its reproductive structures – all important in the identification

Q Books process. There is a distribution map and a description of the main features of the tree, of similar species and of the habitat in which it is found, as well as any human uses of the tree. This is altogether an excellent field guide and would provide hours of entertainment on a long car trip, as well as an indispensible part of your luggage on any trip to a new part of the region.

ramifications. Our transformation into a democracy is called A South African Miracle? – the query indicating the author’s analysis of this transition as less of a miracle and more of a journey into a present in which hard questions still need to be asked and answered. The final chapter, South Africa Today, takes a look at what Wilson sees as the country’s seven most significant achievements and then looks ‘squarely at the seven greatest difficulties facing the country as it peers into the future’. This is a book for scientists and nonscientists alike – read it! A feast of flowers

biomes, which leads to a description of the way in which flowers are named, taking the reader through biological nomenclature and also explaining the origins of vernacular or common names. This is followed by helpful hints on how to identify flowers and how to use the book. The inside front and back covers contain an illustrated glossary of flower parts, flower shapes and so on that are essential to understanding plant identification. There is a photographically illustrated guide to the different flower families, with a detailed description of each group as well as a guide on how to use the family finder, which will make identification far less hit and miss than my efforts after my recent trail run, although admittedly my botanical background did allow me to skip some of the steps! This would be an invaluable book in the classroom in particular, providing a practical approach to botany that would be sure to capture the imagination of anyone interested in the world around us.

A pocket history of South Africa Dinosaurs, Diamonds and Democracy: A Short, Short History of South Africa. By Francis Wilson. (Johannesburg. Random House Struik. 2009)

Field Guide to Wild Flowers of South Africa, Lesotho and Swaziland. By John Manning. (Cape Town. Struik Nature. 2009) While running in the Silvermine area of Table Mountain recently, my running partner and I noticed a truly lovely flower – among all the other truly lovely fynbos plants surrounding us. We knew it was a bulb, but had no idea of its identity. When I got home I was able to identify it as Gladiolus undulatus, which has quite a restricted distribution in that part of the Cape mountains, with the help of this colourful and informative book. However, this book is more than simply a series of photographs, descriptions and distribution maps for all the indigenous flowering plants that you will find in South Africa, Lesotho and Swaziland. The introduction contains a specially written description of southern African

Of frogs and frogging A Complete Guide to the Frogs of Southern Africa. By Louis du Preez and Vincent Carruthers. (Cape Town. Struik Nature. 2009) I love frogs. Unfortunately so does one of my Norwegian forest cats, but

▲ ▲

This truly is a short, short history of our country and fits easily into a handbag or even a pocket. The front inner flap contains a handy little time line of South Africa’s ancient history and the back flap the same for South Africa since 1200. In between is a treasure of information, starting with the fascinating story of South Africa as the ‘cradle of life’. Our rich fossil fields and their importance in understanding how life evolved is covered in remarkable detail in so few words. This is followed by a chapter on the evolution of humans and the importance of the Cradle of Humankind both in our own heritage and the science of human origins. Prehistory continues with an excellent account of the stone age and its hunters, gatherers and fishers, followed by a chapter on the iron age. The colonisation of this area of Africa leads on to the importance of gold and minerals in our history and, in turn, to apartheid with all its political

Quest 5(4) 2009 49

Books Q

I often manage to rescue them alive because she brings them in very carefully as playthings rather than as food. But that does bring me to a major issue with all amphibians – that of their slow disappearance, all over the world. This continuing decline in amphibian species is reason enough to publicise this lovely new book on frogs. I have Passmore and Carruthers’ earlier book South African Frogs on my shelf, given to me way back in 1982. At the time it seemed to be the best book available on the frogs of the region. But this book surpasses it by a very long way. It is a thick, heavy volume, covered in a sturdy plastic dust jacket that would make it quite practical in the field, were it not so heavy! But it is a book that I pick up and leaf through regularly, learning something new each time, for example frogs and toads are actually the same thing. The approach is scientific but without being inaccessible. The introduction details how to identify frogs, their classification, their

