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ISSN 1729-830X

VOLUME 1 • NUMBER 3 • 2005 R20 incl. VAT


Cover stories


Laser light fantastic

Philemon Mjwara, Hardus Greyling, and Skhumbuzo Ntenteni Lasers for industry, environment, and health 8



Ian Meiklejohn and Paul Sumner Your QUESTions answered


VOLUME 1 • NUMBER 3 • 2005

Animals at risk ■ Protecting species the global way Jenny Underhill Taking a biodiversity line


■ Penguins feel the heat Jenny Griffin Cool nests are best

Regulars 7

Careers Working with lasers Science news



■ Kinkle the infrared elephant Rory Paul and Matt Hartley Thermography helps to track injuries

Managing fires: the science behind the smoke

2004 Nobel Prizes in the natural sciences (p.24) • Space mission extraordinary: Cassini reports from Saturn; Huygens reports from Titan (p.43) • 44s smother Earth; Ocean census; Boozy tastes in the genes? (p.45) • Bright birds (p.47) 15

Measuring up Film & noise, beads & honey


Fact file Understanding DNA


The S&T tourist Veld walk in the city Geology, archaeology, and bush in the Melville Koppies Nature Reserve


Brian van Wilgen Dealing with fires in South Africa

Feature 22

Sydney Brenner: a most distinguished biologist

Keith Manchester His part in the DNA and RNA story

Viewpoint interview Why bother with physics? – Frank Nabarro and Robert de Mello Koch


Books Coastal fishes of southern Africa, by Phil and Elaine Heemstra • and other titles


Letters to QUEST


Crossword puzzle


Diary of events


ASSAf news


Subscription form • Back page science

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More understanding s 2005 began, the world was still reeling from the shock of the most recent tsunami in south-east Asia, the thousands of human lives lost, and the devastation from which it will take years to recover. The only way to cope, it seems, is by examining what caused such damage and why so many people died. How should land be cleared for human development without demolishing natural barriers, such as indigenous forests, that protect vulnerable places from destruction? How to prepare for natural disasters? How to recognize warning signs before it's too late? The answers seem to start with the search for more understanding to clear the way for planning ahead. Our authors give responses to some of the most frequently asked questions about tsunamis (p. 8) and consider what might happen if we too were struck by a large tsunami. This kind of activity is surely the role of science. It gathers facts, analyses, and attempts to substitute understanding for ignorance. If good science is science that has predictive value, it is by definition useful science. Understanding and working with the facts as we know them is also the theme of the article on fires in southern Africa, which can damage but also bring new life (p. 26). All this year the world celebrates the understanding of the physical world that Albert Einstein brought. It is the International Year of Physics and the centenary of the year 1905 in which he published five revolutionary papers, where he showed that atoms are real, introduced his special theory of relativity, and helped to put quantum theory on the map. As we now know, he fundamentally revised notions of space and time, and his Nobel Prize for 1921 was for the first of his 1905 papers, about the photoelectric effect, which proved the existence of photons (light as particles). So QUEST opens this year by featuring South Africa's own current work in the fantastic world of laser light (opposite page) and an interview with two of our eminent physicists (p. 36). This issue also carries news of the 2004 Nobel Prizes in the natural sciences and looks back at the work on DNA and RNA of our own South African-born Nobel laureate, Sydney Brenner. We explore far-off worlds with the Cassini-Huygens space mission (p. 42) and we air concerns about the world of nature close by (pp. 14 and 16). We've welcomed your questions and letters and hope for a great many more.


Laser cladding at the CSIR National Laser Centre. Photograph: Courtesy of the CSIR


ISSN 1729-830X

Editor Elisabeth Lickindorf Editorial Board Wieland Gevers (University of Cape Town) (Chair) Graham Baker (South African Journal of Science) Anusuya Chinsamy-Turan (University of Cape Town) George Ellis (University of Cape Town) Jonathan Jansen (University of Pretoria) Colin Johnson (Rhodes University) Correspondence and The Editor enquiries PO Box 1011, Melville 2109 South Africa Tel./fax: (011) 673 3683 e-mail: editor.quest@iafrica.com (For more information visit www.assaf.co.za) Business Manager Neville Pritchard Advertising and Neville Pritchard Subscription enquiries PO Box 5700 Weltevreden Park 1715 South Africa Tel.: (011) 678 7093 Fax: (011) 673 3683 Cell: 083 408 3286 e-mail: pritchardn@mweb.co.za Copyright © 2005 Academy of Science of South Africa Published by the Academy of Science of South Africa (ASSAf) PO Box 72135, Lynnwood Ridge 0040, South Africa (011) 673 3683 Permissions Fax: e-mail: editor.quest@iafrica.com (011) 678 7093 Back issues Tel.: Fax: (011) 673 3683 e-mail: pritchardn@mweb.co.za Subscription rates (4 issues and postage) (For subscription form, other countries, see p.48.)

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Elisabeth Lickindorf Editor – QUEST: Science for South Africa Join QUEST’s knowledge sharing activities ■

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 S&T Questions and Answers column – e-mail or fax your questions to The Editor and win a prize. (Write S&T QUESTION in the subject line.) ■ Inform readers in our regular Diary of Events column about S&T events that you may be organizing. (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.assaf.co.za), and make arrangements to tell us your story. To contact the Editor, send an e-mail to: editor.quest@iafrica.com or fax your communication to (011) 673 3683. Please give your full name and contact details.

Invented four decades ago, lasers gave us CDs, barcodes, surgical tools, industrial cutting implements, and much, much more. The CSIR National Laser Centre is at the heart of South Africa's – and the continent's – laser technology. Its scientists Philemon Mjwara, Hardus Greyling, and Skhumbuzo Ntenteni tell us what this branch of applied physics does for our economy, our environment, and our health. What are lasers? How do they work?

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We all use laser technology in some form or other, but what do we actually know about this sophisticated and powerful source of light? The word 'laser' is an acronym for 'light amplification by stimulated emission of radiation'. Unlike other light sources, a laser is a device normally designed to produce a powerful, highly directional, intensified, monochromatic, coherent, parallel beam of light. Its radiation can be generated in the infrared, visible, and ultraviolet regions of the electromagnetic spectrum (see also p. 19). Traditionally, explains Brian Silver in The Ascent of Science (1998), light comes from heating or burning something (such as a lamp filament or oil), which causes electrons to oscillate in the atoms of the hot body to produce electromagnetic waves of light. The electrons behave independently, so the waves emitted are not in phase but jumbled and disorganized. Because the light is a mixture of frequencies, the waves don't 'fit together', or cohere, but peak at different times and move randomly in different directions away from the light source. Light waves from a laser, however, have the same frequency and are in phase: the effect is very strong. By analogy, writes Silver, "It is as though many people were simultaneously shaking you such that they all pushed and pulled in the same direction together. That's how laser light acts; all the waves in the light are effectively of the same frequency, and they all travel in phase. The effect

of this army of simultaneous shakers can be dramatic. Lasers can burn through steel." In a simple ruby laser, for instance, electrons in the chromium ions are first 'pumped' into an excited state. When they relax again to lower energy states, a photon (a unit of light, or radiant energy) is emitted, which in turn also stimulates neighbouring excited electrons to emit photons. These photons are all the same wavelength (monochromatic), move in the same direction (highly directional), and are all in phase (coherent). To turn the emitted photons into a coherent beam with high energy and very little spread, they are sent up and down an optically transparent cylinder with a reflecting surface at one end and a partially reflecting surface at the other; some then emerge through the partially reflecting end as pulses of highly coherent light.

An industrial laser system capable of cutting, welding, cladding, and hardening components for general manufacturing.

Above: A CO2 laser deposits wear-resistant material onto a shaft used in a pump. Pictures: Courtesy of the CSIR

The inventors 1917 – Albert Einstein laid the foundation for lasers when he theorized that, under the right conditions, atoms could be stimulated to emit photons of a single frequency in a single direction. Late 1950s onwards – American doctoral student Gordon Gould, at Columbia University, New York, started important work on lasers and, in 1959, applied for a patent. Meanwhile, Charles H. Townes and Arthur L. Schawlow at Columbia were researching microwave radiation for transmitting energy and also applied for patents; their research led physicist Theodore Harold Maiman, in 1960, at the Hughes Research Laboratories in Miami, to build the first-ever device to emit laser light (a ruby crystal). Thirty years of bitter controversy and lengthy legal battles later, the courts decided how to distribute ownership of the key patent rights.

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The African Laser Centre (ALC) is a virtual organization with headquarters in Pretoria. It was set up in November 2003 to enable African nations collaboratively to play a major international role in using light to advance science and technology. The objectives include: promoting research and training at African laser research facilities and collaboration among researchers and institutions to serve the whole continent; supplying financial resources, technical assistance, and equipment loans to laser researchers throughout Africa; attracting and retaining laser expertise through enhanced research facilities; expanding infrastructure through flagship projects. Its initial core consists of the following facilities: the CSIR NLC (Pretoria, South Africa) specializing in manufacturing, machining, and materials processing; the University of Cheikh Anta Diop (Dakar, Senegal) specializing in atomic and molecular physics, laser spectroscopy, and processing; the Laser Fibre Optics Centre (Cape Coast, Ghana) specializing in agricultural and environmental science; the National Institute of Laser Enhanced Science (Cairo, Egypt) specializing in medical and biological applications of lasers; Tunis el Manar University (Tunis, Tunisia) specializing in plant and environmental science and molecular spectroscopy; and Advanced Technologies Development Centre (Algiers, Algeria) specializing in laser spectroscopy and surface studies. For more, phone (012) 841 4188 or fax (012) 841 3152 and visit www.africanlasercentre.org

The CSIR NLC The CSIR National Laser Centre (CSIR NLC) combines the activities of the former AEC and the CSIR. The two main areas of expertise were molecular laser isotope separation and mainly military laser research and development (R&D). As an independent 'national asset' – an enabler in academe and a research partner for industry – it was to conduct technology demonstrations, act as a clearing-house for information, and promote the use of lasers in industry. It was also to operate as a business, that is, to conduct contractual R&D and develop laserbased processes, laser systems, and services. In three years, the centre has achieved financially and strategically, and is initiating its consortium approach to research and innovation. Finances. The centre was initially granted some R9 million from DACST (now the Department of Science and Technology). It generated approximately R5 million in 2001 in external income, with a turnover of about R14 million. Now its external income is around R12 million a year and its annual grant has increased to R18 million. Strategy. The competencies inherited from the AEC were mainly the development of special laser sources, the use of lasers in materials processing, and the application of spectroscopy to detect objects. To build on them, the CSIR NLC examined today's challenges, such as sustainable development, health, and the efficiency of manufacturing components. Now its programmes include using lasers in processing advanced materials, such as light metals, and developing specialized laser sources together with spectroscopy to detect atmospheric pollutants. Utilizing lasers initially developed for isotope separation for nuclear activities, we have developed a 'dry cleaning' technique for removing paints and contamination from substrates without damaging the host material. Consortium approach. Taking technological innovation from research idea through to product is worth sharing with the research community. To introduce the use of lasers in health, for instance, we investigated areas where little research had been conducted: the use of lasers to enhance wound healing for diabetic patients, potential tissue damage resulting from laser radiation, and the combination of lasers with specialized drugs to treat cancer. To carry out the last of these, the CSIR NLC established a consortium, including Rhodes University, the University of Cape Town's medical school, University of Johannesburg, the CSIR's Food, Biological and Chemical Technologies unit (BioChemtek), and the Medical Research Council (MRC). Rhodes is developing drugs on a laboratory scale; the CSIR NLC provides the lasers for activating the drugs as well as other diagnostic tools; UCT is responsible for clinical trials and introducing the treatment; CSIR BioChemtek will develop the drugs commercially; and the MRC will assist with the intellectual property protection strategy. This collaboration allows us to engage in the range of activities that take an idea from early stages to commercialization. It also provides for interaction between tertiary education institutions, science councils, and medical specialists at the initial stage of commercialization. – Philemon Mjwara (pictured above)

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Lasers for Africa

Lasers in South Africa South African laser research began at the CSIR in Pretoria at the then National Physical Research Laboratory. In the early 1970s, a group led by George Ritter designed and built the first solidstate laser in Africa, based on a ruby crystal. Other types followed, including gas lasers ranging from large CO2 lasers producing tens of joules per shot to 'ultra miniature' N2 lasers emitting subnanosecond pulses. The group also worked on spectroscopic and holographic applications. An historic example of the holography done at the CSIR is the hologram of the Taung skull produced in 1985 for the November cover of National Geographic Magazine. The importance of the defence industry during the late 1970s and the 1980s meant that laser research also focused on military applications, mainly laser rangefinding. (The technology was later commercialized by Eloptro, now called Denel Optronics.) A parallel laser programme ran from the mid1980s at the then Atomic Energy Corporation (AEC, now renamed the South African Nuclear Energy Corporation, or NECSA) to develop pulsed gas laser technology for nuclear applications. The world-class pulsed CO2 laser sources developed there offer excellent performance, even today. At the time, they were used in an isotope separation process, mainly for enriching uranium. The CSIR group was never large (typically 20 scientists), but the AEC laser programme employed over 250 people at its peak. Funded by the then Department of Mineral and Energy Affairs, it was designed to develop cheaper nuclear fuel for South Africa's nuclear power station at Koeberg. New priorities following the 1994 elections meant reduced support for laser research at the CSIR and AEC. In 1999, the then Department of Arts, Culture, Science and Technology (DACST) evaluated the country's laser technology and, in 2000, the National Laser Centre (NLC) was formed to serve the new South Africa. In 2003 it became part of the CSIR.

Manufacturing and materials The automotive industry, general manufacturing, and minerals industries use lasers mainly for cutting and marking/scribing. There is much laser cutting and even laser marking in the diamond industry, as lasers can cut diamonds very accurately, even against the natural cleavage planes often used to 'break' diamonds into smaller pieces. Lasers can also drill into diamonds, allowing jewellers to remove impurities. Components for automotive body parts are cut by lasers. The beam can be so powerfully focused that intricate patterns and complex components are quickly cut. Because the computer-controlled laser beam is manipulated with respect to the work piece, the engineer can rapidly adjust designs or modify existing ones. The 'non-contact' processing means that the work piece is not distorted by the forces working on it or by tools that get blunt.



There are many ways to use lasers to process and improve materials. ■ Welding – focusing the laser beam onto the joint and melting the weld material fuses the two components to be joined. ■ Laser cladding – this is similar to welding, in that additional weldable material in powder form (such as stainless steel, steel, or aluminium) is melted onto a component's surface to apply a new layer with different properties onto an existing substrate. Components can be made more resistant to wear and corrosion, and the process can even extend the life of old components by building up worn areas. ■ Surface modification includes laser cleaning, corrosion prevention, and laser hardening. If you heat the surface of a steel component to a high temperature and cool it rapidly, for instance, the material undergoes a 'phase change' and becomes much harder. Lasers as a heating source make accurate localized heat treatment of components possible, because the beam is so controllable and precise. Laser pulses can also be used to remove layers of rust, paint, grease, and other unwanted contaminants from components or materials quickly and efficiently without damaging the original.

Clockwise (from top left): 1. An injection mould after wearresistant powder cladding and before final machining. 2. The selective laser hardening of a tool, which is done to increase its working life. 3. A thick layer of grease is removed by means of a transverse excited atmospheric (TEA) CO2 laser. 4. Yttrium aluminium garnet (YAG) laser cladding of a tool steel injection mould. New material is deposited on existing components to improve wear and reduce corrosion.



Good, clean air

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The light detection and ranging (LIDAR) laser technology we probably know best is the device the police use to measure the speed of cars on public roads. But we also use LIDAR to measure air pollution, track wind and weather patterns, and monitor changes in the ozone layer. In fact, scientists are now considering space-based LIDAR systems to monitor the Earth's environment and changes in its atmosphere. LIDAR is a laser remote-sensing technique that works rather like radar – where radar transmits radio waves, the LIDAR transmits laser light. The system consists of a laser transmitter, a receiver telescope, photo-detectors, and data-capturing electronics.

How a LIDAR works. Laser light is transmitted in a specific direction or in multiple directions. It interacts with molecules (the target) in the atmosphere, and some part of the light is reflected or scattered back to the telescope, where it is measured by photo-detectors. The measured light goes through a data-capturing electronic system, from which we can deduce information about the altitude, the different types of gases in the atmosphere, and their concentration.

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For more, contact the CSIR NLC's Public Understanding of Lasers in Science and Engineering (PULSE) programme: tel. (012) 841 4188/3152 or visit www.csir.co.za/nlc Pay a visit to http://stwi.weizmann.ac.il/Lasers/laserweb/index and view the images at http://micromagnet.fsu.edu/primer/ lightandcolor/lasersintro Read O'shea Callen Rhodes, An introduction to lasers and their applications (Reading, MA and London: Addison-Wesley, 1977) and Richard Scheps, Introduction to Laser Diode-Pumped Solid State Lasers (Bellingham, WA: SPIE – The International Society for Optical Engineering, 2002).

How your CD player works CDs were introduced for public use in the 1980s as a convenient way to store music, data, or computer software. How does this small, lightweight disk do its job? The CD is a digital storage device, storing information as a sequence of zeros and ones – in other words, it uses a binary code. Computers also store information in a binary code, so we now have CD-ROMs on our computers. The binary code is stored either as a small bump (called a micro-pit) or no bump, and makes up the track. A CD's single spiral track circling from the inside of the disk to the outside is more than 5 km long and can contain more than 3 billion micro-pits. The CD player or CD-ROM reads the music from the CD. The basic job of the CD player is to focus the laser beam on the track bumps. So, inside a CD player, you have a semiconductor laser, a focusing lens, and a light sensor. The semiconductor laser is a small solid-state light source that produces a reddish laser beam. The lens focuses the laser light into a tiny spot on the shiny surface of the disk. The micro-pits on the CD track reflect the laser light back to the light sensor. When a laser light shines on it, the light sensor produces pulses of electricity; these are converted electronically into the binary code as recorded on the CD.

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Anticlockwise (from top right): 1. The CSIR NLC is developing new laser sources for spectroscopy and materials. The picture shows a diodepumped Nd:YAG laser, which pumps an optical parametric oscillator (OPO). An OPO is a non-linear optical device, consisting of a specialized crystal and two mirrors. Its main function is to change the wavelength (colour) of a laser beam from one wavelength to another more desirable one. A laser physicist typically selects the type of crystal and its orientation to produce a specific wavelength shift. 2. Laser marking of metal components. It is better than conventional ink marking technology in many ways, the most important being that the marks are permanent. 3. A laser ablation system, applying intricate patterns on tools that are used to produce plastic components. 4. Laser marking on an alternator cap.

The CSIR NLC is developing a mobile LIDAR system for detecting atmospheric pollution and pollutant concentrations that threaten human health and produce acid rain. The laser remote measurement of air pollutants (Las-R-MAP) system is customized to detect specific gases in specified quantities. It can detect and map a large number of gaseous pollutants at various ranges, including SO2, NO2, O3, benzene, and butadiene. These are found particularly where chemicals are made, as well as in the petrochemical industries and in hydrocarbon-based power generation. The mobile system will monitor gas emissions into the air and help factory owners understand the impact of their operations on the environment. Travelling countrywide, the system will be used for large-area mapping, short-range toxic or flammable gas warnings, and law enforcement of emission levels. The Las-R-MAP uses the differential absorptions LIDAR (DIAL) technique, where tunable laser pulses are transmitted towards the region to be monitored. A small fraction of the light is scattered by atmospheric particles and aerosols, and the reflected light is collected by a large receiver telescope onto a sensitive detector. The transmitted laser wavelengths are chosen to coincide with the absorption characteristics of the pollutant gas being investigated. The concentration of the gas that's found is derived from the amount of differential absorption of the back-scattered signals. The measurement is sensitive in the range of parts per billion and is pollutant-dependent. Different pollutants have different measurement sensitivities because the absorption of a particular wavelength depends on the spectroscopic properties of the pollutant. We can, for instance, very easily trace SF6 (a gas used in high-voltage switchgear) but it is more difficult to measure H2S (a by-product of burning coal). The CSIR NLC is also developing ways to measure dangerous gases, such as methane, by remote sensing at relatively short ranges, providing accurate measurements over a 50 m distance. Methane explosions are common in coal mines, for example, and the technology could be used at the coalface, down mine shafts, and at all depths to warn of danger levels.

Q Careers in S&T

Working with lasers There's work in laser technology for scientists and technicians of all kinds, particularly those with postgraduate degrees. Here are some examples from the National Laser Centre. Biochemistry

Laser marking can be applied onto almost any material, from paper to diamond. This picture shows examples of laser-marked components: text on aluminium, titanium (the screw in the foreground), stainless steel – even the face of Albert Einstein engraved on a granite slab.

Health and wellbeing The medicinal uses of lasers are many and varied, and South Africa is exploring their effects and their potential. The medical and cosmetics industries, for example, use a treatment called low-level laser therapy (LLLT) (typically less than 50 mW) in the visible to near infrared wavelength range of between 500 and 1 000 nm. Therapists claim (though without incontrovertible scientific proof) that it helps wounds to heal and muscles to recover more quickly after injury, and that it can treat skin problems, sinusitis, and even wrinkles. CSIR NLC researchers are investigating LLLT for the healing of wounds in diabetic patients. Another national collaborative research project involving the CSIR NLC is developing cost-effective drugs for use in photodynamic therapy (PDT), a process used in diagnosing or treating cancer. A photosensitizer is applied or injected into the patient, and is absorbed in cancerous tissue. Later, the cancerous areas are irradiated with a laser tuned to a wavelength that is absorbed by the photosensitizer. In the process, singlet oxygen is produced, which kills the cancer cells. When PDT is used for diagnosis, the fluorescence from the photosensitizer after laser irradiation reveals the area where the photosensitizer accumulates. During irradiation, healthy cells surrounding cancer cells can also be exposed to the laser radiation. A laser–tissue interaction study at the University of Johannesburg is now investigating the side effects or possible longer-term damage to the normal (healthy) cells. ■ Dr Philemon Mjwara is the centre manager of the CSIR NLC, Hardus Greyling is the portfolio manager, and Skhumbuzo Ntenteni is the PULSE coordinator.