taxonomy and their evolution, making it potentially an excellent companion to school biology textbooks from about Grade 10 onwards, with its practical applications of the theory that is being learnt at this stage. But the book is a must-have for anyone with a love of the wildlife of this country and an excellent introduction to amphibian biology. I had no idea that you can identify tadpoles, but this book provides a full page diagram on what to look for, as well, of course, a diagram for identifying adult frogs. The section on classification and taxonomy is particularly detailed. It is not essential if you are simply looking for a field guide, but is certainly interesting enough to capture the casual reader. The evolution of the group is fascinating, particularly since we have representatives of some of the fossil groupings in South Africa. There is also a systematic list of southern African frogs, giving the scientific and common names of each species.

The section on frog biology covers reproduction and vocalisation, used in attracting mates, how eggs and tadpoles develop and a comprehensive list of survival adaptations necessary in eggs and tadpoles, with their dependence on water. The distribution of frogs across southern Africa is uneven, in terms of both species diversity and population numbers, which leads to a discussion of micro- and macro-habitats and how this might affect distribution. The steady decline in amphibians is also discussed in detail and includes a discussion of their parasites and how amphibians are useful bio-indicators of environmental health. The biology section finishes with a chapter on frog-human interactions, including frogs as food. A full field key introduces the species descriptions, which are illustrated with full-colour photographs. This is another book that would be an excellent addition to the shelves of any school biology laboratory, bringing alive the theory of classification and biodiversity. ■

HOW H OW O ON N

... does does rrock ock g get et ffolded? olded? HOW HO OW Wa are re v volcanoes olcanoes fformed? ormed? WHY is Table Mountain ﬂat? WHAT is the Sixth Extinction? WHY is sea water salty? WHERE does Earth’s water come from? These and many more questions answered in this fascinating book from

50 Quest 5(4) 2009

OOK BESKIKBAAR IN AFRIKAANS

Diarise Scifest Africa 2010

f you haven’t already done so, set aside 24 – 30 March 2010 to experience the biggest explosion of science in Africa! Scifest Africa takes place again to amaze visitors at over 500 make-science-fun events and activities! Scifest Africa was launched in 1997 and has since become an annual ‘must visit’ for many thousands of learners, teachers, businesses, universities and the general public. By highlighting science, technology, engineering and maths (STEM), Scifest has helped shape the way people talk and feel about STEM. Breaking down the misconceptions of science is what we are all about. Getting the public involved, interacting with scientists and science teachers and understanding the importance of science and how it affects their daily lives is what we do best. From exciting exhibitions and wowfactor workshops to lectures that will make you laugh, think and ask questions, Scifest Africa has something for everyone. In 2010, Scifest celebrates science in motion and visitors will enjoy exploring a wide range of topics from sport and wind turbines, to car crashes and cooking. Wayne Derman, Cape Town’s medical officer for the FIFA 2010 World Cup, was side by side with Mark Shuttleworth while he was training to become the first African in space. Professor Derman’s lecture will relive the extraordinary behind-the-scenes training for this mission, as well as provide insight into the space tourism industry. Vanessa Lynch, founder of the DNA Project, will talk about the successful use of DNA profiling as a crime-fighting tool throughout the world as well as the potential benefits of expanding and developing the National DNA Database of

South Africa to ensure accountability and deterrence among its criminal population. She will explain why DNA profiling has been called the 21st century detective. Arthur Benjamin, Professor of Mathematics at Harvey Mudd College in California and also a professional magician, brings to Scifest Africa his entertaining and fast-paced performance. Dr Benjamin will demonstrate how to mentally add and multiply numbers faster than a calculator, memorise 100 digits of pi (π), figure out the day of the week of any date in history and many other amazing feats of the mind. Rene Naylor, physiotherapist to the Springbok rugby team, will share her experiences of touring with the Springboks and the role she plays within the medical team. She will also discuss how the game of rugby has changed over the years and how it is no longer just about the playing and coaching. Whether you’re young or old, be at Scifest Africa 2010 for an awesome outof-the-classroom experience – even if you haven’t been in a classroom for years! Be sure to get hold of our flyer, available at museums and tourist information offices nationwide. This flyer has a reply slip in it that you can send back to us to order your programme. Also take note of our competition details! ■ For more information call 046 603 1106, email info@scifest. org.za or visit www.scifest.org.za. Join our mailing list to be the first to know about festival developments!

Quest 5(4) 2009 51

Diary of events Q

Shows and exhibitions For children For the School Holidays! Davy and the Dinosaur Davy Dragon finds a newly hatched creature that he thinks is a baby ostrich. But is it? Davy and his grandfather magically take the creature back to its mother. Join us and discover what kind of creature Davy found and what it has to do with the Milky Way! 12 December–12 January Monday to Friday – 12:00 & 13:00 Saturday – 12:00 Sunday – 12:00 Plus 16, 17, 23, 24, 30 & 31 January – 12:00 Especially for children aged 5 – 12 For adults The Sky Tonight An interesting live lecture on the current night sky is presented every Saturday and Sunday. You will receive a star map and be shown where to find the constellations and planets that are visible this month. Saturday – 13:00 Sunday – 13:00 22 March – 13:00 Suitable for teenagers & adults

Bad Astronomy: Myths and Misconceptions Were the Apollo visits to the moon actually a hoax? Have aliens landed on Earth? Can you tell your future by the stars? Join the ‘Bad Astronomer’ as he takes a critical look at popular myths and misconceptions to show audiences how science can be used to evaluate questionable claims. Starts 12 December Monday to Friday – 14:00 (excluding 24, 25 & 31 December) Tuesday evening – 20:00 (& sky talk) Saturday – 14:30 & Sunday – 14:30 Suitable for teenagers & adults

52 Quest 5(4) 2009

Planetarium entrance fees: Adults: R20,00; Children: R6,00; Adults (children’s show only) R10,00; SA pensioners and students (with cards): R8,00 The Iziko Planetarium will be closed for maintenance on the first Monday of the month (excluding school holidays), 30 November–4 December and 7–11 December. Please note that the last show on 24 & 31 December is at 12:00 and that we are closed on 25 December.

Talks, outings and courses Botanical Society of South Africa, Kogelberg: Talk: Gardening in the fynbos 18h00 Speaker Maryke Honig. Nivenia Hall, HPG. Refreshments will be served. (16 January 2010) Contact: Merrilee Berrisford 028 2729 314 Kogelberg: Talk: Sea Shores of the Western Cape 10h00 Speaker Professor Charlie Griffiths (12 December 2009) Contact: Merrilee Berrisford 028 2729 314 Limpopo: Walk and talk: Spiders, Polokwane Game Reserve 08h00 Professor Susan Dippenaar will get us focused on the smaller, but fascinating creatures of our local reserve. Polokwane Game Reserve charges will apply. (9 January 2010) Contact: Bronwyn Egan: 015 268 2227 or 0766976550

Diarise n World Kidney Day 11 March 2010. World Kidney day is a joint initiative of the International Society of Nephrology (ISN) and the International Federation of Kidney Foundations (IFKF).The theme for World Kidney Day 2010 is ‘We must act on diabetic kidney disease’. Diabetes is the leading cause of chronic kidney disease. The mission of World Kidney Day is to raise awareness of the importance of our kidneys to our overall health and to reduce the frequency and impact of kidney disease and its associated health problems worldwide. If detected early, Chronic Kidney Diseases can be treated, thereby reducing other complications and dramatically reduce the growing burden of deaths and disability from chronic renal and cardiovascular disease worldwide. n International Year of Biodiversity 2010. The United Nations declared 2010 to be the International Year of Biodiversity. It is a celebration of life on Earth and of the value of biodiversity for our lives. The world is invited to take action in 2010 to safeguard the variety of life on Earth: biodiversity. The International Year of Biodiversity is a unique opportunity to increase understanding of the vital role that biodiversity plays in sustaining life on Earth. Biological diversity – or biodiversity – is the term given to the variety of life on Earth and the natural patterns it forms. The biodiversity we see today is the fruit of billions of years of evolution, shaped by natural processes and, increasingly, by the influence of humans. It forms the web of life of which we are an integral part and upon which we so fully depend.