Biochemistry is the chemistry of compounds and processes in living organisms, and scientists in this field examine biology within the context of chemistry. They study the elements, compounds, and chemical reactions that are controlled by enzymes and occur in all living things. Biochemistry focuses on the structure and function of cellular components, such as proteins, carbohydrates, lipids, nucleic acids, and other biomolecules. More recently, biochemistry has concentrated on the chemistry of enzyme-mediated (controlled) reactions and on the properties of proteins. Other areas include molecular biology (DNA, RNA) (see p. 25), protein synthesis, cell membrane transport, signal transduction, and energy decomposition cycles. For ages the sun has been used as a healing source. Wounds heal faster when exposed to controlled amounts of light. This has led biochemists to light and lasers, studying specific aspects of laser–tissue interaction. They examine the mechanisms by which light interacts with biological material. CSIR NLC research, for example, employs techniques to elucidate specific biological pathways involved in the healing processes of light. Through the technique of fluorescent lifetime imaging (FLIM), substances known as chromophores (probes) are introduced to a cell, specifically to bind particular molecules in it – such as proteins – and label or mark them: when such cells are subsequently exposed to light they start fluorescing (glowing). A

probe can, for example, bind selectively to cancer cells – which helps in the early detection process; another might follow the path taken by a drug as it interacts with cells. In this way we can detect pathological conditions without the need for a biopsy. There is plenty of work for biochemists in studying the application of laser technology to medicine.

Electronic engineering An electronics engineer needs proficiency in mathematics and physical sciences. Laser work gives an electronics engineer a unique chance to be involved in research as well as industry. Particularly useful areas include electronic circuit design, digital signal processing, software coding, and project management. At the CSIR NLC, an electronics engineer might, for instance, design power supply circuits for laser diodes or implement a cooling system for laser diodes using a thermoelectric cooler. (A laser diode is a semiconductor device that emits laser radiation – similar to a laser pointer or the laser in a CD player. Laser diodes provide power of milliwatt [CD players and pointers] to kilowatt [hardening and materials processing applications] output.) A current project involves the full integration of the gas detection system Las-R-MAP, involving lasers and electronics. This system provides challenges for both analogue and digital signal processing and offers work in a range of technologies, from complex laser sources down to simple stepper motor controllers.

Optical design and laser technology Optical design is closely aligned with laser technology. We need to design laser resonators that produce laser beams with specified characteristics – such as a particular energy distribution across the light beam or a beam with particular divergence. For most laser applications, the beam needs to be reflected with mirrors and focused with lenses, so optics are crucial. Fundamental optics is covered at undergraduate and postgraduate levels, but much of modern optics is conducted using modelling and optimization software packages. For laser work, you need a sound knowledge of physics, and optics in particular, but programming and applied mathematical skills also help.

Optics designer Liesl Burger at the CSIR NLC.

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? A tsunami is a wave or series of waves that can travel vast distances across oceans, causing flooding and damage when it swamps ocean shores. Historically, Japan has been the country most affected by such waves, and the name comes from the Japanese characters ‘tsu’ (meaning ‘harbour’) and ‘nami’ (meaning ‘wave’). Tsunamis are distinctly different from what we call ‘tidal waves’, which are a product of the gravitational pull of the Moon and other celestial bodies, but the height of the tide at the time of impact can influence a tsunami’s effect. For example, during spring high tide a tsunami has a greater impact because the sea through which the wave is propagated is at a higher level. The reverse holds true at low tide, where flooding would not be as high above the beach but the natural impact on coastal systems, such as coral reefs, may be greater – high water will wash over the reef but, when the wave is low, it is more likely to break on the reef itself and cause damage.

occur at the crustal plate boundaries. Not all earthquakes create tsunamis, however; the magnitude of the quake, sea depth, and distance to shore are deciding factors. Any other type of disturbance that displaces water can also cause tsunamis. Landslides can take place under the surface of oceans on continental shelves, where big buildups of sediment eroded from the land mass accumulate out at sea beyond a self-supporting threshold. Rockfalls into oceans, volcanic explosions, and even anthropogenic effects (in other words, deriving from human activity), such as explosions or mass movements caused by collapsing land fills, can cause waves of varying magnitude. Small meteorite impacts are frequent but they cause only small displacements if they land in the ocean. Most dramatic are megatsunamis, thought to be caused by asteroid impacts that create waves up to 100 m high, many times larger than what is normally considered a large tsunami.

What causes tsunamis?

How are they propagated?

Tsunamis are caused by rapid disturbance of the ocean bed, or to the water column above it. Undersea earthquakes, volcanoes, mass movements (landslides) and rockfalls from cliffs as well as meteorite impacts can all generate waves of varying size. The most common types of tsunami are caused by earthquakes, when the sea floor abruptly shifts and displaces the water above it. Most earthquakes

A displacement below the surface of the ocean releases energy that is distributed throughout the water column above it and then propagated sideways in the ocean in the form of a wave. (A common misconception is that water from the earthquake on 26 December 2004 was displaced across the ocean, but this is not correct: the tsunami moves as a wave, but the main displacement of water is vertical.)

What is a tsunami?

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The characteristics of a tsunami change during its movement as the water depth varies. Velocities of the waves in deep oceans can exceed 1 000 km/h at the surface. Amplitude, or wave height, decreases with the distance from the source because of wave divergence and dispersion. When the wave reaches a coastline, the shallower water slows the wave down to approximately 100 km/h on continental shelves and 40 km/h in water that is 10 m deep. The amplitude increases as the wave approaches the shore, and the wave energy is expressed as potential energy (a function of vertical displacement of water) and kinetic energy (a function of moving water). On impact with the coast, a small proportion of the energy may be reflected back out to sea, particularly on steep coastlines. In such circumstances, movement of water onto the land can occur as a tranquil surge or as a breaking wave. On steep coastlines, the area affected is defined by the ‘run-up’, which is the height reached by the water above sea level at the time of impact, and this is a function of the wave height. If the tsunami reaches the coast as a tranquil on-shore movement, then the run-up is approximately the height of the wave. Where waves break, the resultant kinetic energy causes run-up to exceed wave height. On shallow gradient coastlines, water moves further inland and this is referred to as ‘run-in’ (defined as the distance

Q Your Q UEST ions answered What do we know about tsunamis? What caused such devastation in south-east Asia on 26 December 2004? Could this kind of disaster hit South Africa? These and many other questions have been posed. We asked geomorphologists Ian Meiklejohn and Paul Sumner for answers.

that water floods inland from the shoreline). The extent of run-in is a function of wave height and also of surface roughness, which acts as a drag on the water and slows on-shore velocities. After the full extent of run-up or run-in is reached, much damage can still be caused by the floodwaters receding back into the ocean.

How often do tsunamis occur? Tsunamis occur regularly, mostly in the Pacific Ocean. At least 790 are reported to have occurred worldwide in the past 100 years, giving an average of eight each year, or two every three months. Not all tsunamis are large: not all of them cause damage or loss of life and many go unnoticed by the general public. Most tsunamis are created by earthquakes in the Pacific Rim and around Indonesia, where the earth’s crustal plates are tectonically active. Loss of life is not always known, given the total destruction that can happen to coastal villages and given secondary effects, such as famine and the spread of disease, that increase the death toll. Deaths may also be caused by the trigger mechanism itself – the earthquake, for instance. Economic impacts are even more difficult to assess, as off-site and longterm effects add to the overall cost of a tsunami disaster.

Is the natural environment affected?

What are the warning signs? In the case of an earthquake acting as the trigger of a tsunami, a tremor is likely to be felt some time before the wave hits the coast. As with lightning and thunder, the time between the earthquake and the tsunami reaching you is a function of the distance of the epicentre from the wave’s point of impact. If you’re at the coast and not sure, once you’ve felt a tremor, whether or not a tsunami has been generated, play safe and head for high ground – like animals that, following their incredible sense for disaster, tend to run for high ground in such instances. A report from the nature reserves says: “When in doubt, follow the animals!” The water at the shore begins withdrawing moments before the wave reaches the coast. If you see this happening, run the other way. Just before the Asian tsunami struck

This remarkable sequence of images (from left to right) from the QuickBird satellite shows a detail of Kalutara Beach, Sri Lanka. The first was taken in January 2004; the next shows the water withdrawing before the tsunami arrives on 26 December 2004; the third shows the turbulence of the wave. (The eddy currents are caused by the local topography and interference from waves rebounding off the shore.) The last shows the area after the tsunami had struck, leaving devastation in its wake. (NB: The pictures vary in scale.) Images courtesy of Digital Globe

in December 2004, there were reports of people running out and collecting fish on the exposed seabed, oblivious of the approaching wave, and many of them lost their lives because they didn’t understand what was happening. There’s very little you can do if you’re directly in the path of the wave as it crosses the shore – you will not be able to outrun it. Your best course of action would be to try to climb up a secure structure, but remember that the water will reverse direction and rush back out to sea. As with floodwaters, it’s the debris in the water that is the most dangerous.

What are the facts about south-east Asia’s tsunami of 26 December 2004? The Earth’s crust comprises a number of solid (tectonic) plates that ‘float’ over softer rock. Where these plates meet, considerable stresses develop. In the Indonesian area of our planet there are five moving plates close to one another. An earthquake caused the 2004 Indonesian tsunami when a movement occurred along a fault line,

▲ ▲

The United Nations Environmental Programme (UNEP) has set up a task

force in Geneva to assess the environmental effects of the most recent Indian Ocean tsunami of 26 December 2004. Very little research has been conducted on tsunami impacts, particularly on the vulnerable coral reefs and mangrove swamp areas. On coral reefs, the effect of sediment deposits and secondary damage caused by debris washed offshore during floodwater recession are of greater concern than the wave impact itself. Another concern is the potential effect of pollution caused by flooded and damaged coastal industries.

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Some major known tsunamis: causes and impacts in terms of loss of human life Year

Tsunami impact location

1628 B.C.

Crete, Aegean

Source location (if different from impact) and type Thira (Santorini) volcano; the caldera collapse

1700 A.D. 1737 1755 1815

Sanriku coast, Japan Kamchatka, Russia Lisbon, Cadiz, Tangier, Madeira Flores, Indonesia

Earthquake Earthquake Gorringe Bank, Atlantic Ocean; earthquake Tambora volcano; pyroclastic flow into sea

1863 1868 1883

Eastern Philippines Pacific Rim, especially Chile and Peru Cook Inlet, Alaska

1883 1896 1902 1908 1933 1946 1952

Java, Sumatra Sanriku coast, Japan Martinique Messina, Italy Sanriku coast, Japan Pacific Rim; especially Hawaii Unknown

Earthquake North Chile Trench; earthquake Augustine volcano; pyroclastic flows and debris avalanches into the sea Krakatau volcano; multiple types from eruption Earthquake Mt Pelee volcano; mudflows Earthquake Earthquake Aleutian Arc, Alaska; earthquake Myojin-sho, south of Japan; submarine volcanic explosion

1960 Pacific Rim; especially Chile, Japan, Hawaii 1964 Alaska, California 1976 Eastern Philippines 1983 Hokkaido, Japan 1992 Nicaragua 1992 Flores, Indonesia 1993 Honshu, Japan 1994 Java, Indonesia 1996 Irian Jaya, Indonesia 1998 Sissano, Papua New Guinea Source: www.nerc-bas.ac.uk/tsunami-risks ▲

and the Indian Plate moved diagonally under the relatively small Burma Plate (this process is called subduction). Tectonic plates are constantly moving and, because their margins are not smooth, friction may cause them to stick. If resistance builds up at their margins over a long period, the release that takes place when the plates actually do move is considerable. The last large earthquake along the fault marking the boundary between the Indian and Burma Plates was in 1833, and the long period between that quake and the 2004 quake probably contributed to the large magnitude of this most recent one. Seismic studies indicate that the earthquake occurred over a front of approximately 1 200 km and that the maximum displacement was 20 m over a distance of between 100 and 400 km. Following an earthquake, aftershocks are likely to occur, as a tectonic movement is seldom a ‘oneoff’ occurrence. In the Indonesian quake of 2004, there were at least 14 aftershocks of more than strength 5 on the Richter scale. The Richter scale is logarithmic, and

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Central Chile Trench; earthquake Alaska; earthquake Earthquake Sea of Japan; earthquake Earthquake Earthquake Sea of Japan; earthquake Java Trench; earthquake North Irian Jaya; earthquake Earthquake

a strength-9 quake (as was the case in 2004) is 10 times greater than a strength-8 quake, 100 times greater than strength-7, 1 000 times greater than strength-6, and so on. The power of the 26 December 2004 earthquake that caused the Indonesian tsunami is

Maximum run-up (metres) Unknown; probably several tens of metres Unknown 64* 25+ Unknown; probably several tens of metres Unknown 20 6

Number of deaths Unknown; probably very large 100 000* 50+ 25 000+ 12 000*

35 24 8* 8 20 35 Unknown

33 000* 26 000* 100* 6 000* 3 000* 200* 30 (crew of sunken research vessel) 2 500* 115 3 000* 103 170 1 000* 230 230 160 2 000* * estimate

20 20 Unknown 15 10 26 20 14 11 20

30 000* 25 000* None

estimated by the US Geological Survey as having been the equivalent of 475 megatons of TNT, or 23 000 Hiroshima bombs.