Q CSIR News CSIR inspires learners in Limpopo with space technology

CSIR technology for improved, more durable low-income housing

South Africa’s SumbandilaSAT is now in orbit, and locally the topic of space technology is one of great fascination. To capitalise on this wave of interest, the Satellite Applications Centre of the Council for Scientific and Industrial Research (CSIR) has embarked on a joint space education initiative for learners and educators with three Limpopo-based science centres. Funding for this initiative comes from the Department of Science and Technology (DST). The initiative supports the theme – Space for Education – of the 10th World Space Week (WSW) celebration. WSW is an annual event celebrated worldwide to commemorate the launch of the first man-made satellite, Sputnik 1, on 4 October 1957. The WSW celebration is a week-long event taking place from 4 to 10 October 2009. The CSIR-led awareness campaign will run from 19 to 23 October 2009, targeting learners from Grade 10 to 12 who study physical science, mathematics and geography. It aims to expose the learners to the space industry in all its fascinating facets. Learners from schools in the rural areas will be transported by bus to participating science centres such as the University of Limpopo Science Centre, Bokamoso Science and Technology Education Centre (BOSTEC) and Vuwani Science Centre, on allocated dates. By spreading the allocation, learners from all five districts of the province (Capricorn, Vhembe, Mopani, Greater Sekhukhune and Waterberg) will have an opportunity to hear and see more about space. Through inspiring narratives and presentations on their work at the CSIR Satellite Applications Centre, the CSIR’s Daniel Matsapola and Johnny Rizos plan to thrill their audience and create excitement and a desire among learners to choose science, engineering and technology as their primary career choice.

Communities who depend on subsidised, lowincome houses in South Africa can benefit greatly from technology developed and tested by the Council for Scientific and Industrial Research (CSIR). While much progress has been made with housing provision, the backlog of some 2.1 million homes is still a reality facing South Africans. Numerous initiatives are underway aimed at increasing delivery in this regard. Recognising this as a national priority, the CSIR has applied its collective knowledge to contribute towards finding a solution for the low-income housing sector, comments Dr Sibusiso Sibisi, CSIR President and CEO. ‘Using innovative design and construction technology, CSIR researchers have developed a demonstration house with significantly improved performance and sustainability. If built according to CSIR specifications, and on large scale, such houses will be constructed much faster and at similar costs than when using conventional methods,’ he says. The Department of Science and Technology supports this CSIR research project. The CSIR demonstration house was built according to the regulations of the National Home Builders Registration Council. The complete house has also been accredited by Agrément South Africa, the internationally acknowledged body that provides assurance through technical approvals of non-standardised or unconventional products. Two other houses have also been built on the CSIR campus in Pretoria – both are the standard 40 m2 size and design of subsidised low-income houses. While one is a replica of a properly built subsidised low-income house, the interior and exterior finishing of the other house is according to suburb style, illustrating the difference in appearance and experience when inside the house. While being the same size as the other two houses, the CSIR’s experimental house has an optimised design with the added advantage that it can be extended easily by home owners. ‘The house was constructed combining technologies and materials in an innovative way to improve living conditions and the durability of the home,’ explains Hans Ittmann, Executive Director of CSIR Built Environment. Some contractors in the low-income market do not lay foundations to standard. To eliminate cracked walls resulting from sub-standard foundations, a CSIR technology developed for roads was adapted to form the foundation slab of the house. ‘Local labour can be used to construct such foundations, which is based on ultra-thin, continuously reinforced concrete technology,’ says Ittmann. ‘We used a modular, design-to-fit approach similar to a Lego set where pieces have to fit together correctly to form the bigger unit,’ explains Llewellyn van Wyk, senior researcher at the CSIR. One big difference to current lowincome houses is the design of the bathroom and kitchen area, and the use of a waste outlet manifold that is pre-manufactured, quality-tested and installed on site. This reduces the extent of the plumbing installation substantially while

Johnny Rizos (second from right) of the CSIR Satellite Applications Centre with some of the learners.