The impacts The wave emanating from the 26 December 2004 tsunami was

Tectonic plates, the location of the Indonesian earthquake that caused the 26 December 2004 tsunami, and a schematic section of the faulting that caused the earthquake. (Based on data from the US Geological Survey)

Areas in South Africa (in red) that might be most at risk if a tsunami were to strike there. Map: Ian Meiklejohn

estimated to have had a maximum height of 17 m. All the damage was in low-lying coastal areas. More than 292 000 people lost their lives – which is more than twice the capacity of the First National Bank stadium at Soccer City and more than three times the capacity of Johannesburg’s Ellis Park rugby stadium. Estimates are that more than 2 million people were left homeless – a number greater than the entire population of the Tshwane metropolitan area. Damage and the impacts extended to the Indian Ocean islands of the Seychelles and Reunion, and, on the African continent, to Somalia as well as Kenya, which is over 6 000 km away from the epicentre of the earthquake. Tourism is the main income earner in most of Indonesia and could take decades to return to normal. Till now, no accurate estimates of the economic impact of the tsunami are available. Most damage was caused to human-made structures and places where people had changed the natural environment. In the images (right) from the IKONOS satellite of the Lhoknga region of Aceh Province, Sumatra, Indonesia, we can see clearly that the damage was greatest in areas where the natural vegetation had been removed for human development. The lesson to be learnt is that, for our own safety, we need to ensure that the natural environment is preserved. The impact of the earthquake off Indonesia on 26 December 2004 caused the Earth’s rotation to speed

up, thereby shortening our days by nearly 3 microseconds. The cause was a displacement of the Earth’s crust (the Indian Plate) inward, which increased rotational velocity. The effect was similar to that of ice skaters speeding up when they pull in their arms while rotating on the ice. This change in the length of the day is too small to be noticed except by precision instruments.

What would happen if South Africa were hit by a tsunami of similar size? South Africa has a relatively steep coast, so would not experience as much devastation as was recorded in Indonesia. Using Geographic Information Systems (GIS) and a Digital Elevation Model, we identified areas in South Africa where altitudes were less than 20 m, representing parts of the country with elevations that would put them at risk if they were in the path of a large tsunami. The results show that most at risk would be the low-lying areas of northern KwaZulu-Natal (i.e. St Lucia and its surroundings), the southern parts of the Western Cape, the Cape Flats, St Helena Bay, and the Langebaan Lagoon. Obviously, the state of the tides, weather conditions, and local topography would also influence the extent to which a tsunami might affect the country. ■ Professor Ian Meiklejohn and Dr Paul Sumner are in the Department of Geography, Geoinformatics and Meteorology, University of Pretoria.

Images of Lhoknga, Aceh Province, Sumatra, Indonesia, taken by Space Imaging’s IKONOS satellite. Top: Taken before the tsunami, on 10 January 2003. Below: Taken after the tsunami, on 29 December 2004. Note that the greatest damage occurred where humans had cleared the natural environment for development. Courtesy of Space Imaging/CRISP–Singapore

For further details visit the National Oceanic and Atmospheric Administration’s Pacific Marine Environmental Laboratory web site at www.pmel. noaa. gov; News@Nature at www.nature.com/ news/infocus/tsunami; the Tsunami Risks Project at www.nerc-bas.ac.uk/tsunami-risks/index; the United States Geological Survey at www.usgs.gov; Spaceimaging (IKONOS satellite) at www.spaceimaging.com (for images); Digital Globe (QuickBird satellite) at www.digitalglobe.com (for images); and NASA’s Earth Observatory at earthobservatory.nasa.gov

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A new biodiversity-driven approach is being devised to conserve endangered species more effectively, writes Jenny Underhill. Some conservation complexities Conservation is a complicated activity. For a species simply to occur within a protected area, for instance, does not necessarily ensure its long-term survival, nor is every protected area optimal for the survival of the species located within it. To protect a species, what it needs at different stages throughout its life cycle has to be taken into account, e.g. ■ certain fish species, such as salmon, breed in rivers but spend their lives at sea ■ migrant birds need protected areas not only where they breed but also at their migration destinations and along the routes to and from these places. Conservation strategies must consider a multitude of factors when protected areas are being planned, e.g. ■ minimum viable population sizes ■ levels of endemism ■ shifting species distributions in the face of global climate change ■ evolutionary processes. For parks and reserves to conserve endangered species in the most effective way, their location needs to be in areas of high diversity and inhabited by species with limited ranges. As human populations increase, competition for land becomes more intense and conservation is often not a priority, even in important ecosystems.

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cientists believe that the current rate of extinction of species is 1 000 times higher than at any previous time in Earth’s history. At present, approximately 20 000 species are listed as ‘threatened’ on the Red Data List of the Species Survival Commission of the World Conservation Union (IUCN). Human pressure and exploitation of natural resources cause widespread loss of biodiversity. A new approach is called for.


Protected areas National parks and reserves have been effective in conserving species in their natural habitats. Many species facing extinction are restricted to their last remaining refuges within protected areas. The Umfolozi Game Reserve, for example, created in KwaZulu-Natal in 1952, has saved the southern white rhino (Ceratotherium simum) from extinction in southern Africa. In 1996, countries involved in the Fourth World Parks Congress in Caracas, Venezuela, proposed a target of protecting 10% of Earth’s terrestrial habitat. There is deep concern among conservationists, however, that this uniform, percentage-driven approach is inadequate. Biodiversity is unevenly distributed across our planet and certain regions require larger proportions of protected area than others. In many instances, countries close to – or that have already surpassed – the 10% target may still have insufficient protected areas. In countries with less than 10% of their area protected, increased expansion may not be an

immediate priority. It is unrealistic and shortsighted merely to use area targets to determine what protected areas are required for adequate conservation.

The Global Gap Analysis To explore the alternative of using information about biodiversity as a basis for policy, a group of 21 scientists representing all six continents has developed a new approach, the Global Gap Analysis, to assess the global effectiveness of existing protected areas. Two South African scientists were involved, Les Underhill of the Avian Demography Unit (University of Cape Town) and Richard Cowling (University of Port Elizabeth), and the results were first presented at the Fifth World Parks Congress in Durban in September 2003. The main objective of the analysis is to make sure that the Earth’s wealth of biodiversity is adequately represented in a global network of protected areas. The first step was to assess the efficiency with which the current number of protected areas is conserving species. This was only possible once databases containing the exact boundaries of the world’s protected areas became available in 2003. Species distributions were overlaid onto protected area maps using computer-based Geographic Information Systems (GIS) and distribution maps for a total of 11 633 species of terrestrial vertebrates – these included globally threatened bird species, all mammal species, freshwater turtles and tortoises, and

Q Measuring up

Odd measurements How do you measure... ...the speed at which an image registers on photographic film? The American Standards Association (ASA) number measures the speed of developing a photographic emulsion. The speed at which the image registers on the film is proportional to the ASA number. So, ASA 400 film registers an image four times as fast as an ASA 100 film, and twice as fast as ASA 200. The Deutsches Institut für Normung (DIN) number rates speed, too. A difference of 3 in the DIN rating corresponds to a doubling of the film speed; that is, DIN 27 film (ASA 400) is twice as fast as DIN 24 (ASA 200). The International Organization for Standardization (ISO) rating now combines ASA and DIN ratings. For example, ASA 200 film is now marked ISO 200/24°.

Above: The Cape Floristic Region is one of the richest hotspots of floral biodiversity. In this smallest of the world’s six floral kingdoms, more than 9 000 species of plant occur, 6 000 of which are endemic. Establishing areas to protect them is essential. Right: To conserve migratory species such as this grey plover (Pluvialis squafarola), there need to be adequate protected areas at breeding and nonbreeding grounds, at migration ‘stopover’ destinations, and along the access routes. Colour marks and rings, like the ones on this bird, enable scientists to track these routes. Left: The white rhino (Ceratotherium simum) is restricted to a few remaining refuges in protected areas. The creation of the Umfolozi Game Reserve ensured the escape of this charismatic species from extinction in southern Africa.

amphibians. Species were classified as either “covered” (having distributions that overlapped protected areas) or as “gap” (having distributions totally outside protected areas). Of the species analysed, as many as 12% do not inhabit any protected area. Species listed as “threatened” in the IUCN’s Red List were less likely than others to occupy protected areas. Furthermore, the gap species were more localized and had a smaller range than covered species, indicating areas to which many species are endemic*, have restricted ranges, and are most in need of conservation effort. These areas are primarily located in the tropics and on islands. The scientists determined priority areas, using information about ‘irreplaceability’ or ‘threat’. Irreplaceability is a measure of how vital a particular site is to the conservation network: if that site is omitted, certain species will not be located in any protected areas. Threat, or vulnerability, can be defined in terms of the number of threatened species present at a site and is weighted around those at greatest risk of extinction. Sites that combine high irreplaceability with exceptional threat were given the highest conservation priority – here, urgent action is necessary to prevent the loss of unique suites of species. South Africa (like Brazil, Madagascar, and Indonesia, for example) is one of the 17 megadiversity countries, that is, those with a large number of endemics and needing urgent attention to ensure that all these species are covered by the

global protected area network*. Computer analyses of the data yielded further interesting results. If protected areas were equally distributed across the Earth’s land surface, the number of gap species would be higher than it is in the existing network of protected areas. Species would be more effectively represented, however, in a model that incorporated more tropical landmass into parks and reserves than is currently the case. Highest species diversity occurs at lower latitudes. Even though Global Gap Analysis needs refining through the distribution mapping of more species, it shows the need to shift focus away from slavishly following recommended percentage area targets and to plan for greater species representation in protected areas. Most regions needing additional protected areas are in the world’s poorer nations: if conservation is conducted at a global level, however, institutions, foundations, private corporations, and individuals worldwide could meet conservation costs. This might be the only logical path forward to ensure the continued survival of the earth’s living treasures. ■ Jenny Underhill has a special interest in ornithology and in conservation strategies that will most efficiently preserve the world’s wealth of flora and fauna. For more on the Global Gap Analysis, consult A.S.L. Rodrigues et al., Global Gap Analysis: Towards a representative network of protected areas, Advances in Applied Biodiversity Science 5 (Washington, D.C.: Conservation International, 2003), and A.S.L. Rodrigues et al., “Effectiveness of the global protected area network in representing species diversity”, Nature, vol. 428 (2004), pp.640–643.

... the size of small beads? Small ('seed') beads are measured in aughts (/0) ('aught' means nought, zero, nothing). For example, beads of size 11/0 (11 aughts) are slightly less than 2 mm in diameter and you would need about 11 of them for every 20 mm of cord or string. The aught scale is inverted: the smaller the bead, the larger the number of aughts. ... the spaces between honeycomb frames? A beekeeper wanting to dismantle a hive to remove the honey should carefully space the comb frames one bee space apart. Bees seal up an opening that is smaller than a bee space and fill one larger than a bee space with new honeycomb. If, however, the opening is equal to a bee space, the bees leave it open as a passage. The size of a bee space is generally 6.5 mm, but varies according to the strain of bees. ... perceived noisiness? A noy (plural: noys, pronounced 'noise') is the unit used to describe the noise level experienced. One noy, the standard level, is the noisiness of a random noise signal that falls between 910 and 1 090 hertz (Hz) and has a sound pressure level of 40 decibels. The noise of a jet aeroplane taking off is rated at about 100 noys.

* Endemic species (endemism): species located in a particular region and found nowhere else. * Protected area network: a logically chosen collection of protected areas.

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Above: An adult bird and two large chicks in an open nest. Such nests are susceptible during the day to hot temperatures, which then drop dramatically at night. Eggs and chicks are in danger from predators if the adult leaves the nest unattended. Right: African penguins on the shoreline at Robben Island.

Researcher Jenny Griffin explains the difficulties that heat waves bring to penguins when they’re breeding.

Penguins feel the heat hen conditions get too warm, penguins overheat and abandon their nests, especially those species living in warmer temperate regions such as those of Australasia, South America, and southern Africa. Increased temperatures due to global warming could seriously threaten their breeding patterns. To conserve these birds, we needed to find out about their nesting environments, how they react to changes in temperature, and what artificial environments could be created to help them.


African penguin at risk

An active nest in an artificial nest box made of wood, with an A-frame design, a front opening, and a small opening in the back wall near the roof apex. Photographs: Jenny Griffin

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The African penguin (Spheniscus demersus) is endemic to southern Africa and breeds along the coast from Algoa Bay in the east to the Namibian islands off the west coast. It lives in one of the warmest environments of any species of penguin. In the medium-term future it is at risk of extinction in the wild and is listed as “vulnerable” on the Red Data List. Its population has decreased by 90% from an estimated total population of two million in the early 1900s to 170 000 a century later. At first, the reduction in numbers was mainly caused by people collecting penguin eggs for food and scraping guano. This last activity denuded most islands of the kind of substrate within which penguins burrow to protect their nests against

predators and from harsh weather during their breeding cycle. Now that these practices have been stopped, penguin numbers are limited by the availability of food and, crucially, breeding sites that suit them.

Nests for breeding success African penguins come ashore to breed from midJanuary/February and lay clutches of 1–2 eggs. During heat waves in February/March, however, they often abandon their eggs, and it is not unusual for an entire colony to leave their nests. The penguins are adapted for life in coldtemperate waters. They have insulating fatty deposits to prevent hypothermia, and black and white colouring that provides camouflage from predators at sea. These adaptations cause problems of overheating while they are on land incubating eggs and brooding chicks during the breeding season. In southern Africa, penguins are often exposed in late summer to temperatures over 30˚C – and in winter on the Namibian islands too, when hot, dry, east winds often blow from the desert. Robben Island in Table Bay is one of the few breeding colonies of the African penguin where the population is growing. After being exterminated in the 1800s, nine pairs were observed breeding on the island in 1983. The

Fluctuations in nest temperature over time 60 55

What now? The ADU findings echo those of a study conducted in 2002 by Yan Ropert-Coudert’s team from Japan’s National Institute of Polar Research on artificial nest boxes used at a breeding site of little penguins (Eudyptula minor) on Penguin

Temperature (˚C)


numbers steadily increased to over 7 000 pairs recorded in 2002, and between 1992 and 2003 the number of breeding birds more than tripled, reflecting a growth rate of 12.4% per year. This is now the second largest breeding colony of African penguins, with the capacity to expand further. The University of Cape Town’s Avian Demography Unit (ADU) is researching factors that affect the breeding success of African penguins on Robben Island, such as habitat choice, nest type, and microclimates experienced by incubating parents. Our first concern was that removing invasive alien plants (see “Crackdown on invasive aliens” in QUEST vol.1, no.1) such as rooikrans, pines, and eucalyptus, which give shade and protection to nesting penguins, might reduce their breeding productivity, so we tried to assess the suitability of the nest boxes currently used in the colony as an alternative ‘habitat’ option should alien vegetation be targeted for eradication on Robben Island. Second, we suspected that mass abandonment of clutches of eggs during heat waves is not entirely due to the extreme heat stress experienced by all the nest deserters. Penguins breed in dense colonies for the various benefits that big numbers provide, and they synchronize the building of nests and laying of eggs at the start of the breeding season. It seemed possible that, when their neighbours desert their nests because of exposure to high temperatures, birds nesting in cooler shady sites may do the same, not so much because of heat stress as because they then lose the security of numbers. In a sample of nests of various types and different habitat we placed mini-biologgers to record temperatures at 15-minute intervals. Mean temperatures were similar in different types of nest, but the range of variation was of special interest. Variability was greatest in artificial nest boxes, where temperatures were low at night and soared during the heat of the day – possibly owing to poor ventilation and a reduction in the mitigating effect of the cool sea breeze. Temperatures recorded in nests in burrows were more constant than in any other nest types, and these were the only nests not abandoned during a February 2003 heat wave. Temperatures in the nests situated under the shady canopy of alien eucalyptus forests showed the least variation of the nests above ground, but it was still substantially greater than in the burrow nests. Although the canopy nests do not suffer direct radiation from the sun, they are further inland and so are not cooled by the sea breezes. Given reduced air circulation, these nests still have rising temperatures during the day even though they are completely shaded.

45 40 35 30





Nest box


Shade Canopy

10 6

Temperature Minimum Maximum Mean Standard deviation Range



Burrow 18.0 26.5 21.3 1.8 8.8

9 10 Date in February 2003

Open 14.9 43.1 22.9 6.8 28.2



Nest box 15.6 57.7 23.1 7.0 42.1


Shade 13.8 42.1 21.7 5.9 28.3

Canopy 14.3 38.5 21.1 4.5 24.2

Changes in nest temperature (˚C) of various nest types recorded over the period of a week.

Above: Two large chicks in a burrow nest, which offers the best breeding habitat. It is shady and cool with constant temperatures and it protects eggs and small chicks from predators such as kelp gulls.

Island in Western Australia. Temperature was recorded continuously over a 37-day period inside seven nest boxes and the surrounding bush. Temperatures inside nest boxes were always higher than in the surrounding bush, with the difference between the two being greatest around noon. Differences in temperature between boxes and bushes were smaller on windy days, suggesting that better ventilation is needed in the design of nest boxes. ADU researcher, Jessica Kemper, is examining the breeding success of African penguins on Namibian islands. She has used plastic bins cut in half and dug into the ground to form a burrowlike structure. The bins provide suitable protection from the harsh environmental conditions; they limit predation by kelp gulls, are well drained, and have ample space to accommodate two adult penguins with two large chicks. Comparing the breeding success of birds using bins with surface nesters and with those using the abandoned buildings of the guano scrapers, she found that the birds breeding in bins were more successful. Burrows are the optimal habitat of breeding penguins, but these are scarce. Providing artificial nests may be needed to preserve penguins in an environment that is getting warmer, and these need to be carefully designed to mimic the optimal habitat found in nature. ■ Jenny Griffin, a research officer at the Avian Demography Unit, University of Cape Town, is investigating factors that affect the breeding success of African penguins on Robben Island.

Visit the ADU web site for more on its activities and research projects, and for African penguins visit its African penguin page at http://aviandemographyunit.org/ species/sp003_00 and the Southern African Foundation for Conservation of Coastal Birds (SANCCOB) at www.sanccob.co.za/African_penguin Also read R.M. Randall, “Jackass Penguins” in Oceans of Life off Southern Africa edited by A.I.L. Payne and R.J.M. Crawford (Halfway House: Vlaeberg, 1995), pp.34–256; and M. du Toit, L.G. Underhill, and R.J.M. Crawford, African Penguin populations in the Western Cape, South Africa, 1992–2003. (Cape Town: Avian Demography Unit (UCT), 2004). For more on effects of global warming on Antarctic penguins visit http:// explorations.ucsd.edu/penguins/ and go to the National Geographic site http:// news.nationalgeographic.com/news/2002 /01/0117_020117antarcticpenguins for

the article “Ice buildup hampers penguin breeding in Antarctica.” Read the details of artificial nest experiments in Y. RopertCoudert, B. Cannell, and A. Kato, “Temperature inside nest-boxes of little penguin”, Wildlife Society Bulletin, vol. 32 (2004), pp.177–182, and J. Kemper, “African penguins and rubbish bins: population dynamics and conservation in Namibia”, Bird Numbers, vol. 10 (2001), no. 2, pp.25–26 at http://web.uct.ac.za/ depts/stats/adu/bn10_2_00 For information about biologgers visit www.mcsystems.co.za (Used to monitor environmental and physiological parameters, these low-cost instruments weigh 9 g, measure 30  20  10 mm, and can record temperatures in a range from 20°C to 50°C to an accuracy of 0.2°C at intervals from 1 minute to 24 hours; the data are downloaded onto a computer to be viewed graphically.)

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Caption (Kinkle 2)

Rory Paul and Matt Hartley write about the first time they saw a pink elephant. inkle, the Johannesburg Zoo’s large male elephant, had an injured leg with a very swollen elbow, but we didn’t know the cause. Quite by chance, in the middle of July 2004, Kinkle became a test case for a diagnostic procedure that showed us where the problem really lay. Finding out what ails an elephant is not easy. X-ray machines, for instance, are often too small to use on such a large animal. When we came across an article about infrared (IR) thermography used for diagnosing an Indian


18 Quest 1(3) 2 0 0 5

elephant’s injury at a Vancouver zoo, the method seemed to have many advantages, so we applied it to Kinkle. The beauty of using a sensitive IR camera is that it is a ‘passive’ sensor – it does not emit any potentially harmful radiation and it is non-invasive. The animal can be examined speedily and without being touched, so it causes no stress or discomfort. It creates images in ‘real’ time, so Kinkle would not have to endure sedation to immobilize him or transport him anywhere – these are extremely difficult procedures with large animals.