Johnny and Daniel Matsapola of the CSIR Committee on Earth Observation Satellites (without uniforms) and some of the learners.

Using innovative design and construction technology, CSIR researchers have developed a low-income demonstration house. While being the same size as a government-subsidised unit (40 m2), it has significantly improved performance and sustainability.

Prefabricated plumbing used in the CSIR lowincome house, which has been developed using innovative design and construction technology. ensuring that the installation is done to the required standard. ‘Standard low-income houses have no ceilings and thus no insulation, which results in incredible variations in temperatures,’ says Van Wyk. The thermal performance of the roof was improved dramatically with the addition of an insulation material that doubles up as a ceiling. The house faces the appropriate direction for ensuring bedrooms can benefit from sunlight, while the living room faces north. The CSIR low-income housing initiative is a research project-in-progress. The most recent additions include a solar-powered geyser on top of the roof and a photo-voltaic panel above the front door for powering lights inside the house. ‘CSIR researchers will continue to pursue improved performance and sustainability for the low-income housing sector to impact on the quality of life of communities,’ concludes Sibisi. Incorporating most components of the CSIRdeveloped low-income house, local authorities will have demonstration units constructed in the Buffalo City Municipality in the Eastern Cape and at Kleinmond in the Western Cape.

Quest 5(4) 2009 53

Science news Q

Wits University announces the discovery of ‘Earth Claw’, a juvenile dinosaur found in the northern Free State, South Africa The discovery of a new species of dinosaur from the Early Jurassic period (approximately 195 million years old and seven metres long) was announced and described by Dr Adam Yates, the primary investigator and a palaeaontologist from the Bernard Price Institute for Paleontological Research (BPI) from the University of

The right premaxilla, a bone from the tip of the snout. The two prongs partly enclose the giant nostril characteristic of this species. The tips of two teeth can be seen protruding from the bottom edge.

the Witwatersrand, Johannesburg, South Africa, on 11 November 2009. The vegetarian dinosaur, one of three discovered at the same site, was named Aardonyx celestae – the genus name (Aardonyx) means ‘earth claw’, (Aard – Afrikaans for earth) and (onyx – Greek for claw) an appropriate name, given that the large, earth-encrusted foot claws were some of the first bones to be discovered in the town of Senekal, near Bethlehem in the northern Free State, in South Africa. The species name (celestae) is given to acknowledge the work of Celeste Yates, who prepared much of the fossil. ‘This species is important as the Aardonyx was an animal close to the common ancestor of the gigantic sauropod dinosaurs,’ explains Yates. ‘Sauropods, known popularly as “brontosaurs”, were the largest backboned animals to walk on land with their long necks, tree-trunk legs and whip-like tails. Some were even longer and exceeded 30 metres in length. Aardonyx gives us a glimpse into what the first steps towards becoming a sauropod involved.’ The discovery was made by a Wits postgraduate palaeaontology student, Mr Marc Blackbeard, who began excavating two sites in the northern Free State, five years ago, under the leadership of Yates. ‘We knew that there was likely to be some fossils in these “bone beds” discovered by

A reconstruction of the skull of Aardonyx. The known parts are shaded in. Drawn by Adam Yates.