How infrared (IR) thermography works

▲ ▲

In a live body there is a high degree of thermal symmetry (in other words, there is a similar heat profile on both sides of it) so abnormal or asymmetrical changes normally indicate a problem. An imaging radiometer (a kind of IR camera) can ‘see’ in the IR range and calculate the temperature of an object, or an area within it, extremely accurately between 40°C and 2 000°C. Sometimes an injury in an animal isn’t where you first thought it was. A symptom can often show up in one place, while its root cause is in fact somewhere else. In a racehorse, for example, back pain can be a secondary symptom when the root cause is actually in the foot – in such a case the horse is compensating for the foot injury by transferring its weight to the other leg, which causes twisting and stress along the spine. In Kinkle’s case we found that, although his leg was swollen at the elbow, there was, unexpectedly, a major ‘hotspot’ at his ankle caused by blood surging to an injury there. We did not know what had caused the problem but thought that perhaps he had slipped on frosty ground. Kinkle was put on a course of anti-inflammatory medicine (cunningly administered in loaves of bread). After a week we scanned him again to see how he was responding. The treatment was working well and the proof was in the images: the temperature of his elbow and ankle had dropped dramatically. IR thermography has mainly been used for industrial inspection of electrical, mechanical, and structural systems. When we used it on Kinkle, this was the first time that we had applied the technology to assist a live animal patient in the Johannesburg Zoo. The method is not new to veterinary medicine but it is not widespread because the equipment is very expensive, although it is gaining ground in the treatment of racehorses. At the Johannesburg Zoo, we are currently experimenting with thermography to find out whether or not eggs are fertilized. We are also following a number of species, using IR imaging to determine their general health and whether or not they are pregnant. This is helping to build a thermal image database to assist other zoos with diagnostic and reference data. Rory Paul of Phosphor Technologies is a thermographer who works as a volunteer at the Johannesburg Zoo, where Dr Matt Hartley is the manager of veterinary services. For details, contact Rory Paul at roryp@phosphor.co.za and Matt Hartley at pzc@jhbzoo.org.za You’ll find a training provider when you visit www.snellinfrared.com; medical thermography at www.iact-org.org, and infrared imaging news at www.maxtech-intl.com/irnews

Infrared (IR) thermography is the process of remotely monitoring the temperatures and thermal patterns of a wide range of objects and producing ‘heat pictures’, or thermograms. An IR thermography camera measures the IR radiation (‘heat’) emitted from the surface of an object, then converts this measurement into a visible image of the equivalent surface temperature. The camera accurately measures temperatures between 40˚C and 2 000˚C and can display around five temperatures simultaneously in instruments developed for industrial applications. The thermal images are saved to an internal memory card for downloading to a personal computer. The warmer the object or area, the brighter it appears on the camera: white (hottest) through red, yellow, green, blue to black (coldest).

The electromagnetic (EM) spectrum ranges from extremely high-frequency, short-wavelength gamma rays to extremely lowfrequency, long wavelength radio waves. Visible light falls within a narrow range between the two extremes. Colour is a manifestation of wavelength: short waves are violet and longer ones are red. Infrared (‘below red’) and ultraviolet (‘beyond violet’) radiation is unseen energy on either side of the spectrum of visible light. IR radiation (with a wavelength range of approximately 0.7 µm to 1 mm) has an energy level that is easily absorbed by molecules. Absorbed energy causes molecules to rotate and vibrate faster, so we associate the transmission (or radiation) of IR energy with radiation of heat. All objects ‘emit’ heat energy unless they are at absolute zero 273.15˚C (or 0 kelvin), where particle motion no longer occurs. All objects at temperatures above absolute zero, therefore, emit energy that can be detected with equipment sensitive in the IR part of the spectrum. Discovering the infrared part of the electromagnetic spectrum ... The German-born British astronomer, Sir William Herschel (1738–1822), who in 1781 discovered the planet Uranus, is also credited with discovering the infrared part of the electromagnetic spectrum while conducting temperature experiments. He directed sunlight through a glass prism, which broke up the light into colours (ranging from violet, indigo, blue, green, through to yellow, orange, and red). Then, using a thermometer, he measured the temperature of each colour. He found that the temperature increased as the instrument moved from the cooler colours, such as indigo and blue, to the warmer colours, such as orange and red. ‘Beyond’ the red colours he found a large increase in temperature that was not associated with a visible colour. This region is now referred to as the ‘infrared’. The energy in this part of the spectrum cannot be detected with the naked human eye. We scanned large animals as well as some of the smaller ones in the zoo's hospital. Left to right: Kinkle's leg shows the 'hotspots' at ankle and knee; Kinkle's leg after the infrared image was adjusted to show the 'hotspot' temperatures; a healthy rhino (the image shows the live and dead tissue of the horn area); a lame duck with a limp, whose injury showed up in the left leg (red indicates higher temperature); the emu who didn't limp but whose knee was clearly 'hot' – was she hiding the injury so as not to give herself away to a predator?

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... and using infrared (IR) thermography ■ From the mid-1950s onwards, the US military used IR imaging to help with

accurate targeting and surveillance, especially at night. ■ In the 1960s, AGA in Sweden made systems commercially available. They were

heralded as revolutionary, but so large that a truck was needed to move them and their cryogenic cooling systems. (Since then, smaller, lighter, handheld cameras have been developed that do not require cooling. They run on batteries and have higher resolutions, take more reliable radiometric measurements, and have more powerful in-camera analytical software.) ■ In the 1980s the first direct measurement scanning systems became available, allowing for radiometric temperature measurement directly on the image.

Spies in the sky Aerial and orbital IR photography from satellites is used to monitor crop conditions, insect and disease damage, and pollution, as well as to locate mineral deposits. ■ The US Environmental Protection Agency uses thermography to identify sources of pollution such as leaking sewage lines and illegal connections to storm-water drainage systems. (As these sources of pollution leak, seep, or empty into streams, rivers, and lakes, they can be detected because they are normally warmer than the surface of the larger body of water, especially during relatively cool times of the year.) ■ Aerial IR photography is also used in search and rescue operations and in covert surveillance or to ‘see’ military targets. In World War II, IR devices allowed snipers to see their targets in the dark. An IR lamp sends out a beam of IR radiation (also called ‘black light’) and a telescope receiver picks up the returned radiation from the object and converts it into a visible image. Seeing beneath the skin In human medicine, thermography is used to measure body heat emitted by the skin and to detect abnormal variations in temperature that can help to show up a disorder that is invisible to the eye or does not show up on an X-ray film. An unusually cold spot could signal a blockage in the bloodstream; a warm spot may indicate cancer. Thermography can also help to detect back injuries, arthritis, jaw dysfunction, and sports injuries, for example. Industrial applications Today, small units with onboard analytical tools are becoming more common in industry as preventative maintenance tools. Equipment, such as pumps, motors, bearings, pulleys, fans, and engines can be monitored while they are running. One of the biggest problems in mechanical systems is excessive temperature, which can be generated by friction, material loss, or blockages. Excessive friction, in turn, can be caused by wear, misalignment, underor over-lubrication, and misuse. The heat normally produced within a component is not directly visible to the IR camera: for the camera to sense it, it must conduct up through the material and present itself as a pattern on the surface of the object. Once a problem area has been identified, the root cause can be determined through, for example, vibration or oil analysis and ultrasound. Other applications of thermography include: ■ evaluating moisture contamination in buildings, air-conditioning equipment, the flames inside a furnace, heat distribution in underfloor heating, brake and engine systems for performance and cooling efficiency, printed-circuit boards ■ detecting water leaks in flat roofs, gas leaks in boilers, and loss of cooling in cold-storage facilities ■ diagnosing suspension and tyre contact in racing cars ■ inspecting pipelines for leaks and stress corrosion ■ analysing explosions and flame propagation ■ monitoring the condition of high voltage insulators and electrical connections. ■ From the top: A pickup truck (horizontal surfaces exposed to open sky cool faster than vertical surfaces; the cold sky is reflected in the front window and bonnet while the rear wheel is in sunlight); a bearing running hot; infrared image of a faulty electrical fuse; an electricity substation; a hot water shower. Pictures: Courtesy of Phosphor Technologies

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Keith Manchester captures the highlights of the long and productive career of Sydney Brenner, South African-born Nobel laureate. NOTE: An asterisk following a term indicates that it is defined on p. 25. he latter half of the 20th century, the golden age in the history of biology, had Sydney Brenner as a principal contributor. From modest beginnings, he became one of the most distinguished and influential scientists of his time. Now in his 78th year and still active, Brenner has been at the forefront of many major developments of the subject area called molecular biology.

Early years Brenner was born of poor and illiterate Lithuanian and Latvian Jewish immigrants in Germiston in 1927. As a small boy he would visit a widowed family friend whose kitchen table was covered with newspapers in place of a tablecloth, so by the age of four he could read quite fluently. By the time he matriculated at 14 he was three years younger than the others in his class. The following year he entered the University of the Witwatersrand to study medicine. Because he would have qualified before the legal age to practise, he interrupted his medical curriculum, first to take a medical B.Sc. in anatomy and physiology in 1945,

22 Quest 1(3) 2 0 0 5

then a B.Sc. (Hons) in histology in 1946, followed by an M.Sc. in anatomy in 1947. His M.Sc. dissertation reflected an increasing interest in staining properties of chromosomes* (that is, the properties of chromosomes that allow them to take up coloured dyes, making them visible under a microscope – particularly important because chromosomes are associated with cell division and the passing on of genetic properties) and their relationship with genes*. In this work, Brenner determined the chromosome number of the little shrew, Elephantulus. By now he had no interest in practising medicine and wanted to pursue a career in science. Professor Raymond Dart, the charismatic head of Anatomy and dean of the faculty, persuaded him to complete his medical degree, which he did in 1951, since this would help him to develop a career as a biochemist.

England To further his studies abroad, Brenner first applied to the Biochemistry Department at Cambridge University, which failed to reply (a long-standing

grievance). Instead he worked for his doctorate with the professor of physical chemistry at Oxford, Sir Cyril Hinshelwood, who was working on drug resistance in bacteria and suggested to Brenner that he work on bacteriophage* resistance in bacteria to show that this phenomenon is an adaptation not a mutation. Brenner took up the project enthusiastically – but had to convince his supervisor that the phenomenon was in fact due to mutation not adaptation! England gave Brenner the break he needed. He heard Fred Sanger lecture on the recently elucidated amino acid* sequence of the two-chain insulin molecule, the first real proof that proteins* had a precise and fixed structure. He met James Watson and Francis Crick early in 1953 and saw the epoch-making model of the double helical structure* for DNA* which they had just proposed. As Brenner says in My Life in Science, “When I saw the DNA structure [it] was the first time I recognised the real concept of the genetic code.” The structure made him understand clearly the underlying explanation – that one

linear sequence (the sequence of bases* in DNA) could map directly onto another linear sequence (the sequence of amino acids in protein) – and provided a single central principle of great explanatory power. As he himself said, “It made copying DNA easy to understand. It made gene expression easy to understand. It made gene mapping easy to understand. And it made mutation* easy to understand.” It also united genetics and biochemistry. At the end of 1954, Brenner, armed with his Oxford D.Phil., returned to South Africa to the Department of Physiology at the University of the Witwatersrand, where he successfully set up a laboratory to work on phage* genetics, but he left again at the end of 1956 for the Medical Research Council Unit in the Cavendish Laboratory in Cambridge, where his long and fruitful collaboration with Francis Crick began in earnest. “The important thrill about research,” maintained Brenner, was “the social interaction, the companionship that comes from two people’s minds playing on each other.”