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James Kitching about 20 years ago, but we did not expect to find anything of this magnitude,’ says Yates. Yates elaborates on the anatomy of Aardonyx celestae: ‘the dinosaur had a wide-gaping mouth, bracing joints in the back vertebrae that made the backbone rigid enough to support great weight and a forearm and hand capable of grasping and supporting weight. Growth rings in the rib and shoulder blade sections show that Aardonyx was not full grown – it was probably less than 10 years old when it died near a river or stream.’ He adds: ‘Aardonyx probably walked on its hind legs but could drop onto all fours as well. It had flattened feet with large claws that supported body weight on the inside of the foot and a robust thigh bone (femur) for supporting weight.’ Dr Chinsamy-Turan, a Wits graduate and a vertebrate palaeohistologist at UCT agrees: ‘My analysis of the bone microstructure in the ribs and shoulder blades of Aardonyx suggests that while it had experienced at least seven spurts or cycles of growth, it was not a fully grown animal.’ According to Dr Matthew Bonnan, a vertebrate palaeobiologist, Department of Biological Sciences and an author of the paper, they already knew that the earliest sauropods and nearsauropods would be bipeds. ‘What Aardonyx shows us, however, is that walking quadrupedally and bearing weight on the inside of the foot is a trend that started very early in these dinosaurs, much earlier than previously hypothesised. The bones of the forearm are shaped like those of sauropods – this means that the forearm and hand could bear weight and that Aardonyx could drop onto allfours as well as walk bipedally.’ Dr Johann Neveling, a geologist from the Council for Geosciences in Pretoria, also an author of the paper, says that geology suggests that Aardonyx lived near an oasis on the outskirts of a vast desert. The discovery was published on 11 November 2009 in the Proceedings of the Royal Society in a paper entitled ‘A New Transitional Sauropodomorph Dinosaur From The Early Jurassic Of South Africa And The Evolution Of Sauropod Feeding And Quadrupedalism’.

Q ASSAf News

Professor Coutsoudis with Professor Robin Crewe and Minister Naledi Pandor.

Professor van Helden with Professor Robin Crewe and Minister Naledi Pandor.

ASSAf honours for top SA scientists The Academy of Science of South Africa recognised some of South Africa’s top scientists in their Awards line-up for 2009. The awards recognise the work of a range of scientists from a variety of backgrounds. Two prestigious ASSAf Gold Science-forSociety medals are awarded annually. This year, the two medals were awarded to Professors Anna Coutsoudis and Paul van Helden. Professor Coutsoudis is a public health scientist in the Department of Paediatrics and Child Health at the Nelson R Mandela School of Medicine at the University of KwaZuluNatal, and is held in the highest esteem for the quality of her research, the global impact of her findings on exclusive breastfeeding, and her personal commitment to improving the lives of poor children. She has made groundbreaking contributions in the areas of the impact of vitamin A in lowering measles-related morbidity, and later on the positive effect of vitamin A on the morbidity of infants born to HIV-positive mothers. She established for the first time the association between non-exclusive breastfeeding and increased risk of mother-to-child transmission of HIV. This has had an impact both in South Africa and internationally, first in re-establishing the importance of exclusive breastfeeding as the normative pattern of breastfeeding, and later on international UNAIDS guidelines on HIV and breastfeeding policy. She persisted in the latter despite the fact that initially these findings met with surprise bordering on derision from the local and international scientific community. It was only the rigour of her continuing research which convinced the doubters and spawned other similar work. A number of ancillary studies arising from these publications are also of the

highest standard. These studies have specifically looked at ways of making breastfeeding safer for HIV-exposed infants in all communities. Van Helden is the head of the new Department of Biomedical Sciences in the University of Stellenbosch Health Sciences Faculty, and also heads the molecular biology and human genetics divisions. He has initiated major new directions of TB research, obtained necessary funding, found local and international collaborators and co-ordinated and managed the projects, all in the interest of finding new tools to diagnose, treat and prevent one of the world's most devastating diseases. Under his leadership, the group has set out to understand the mechanisms of drug resistance; challenge all the existing conceptual frameworks and re-examine fundamentals; introduce rapid diagnostics; and to assess whether drugresistant TB cases are caused by acquisition of resistance or transmission of already resistant microorganisms. He has shown that SA has a very high proportion of recently-transmitted TB; that the incidence in the Western Cape is particularly high in the absence of HIV; that reactivation of latent disease is not as frequent as was previously thought; that multiple infections are common and that drug resistance can be identified with a few simple tests which can then direct treatment. The resulting new technology can identify micro-epidemics as they occur.

Dr Chaya Herman from the University of Pretoria giving her presentation at the symposium.