Messenger RNA

fewer than 1 000 cells, was the first (and is possibly still the only) animal for which the complete cell lineage and entire neuronal wiring diagram is known. For this work, carried out in Cambridge, the Nobel committee honoured Brenner with the 2002 Prize for physiology or medicine. The award “for their discoveries concerning genetic regulation of organ development and programmed cell death” was divided equally between Brenner, now a Distinguished Research Professor at the Salk Institute in California, Robert Horvitz of the Massachusetts Institute of Technology, and John Sulston, formerly Director of the Sanger Institute in Cambridge. The choice for the Nobel committee of names to honour could not have been easy. Sulston, with unprecedented precision in experimental manipulation, worked out the complete embryonic cell lineage of C. elegans from zygote to newly hatched larva. John White, in the same laboratory, but not included in the prize, performed the also unprecedented feat of determining the complete ‘wiring diagram’ of the worm’s nervous system consisting of

‘The Worm’ Despite spectacular achievements to date, by the early 1960s Brenner’s restless mind felt that it was time for him to seek new pastures: “The most important thing we know about living systems is that they’ve got genes in them. It is through genes that one living system propagates descendants that look like it. Thus all explanations of living systems have to be couched in the form of genes. That in nature like produces like is surely the oldest biological observation.” Because the development of an organism is written in our genes, we need to learn how our genes build that organism and, in particular, how they build a brain and a nervous system. It was Brenner who decided, after years of searching, that for such a study the soil nematode (Caenorhabditis elegans)* was the most suitable model organism. This tiny worm, comprising

▲ ▲

The postulation of the double helix in 1953 by Watson and Crick explained the physical nature of genes and how information can be stored, but the following years were a period of intense speculation on the mechanism by which this information is used in protein formation. A breakthrough was the famous Good Friday meeting in 1960 when, in the course of a discussion with a group of visiting scientists, Brenner first conceived of the existence of messenger RNA*. By this time, it was widely known that particles called ribosomes* joined amino acids together to form proteins. Brenner realised that when a gene is expressed, its coded information for a particular protein is handed on to a newly synthesised and short-lived species of RNA, which constitutes a message. This then becomes physically associated with the ribosome*, where it specifies the joining of amino acids in a particular sequence without the need for new ribosomes to form. These views were substantiated experimentally with François Jacob of the Pasteur Institute in Paris, and published in 1961. (In

fact, the existence of RNA, which proved to be the messenger, had already been observed, but its function not understood.) In that year, Brenner and Crick published a key paper on the general nature of the genetic code for proteins, the result of genetic experiments.

Left: A wild type Caenorhabditis elegans that was partially immobilized by placing dry ice on the slide on which it was resting. This caused it to coil slightly. Photograph: Courtesy of Erik Jorgensen, University of Utah

Below: The basic body plan of the soil nematode C. elegans (adult anatomy). Pharynx Dorsal nerve chord


Anus Hypodermis

Ventral nerve chord

Nematode worms – ideal for experiment and observation The soil nematode, Caenorhabditis elegans [C. elegans], is small in size (1 mm long and 40 micrometres in cross section). It lays 200 eggs at a time, which hatch within 12 hours, and the larvae grow rapidly to 1 mm in three and a half days. These worms can be bred in large numbers in glass petri dishes and fed on bacteria or liver extract. They can be stored frozen (to halt cell division) and revived, and, because they are transparent, their cells can be watched through a microscope as they divide. They also have the right sexuality for genetic experiments, being self-fertilizing hermaphrodites with about 0.1% males, so the genes are identical in all individuals: they are ‘clones’. C. elegans has only 6 different kinds of chromosome. Its 15 000 genes (humans have perhaps about 25 000) control the production of only 959 adult cells (humans have 100 trillion adult cells). The small size and small number of cells make this work suitable for a study by electron microscopy aimed at resolving the entire wiring diagram (that is, the intercellular connections) of the nervous system.

* Bacteriophage (or phage): a virus that can penetrate a bacterial cell, multiplying there and killing the bacterium. * Phenotype: the outward appearance of an organism, determined by the interaction of its genetic constitution and the environment.

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about 5 000 chemical synapses, 2 000 neuromuscular junctions and 600 gap junctions. Sulston’s work led to the discovery that certain cells always die at specific developmental stages through programmed cell death* (apoptosis*). Horvitz identified the first two genuine ‘death genes’ (ced-3 and ced-4) and showed them to be absolutely required for apoptosis to proceed. Sulston and his team subsequently sequenced the C. elegans genome of 100 million base pairs, and made the complete sequence – the first of a multicellular organism – available in 1998. Now several hundred laboratories worldwide actively work on C. elegans, substantiating Brenner’s claim that initiating this as a model experimental organism was “a monumental achievement because it generated a kind of industry of science”. The system could be fully exploited only with the

(Left to right) Professor Sydney Brenner, Minister Mosibudi Mangena, and Professor Phillip Tobias at the Inaugural Professor Phillip Tobias Lecture 2004, delivered by Professor Brenner in Midrand, Gauteng on 2 November 2004. Photograph: Courtesy of the Department of Science and Technology

advent of what he called ‘inside-out’ genetics – the possibility of making modifications to the gene, then looking for phenotypic* changes. Brenner has always been an extraordinarily hard laboratory worker and by 1973 he had identified a set of 77 genes in the C. elegans organism (which he named ‘unc’ genes), mutants of which produce uncoordinated movement and seem to play a key role in developmental or functional neurobiology.

Puffer fish By 1983, Brenner felt that the pioneering work with C. elegans was over and that, again, it was time to focus elsewhere. Cloning and sequencing techniques had developed to allow characterization of genes directly instead of having to deduce their properties from their effects. Since it was known that the genomes of tetraodontoid fish are particularly small, and, seeking a model vertebrate genome for developmental study at a time when the sequencing of the human genome lay in the future, he alighted on the Japanese puffer fish (Fugu rubripes), whose number of genes (around 31 000), determined from homology searches, is not so different from ours. Though its genomic complexity is so much less, due to a very small amount of repetitive sequences and small introns*, its information content is very similar to that of the human genome. Its haploid genome* contains 365 million base pairs* of DNA, of which more than 90% are unique. This genome is

8 times smaller than the human genome and, because it has a similar repertoire, it is the best model to use for discovering human genes. Indeed, almost 1 000 novel putative human genes have been thus identified.

Coda In his Nobel lecture in Stockholm in 2002, Brenner described his continuing excitement at research and the prospect of what can be done in biology. In November 2004, in his Inaugural Professor Phillip Tobias Lecture at Midrand, he proposed that “we need [now] to create human based research because Man is the next model organism, and the technical developments in the life sciences now allow us to approach and solve many of our medical problems directly in human beings.” ■ Emeritus Professor Keith Manchester is attached to the School of Molecular and Cell Biology at the University of the Witwatersrand. Former head of the Department of Biochemistry there, he has a longstanding interest in the history of science. For more, read Sydney Brenner, My Life in Science: as told to Lewis Wolpert (London: BioMed Central, 2001), and for Brenner’s Nobel lecture of 8 December 2002, visit http://nobelprize.org/medicine/ laureates/2002 For local perspectives read Phillip V. Tobias, "Sydney Brenner, Nobel laureate 2002: his early years at Wits", South African Journal of Science, vol. 99 (2003), pp.11–12; and Jane Dugard, "Sydney Brenner, South African-born Nobel laureate", in DART, newsletter of the Institute for the Study of Mankind in Africa, vol. 4, no. 2 (2003). Read about the human genome in Matt Ridley's Genome (London: Fourth Estate, 1999) and John Sulston and Georgina Ferry's The Common Thread (London and New York: Bantam Press, 2002).

2004 Nobel Prizes in the natural sciences Physiology or medicine – Richard Axel (Columbia University, New York) and Linda Buck (Fred Hutchinson Cancer Research Center, Seattle) "for their discoveries of odorant receptors and the organization of the olfactory system". They have explained the basis of our sense of smell and how we recognize and remember about 10 000 different odours. These laureates identified a family of about 1 000 different genes (3% of our genes) that give rise to an equivalent number of olfactory receptor types, and described the complex mechanism by which we consciously experience the scent of a lilac flower in spring and recall this olfactory memory later. Physics – David J. Gross (University of California, Santa Barbara), H. David Politzer (Caltech, Pasadena), and Frank Wilczek (MIT, Cambridge) "for the discovery of asymptotic freedom in the theory of the strong interaction". The strong force, or 'colour force', is dominant in the atomic nucleus and acts between the quarks inside the proton and the neutron. These laureates theorized that when the quarks approach each other the 'colour charge' weakens till, when they're close enough, it so weakens that they behave almost as free particles – a phenomenon called 'asymptotic freedom'. With distance the force becomes stronger (like a rubber band: the more the band is stretched, the stronger is the force). Their discovery led to a new theory (called quantum chromodynamics [QCD]) helping to explain why quarks behave as free particles only at extremely high energies. Physics has come a step closer to its dream of formulating a unified theory that also encompasses gravity. Chemistry – Aaron Ciechanover and Avram Hershko (Israel Institute of Technology, Haifa) and Irwin Rose (University of California, Irvine) "for the discovery of ubiquitin-mediated protein degradation". They showed that the cell functions as a checking station where proteins are built up and broken down at a furious rate. In the controlled degradation process, the proteins to be broken down are given a molecular label called ubiquitin (a 'kiss of death'), then destroyed. Now we understand at molecular level how the cell breaks down certain proteins and not others (for example, in cell division or DNA repair). When the degradation fails to work correctly, we fall ill. Cervical cancer and cystic fibrosis are two examples. Understanding this process gives opportunities to develop drugs against such diseases. For more, visit http://nobelprize.org

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Q Fact file

DNA (deoxyribonucleic acid) is our hereditary code script and genetic repository. The abundant proteins in the cells of our bodies are the chemical workhorses that carry out our metabolism: their structure and formation depend on the blueprints stored in the DNA. Proteins have 20 different building blocks, amino acids, joined in a specific linear fashion several hundred to more than a thousand times. Nucleotides are the building blocks of molecules of DNA and RNA (see below). They are joined together linearly millions of times. Each nucleotide has three parts: a pentose sugar (deoxyribose in DNA and ribose in RNA), a phosphate unit, and one of four nitrogen bases – in DNA, the bases are adenine, cytosine, guanine, and thymine (that is, A, C, G and T). The amount of A is always equal to T and that of C is equal to G, whereas the amounts of A and T relative to C and G vary widely in different organisms. This and other information suggested to James Watson and Francis Crick that the DNA molecule was three-dimensional and comprised two chains, not one, wound around each other in a helical fashion such that opposite an A in one chain was always a T in the other, and, similarly, C was always opposite G. Each chain is complementary to, not the same as the other, and the two chains run in opposite directions. The outer part of each helix comprises alternating sugar (deoxyribose) and phosphate molecules, with pairs of bases in the centre, like the rungs of a ladder joining the two chains together. A long strand of DNA is easily broken, a serious problem where DNA is our hereditary blueprint. The double helix consolidates the two chains, making them less fragile and protecting the bases from external influences. The coding information contained in DNA is built on the four bases, consisting of a vast linear sequence. Every succession of three bases codes for one of the 20 amino acids used to make protein. If we read off the letters of the DNA code three at a time, we know to what amino acid sequence it corresponds. (Codon is the term – coined by Brenner – for a code of three letters at a time, that is, of each sequence of three nucleotides in a DNA or a messenger RNA molecule.)