Symposium discusses PhD production in SA South Africa needs to increase its PhD production tenfold by 2018, says the strategic plan of the Department of Science and Technology. Currently, output statistics show that only 23 to 27 PhDs are produced per million of the population per annum. ASSAf’s PhD study aims to identify and investigate the issues surrounding PhD production in South Africa, and as the first step in this process, a PhD symposium was held in early October at the CSIR Convention Centre in Pretoria. A number of issues were raised, such as South Africa’s capacity to produce this number of graduates, critical partners and cross-sectoral cooperation. The study aims to identify problems areas where money can best be invested to boost the numbers and quality of PhDs in the country. It is also hoped that the data collected will be of direct benefit to South African higher education institutions. Minister of Science and Technology, Naledi Pandor, addressed the audience at

the symposium, and commended this effort of ASSAf, noting its value in redressing the inequalities brought by the past regime in the generation of knowledge economy.

Senior scientists from TWAS and Minister Naledi Pandor present South African President, Jacob Zuma, with the TWAS medal.

Much to talk about at the 2009 TWAS conference A total of six symposia were presented at the 11th General Conference of the Academy of Sciences for the Developing World (TWAS), taking an in-depth look at some of Africa’s most pressing problems and the role that science and technology (S&T) can play in development. Symposium one, convened by Dr Albert van Jaarsveld, President of the National Research Foundation (NRF), highlighted the S&T sector in South Africa. Presentations included an overview of the science and technology landscape by Dr Phil Mjwara, Director-General of the Department of Science and Technology and an overview of the new book on The State of Science in South Africa published by the Academy of Science of South Africa. Each of the seven NRF-DST centres of excellence was represented in the symposium. The second symposium investigated the topic most relevant at present to communities worldwide: the credit crunch. This symposium focussed specifically on how the global economic crisis has impacted on research and education in developing countries. The session was convened by the Executive Director of TWAS, Professor Mohamed Hassan, and featured the South African Minister of Science and Technology, Ms Naledi Pandor, as a speaker. In honour of the International Year of Astronomy, the third symposium was dedicated to ‘Astronomy in Developing Countries’. Professor George Ellis of the University of Cape Town convened the session. Symposium four investigated human pre-history in Africa, with topics such as a genomic reconstruction of evolution and migration, and origins of the human brain under discussion. Another highly relevant topic was that of infectious diseases. The fifth symposium was dedicated to a discussion thereof. The last symposium looked at science and technology education for development, and included discussions on the value of science academies in science education, as well as innovation in education.

Quest 5(4) 2009 55

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56 Quest 5(4) 2009

Q Back page science MESSENGER spacecraft reveals more hidden territory on mercury A NASA spacecraft's third and final flyby of Mercury has for the first time given scientists an almost complete view of the planet's surface and provided new scientific findings about this relatively unknown world. The Mercury Surface Space Environment Geochemistry and Ranging spacecraft, known as MESSENGER, flew by Mercury on 29 September and used the planet’s gravity in a way that means that it will go into orbit around Mercury in 2011. Many new features were revealed during the third flyby, including a region with a bright area surrounding an irregular depression, thought to be volcanic in origin. Other images revealed a double-ring impact basin about 290 km across. The basin is similar to a feature scientists call the Raditladi basin, which was viewed during the probe's first flyby of Mercury in January 2008. The flyby not only allowed for the first detailed scans over Mercury's north and south poles, but also helped scientists observe how Mercury's atmosphere varies with its distance from the sun, and it also revealed new information on the abundance of iron and titanium in Mercury's surface materials. The spacecraft has completed nearly threequarters of its 4.9-billion-mile journey to enter orbit around Mercury. The full trip will include more than 15 trips around the sun. In addition to flying by Mercury, the spacecraft flew past Earth in August 2005 and Venus in October 2006 and June 2007. For more information about the mission visit: http://www.nasa.gov/messenger. Source: NASA

Why are many large craters on Mercury relatively smooth inside? Images from the MESSENGER spacecraft that flew by Mercury in October 2008 show previously uncharted regions of the planet that have large craters with an internal smoothness similar to Earth's own moon, and are thought to have been flooded by lava floes that are old but not as old as the surrounding more highly cratered surface. Image: NASAcratered surface.

Now here’s a shining light!

Here’s history in 3D

Polishing metal surfaces for moulds for various items such as plastic and glassware is a demanding, but monotonous, task and it is difficult to find qualified young specialists. Polishing machines do not represent an adequate alternative because they cannot get to difficult parts of the surface. A new solution is provided by laser polishers. Dr-Ing. Edgar Willenborg, group leader at the Fraunhofer Institute for Laser Technology ILT in Aachen, Germany, explains: ‘The laser beam melts the surface to a depth of about 50 – 100 micrometres*. Surface tension ensures that the liquid metal flows evenly and solidifies smoothly.’ As in conventional grinding and polishing, the process is repeated with increasing degrees of fineness. In the first stage the researchers melt the surface to a depth of about 100 micrometres; in further steps they gradually reduce the depth. Laser polishing does not achieve the same surface smoothness as perfect hand polishing – hand polishers can achieve a roughness (Ra) of 5 nm; the laser at present can only manage 50 nm**’. But Willenborg still sees considerable market potential for the system. ‘We will concentrate on automating the medium grades: a roughness of 50 nm is adequate for many applications, including the moulds used for making standard plastic parts.’ The high-end levels of smoothness will therefore remain the domain of skilled hand polishers.

Three-dimensional computer graphics are moving into museums. Works of art are being digitally archived in 3D, simplifying research into related artefacts and providing the public with fascinating three-dimensional displays. If you don’t have the time to travel to Florence, you can still see Michelangelo’s statue of David on the Internet, revolving in true-tolife 3D around its own axis. This is a preview of what scientists are developing in the European joint project 3D-COFORM. The project aims to digitise the heritage in museums and provide a virtual archive for works of art from all over the world. Vases, ancient spears and even complete temples will be reproduced in 3D. In a few years’ time museum visitors will be able to revolve Roman amphorae through 360° on screen, or take off on a virtual flight around a temple. The virtual collection will be especially useful to researchers seeking comparable works by the same artist, or related anthropological artefacts otherwise forgotten in some remote archive. The digital archive will be intelligent, searching for and linking objects stored in its database. For instance, a search for Greek vases from the 6th century BC with at least two handles will retrieve corresponding objects from collections all over the world. 3D documentation provides a major advance over the current printed catalogues containing pictures of objects, or written descriptions. A set of 3D data presents the object from all angles, providing information of value to conservators, such as the condition of the surface or a particular colour. As the statue of David shows, impressive 3D animations of art objects already exist. ‘A 3D scan is basically a cloud of measured points. Further processing is required to map the object properly,’ says Dr André Stork, Head of Department at the Fraunhofer Institute for Computer Graphics Research IGD in Darmstadt, Germany. Researchers are developing calculation specifications to derive the actual object from the measured data. The software must be able to identify specific structures, such as the arms on a statue or columns on a building, as well as recognising recurring patterns on vases. A virtual presentation also needs to include a true visual image – a picture of a temple would not be realistic if the shadows cast by its columns were not properly depicted. The research group in Darmstadt is therefore combining various techniques to simulate light effects.

* A micrometre is one millionth of a metre, or 1 000th of a millimetre. A human hair is about 50 micrometres wide ** A nanometer (nm) is one billionth of a metre – or one millionth of a millimetre, so a human hair would be about 50 000 nm wide

Source: Fraunhofer-Gesellschaft

Metal mould for glass manufacture: the lower part of the mould has been left unprocessed; the upper part has been laser-polished. On the right, the product that can be made using a mould of this type. Image: Fraunhofer-Gesellschaft

Source: Fraunhofer-Gesellschaft

MIND-BOGGLING MATHS PUZZLE FOR Q uest READERS Q uest Maths Puzzle no. 12 What letter should replace the ? in the oval below?

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, 5 February 2010. 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. 12’ and send it to: Quest Maths Puzzle, Living Maths, P.O. Box 478, Green Point 8051. Fax: 0866 710 953. E-mail: livmath@iafrica.com. For more on Living Maths, phone (083) 308 3883 and visit www.livingmaths.com.

Solution to Q uest Maths Puzzle no. 11 16 since A=4 and B=12. The winner is Jamie-Kate Loukes from Fourways

Quest 5(4) 2009 57