A string of codons of DNA provides the information for joining amino acid molecules in a specified sequence, thus producing a particular protein. Codon sequences, therefore, by prescribing what proteins are synthesized, determine what kinds of plants or animals develop from seeds or eggs. A chromosome is a rod-shaped body in the cell, made up of structural protein and the DNA, whose genetic information constitutes the genes. Each human cell has 46 chromosomes, or 23 pairs (22 of which occur in identical pairs, while the 23rd pair is the sex chromosomes – XX for females and XY for males). A genome is the entire base sequence of all the DNA (all the chromosomes) of an organism. Genes are sequences of base triplets. Each length of DNA that codes for a specific protein, together with various ancillary features involved in its reading, constitutes a gene. (Strangely, in higher organisms, genes often possess long sequences of bases, called introns, that are in fact not part of the coding sequence [exons] and have to be excised in the production of messenger RNA.) A gene, as part of the cell's DNA, can replicate and mutate; it passes on a trait from parent to offspring. Genes control the division and differentiation of cells to form tissues and organs. RNA (ribonucleic acid) is also a chain of nucleotides and is needed by all organisms for protein synthesis. In contrast to DNA, it is single stranded and includes: ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA (mRNA, which transports codon sequences from DNA to the ribosomes in cell cytoplasm [fluid]). In certain viruses, RNA also acts as the hereditary material transmitted from one generation to the next. Highly specific sequences of bases provide blueprints for the synthesis of different proteins. Ribosomes are structures in the cytoplasm of a cell. They consist of RNA and protein and, when primed with mRNA, synthesize proteins from amino acids. Clusters of ribosomes linked together by a strand of mRNA are called polyribosomes (or polysomes). In protein synthesis, a specific gene directs the production of a particular protein on the ribosome. The gene acts as a template for the manufacture of mRNA.

The mRNA detaches from the DNA and attaches to the ribosomes; tRNA carries amino acids to the ribosomes. The amino acids are linked together (in the order coded by the mRNA) to form protein, in a process called translation. The way in which genes bring about development is through the process of cell differentiation. A multicellular organism, such as a human, starts life as a fertilized egg, which divides repeatedly to produce an embryo consisting of many cells. The cells become 'differentiated' as they mature and some of them become specialized in some aspect of structure and function. Groups of similar cells form 'tissues' such as fat tissue, muscle tissue, nerve tissue, and so on. Different combinations of tissues make up 'organs' like the heart, the liver, and the stomach. New cells are formed by cell division all the time – in human adults, about a thousand billion cells each day. Many old cells die daily. This controlled death of cells is called programmed cell death (or apoptosis). ■ Did you know? ■ There are around 100 000 000 000 000

= 1014 cells in the human body, each containing the same number of genes and (except for the germ cells) the same number of chromosomes and the same amount of DNA. ■ The human genome contains about

3 billion nucleotide units (3 000 000 000 or 3 x 109 base pairs), in 23 sections (one section in each chromosome). ■ The linear length of a chain of 3 billion

nucleotides is about 1 metre. ■ The DNA of all the (1014) cells in our

body put together in a continuous piece would stretch to the sun and back 350 times. (DNA strands are normally tightly coiled to allow their long linear length to fit the minute dimensions of our cells.) ■ We are thought to possess about

25 000 different genes (October 2004 estimate). ■ We now know the precise sequence of

all the bases, A, C, G, and T in human DNA. Its 3 billion letters represent the contents of about 200 telephone directories with 1 000 pages in each.

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How can fire science help to guide ecosystem management and what are the challenges for South Africa? Brian van Wilgen examines the contentious role of fire.

Summer fire in fynbos vegetation in the Cedarberg. Such fires are common in the Western Cape and a vital part of fynbos ecology. Photograph: B.W. van Wilgen

ire is one of the oldest issues in Africa’s vegetation ecology. Aspects of its role remain contentious, and its use in ecosystem management continues to be debated, but much of this dialogue can be informed by good science.


Fires in African landscapes More of Africa burns each year than any other continent on Earth. Fires always happen when three necessary elements come together: enough fuel of the right kind; warm, dry weather; and a source of ignition. Most fires in Africa are fuelled by grasses that grow in its vast savannas – Africa has the largest area of savannas in the world, and most areas of this continent enjoy an extended warm, dry Fire statistics for Africa south of the equator Vegetation type

Total area (1 000 km2)

Fire return period (years)

Forests Savannas Grasslands Fynbos Karoo and desert

1 149 7 033 638 74 665

10–100 2–10 2–10 10–20 Almost never burn

Area that burns each year (1 000 km2) 59 1 427 166 6 4

season. Humans and lightning provide ample sources of ignition. So frequent veld fires are inevitable. Without fire, our ecosystems would look quite different, since the fires promote the growth of grasses and they prevent the development of dense woodlands and forests. Long before human evolution, fire was a significant factor determining vegetation structure. The evolution of C4 grasslands* 6–8 million years ago was accompanied by increased occurrence of fire. If it were possible to exclude fires, we would see increases in tree density and size in drier areas where annual rainfall is below 650 mm; and fire-sensitive forests would develop in wetter areas where rainfall exceeds 650 mm. Forests can and do develop in areas sheltered from regular fires, and they tend to have fuel properties that do not promote fire, which ensures their survival in the fire-prone landscape, but they cover less than 0.25% of the landscape of Africa. Fires, therefore, are integral to the ecology of most African ecosystems and ecologists need to know about fires if they want to study vegetation dynamics or to manage ecosystems

* C4 grasslands: The photosynthetic pathways of grasses are either of the C3 type (which is a carbon-fixing pathway that is most efficient where the growing season is cool in temperate or high altitude environments), or the tropical C4 type (which is more efficient where the growing season is warm).

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Top left: Abundant grasses growing in the Kruger National Park after good rainfall. Below: Low levels of grass fuel after a year or two of below-average rainfall. Such areas cannot burn even in very hot and dry climatic conditions. Right: Island of indigenous forest among fire-prone grasslands at Cathedral Peak in the Drakensberg. Photographs: B.W. van Wilgen

Why some ecosystems burn and others don’t In the Drakensberg in KwaZulu-Natal, the high annual rainfall of 1 400 mm would normally mean that forests develop. However, regular fires restrict the fire-sensitive forests to sheltered areas where fires do not penetrate. These areas develop ‘fuel’ properties that make it difficult for fires to burn, such as moist, compacted litter layers and widely-separated leaves with high moisture content. In the savannas of the Kruger National Park, where rainfall is far more variable from year to year, the same area may burn in some years (when rainfall is high, and enough grass grows to support a fire) and not in others (when rainfall is low, and grass fuels are sparse or absent).

properly. Many plant species are ‘firedependent’ in that they need fires to complete their life cycles and would become extinct without them. So ecological fire science combines an understanding of organisms’ dependence on fires with the physics of fire, to help us manage fire-prone ecosystems better.

Left: Fire lily (Cyrtanthus contractus) flowering two days after a fire (Hluhluwe Game Reserve, KwaZulu-Natal). These plants flower only and immediately after fires, releasing seeds to germinate in the post-fire environment. Photograph: B.W. van Wilgen Right: Species such as these aristeas (Aristea major) are stimulated by fires into mass flowering. Fires are the trigger for most of their germination and reproduction. Photograph: G.G. Forsyth

How and why ecosystems burn

Plant adaptations to fire There is much evidence that plants in fire-prone environments are well adapted to surviving fires, and that in many cases they need fires to survive. Examples include: ■ Sprouting – a large proportion of plants in fire-prone areas are able to sprout after fire, either from below-ground roots or bulbs, or from epicormic buds* protected below thick bark. ■ Serotiny* – some plants (for example proteas) hold their annual production of seeds in ‘fire-proof’ flowers. When the plants are killed in fires, the seeds are released and germinate following the next rains. For such species fires are essential: without fire to clear away competing plants, the seeds cannot germinate. ■ Smoke-stimulated germination – the seeds of many plant species are stimulated to germinate by the chemical cocktails contained in smoke. (‘Smoke extract’ is sold commercially to help seeds to germinate.) ■ Fire-stimulated flowering – many species are stimulated to flower, often en masse, following fires. Fires thus offer the best opportunity for seed production and germination of these plants. ■ Flammability – some plants may even have evolved properties that make them more prone to burning, such as the ability to produce lots of dead material and high flammable oil contents in their leaves. This may have given them an evolutionary advantage through killing their neighbours and creating space for their own progeny to thrive!

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Fire ecology begins with an understanding of how and why plants burn. Attributes that make some plants prone to fire include the ability to produce a lot of dead material (such as grasses that die back each year), low moisture content in live leaves, and a particular arrangement of plant parts that allows for an optimum air-fuel mix. (If material is tightly packed, for instance, it is less likely to burn because there is not enough air space in between. An optimal arrangement allows enough air space to feed the fire, with sufficient material close by for fire to be able to spread.) Fire-prone vegetation is made up of many plant species that collectively have attributes that promote fire. These include low decomposition rates (allowing for dead plant material to accumulate) and low palatability (which means

* Epicormic buds are buds, situated under the bark of trees, that sprout after fire. * Serotiny: serotinous species are those that protect their seeds in cones or other structures that open on the death of the plant (e.g. in a fire) and release the seeds into the post-fire environment.

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Managing fires on a landscape scale The terms ‘controlled’ or ‘prescribed’ burning often describe the practice of burning the veld deliberately. Reasons include: ensuring that fires occur in vegetation that needs it (for conservation reasons); to remove old growth and stimulate the growth of green grass (for grazing); and to remove fuel by burning under moderate weather conditions, with the aim of pre-empting dangerous wildfires at the peak of the fire season. Nature is in a constant state of flux, significantly influenced by factors such as variable and unpredictable rainfall cycles. Most attempts to impose regular fire regimes onto ecosystems have proved naive. Variation in fires is necessary to promote biodiversity (that is, the full suite of organisms that occur in the landscape). Certain fire return periods may favour one species over another, and variation in the long term is needed for both to survive. On a larger scale, forest patches occur embedded in fire-prone grasslands and fynbos shrublands, and their continued existence requires regular fire in some places and infrequent fire in others. Variation in the intensity of fires may be the reason that trees and grasses coexist in savannas. Imposing regular low-intensity fires may promote ‘bush encroachment’ at the expense of grasses. Recent evidence from the Kruger National Park suggests that attempts to manipulate the fire regime through imposing prescribed burning, or fire suppression, over the past 50 years have had little real effect on the actual area that burns each year. Rather, the area that burns is related to rainfall, which in turn determines how much grass there is to burn. In the Cedarberg wilderness in the Western Cape, a policy of ‘no fires’ (suppressing all fires that occurred) failed to prevent the many wildfires. When this was replaced by one of prescribed burning in an attempt to reduce the incidence of large wildfires, the number and size of wildfires was found to be unaffected despite regular prescribed burning for 14 years. Fire managers in conservation areas now talk about ‘adaptive management’, where approaches to fire management are based on best available knowledge, but are deliberately changed as new evidence or understanding develops. Attempts to ‘command and control’ fire regimes are becoming less common.

that, because of its taste, herbivores don’t eat the vegetation). So, for example, ‘sour’ grasslands and fynbos shrublands are sparsely grazed, and fires remove the accumulated fuel. Many vegetation types are not fire-prone, however: deserts and karoo shrublands do not accumulate much fuel; forests have high moisture contents and high decomposition rates; and grazing animals consume most of the ‘fuel’ in ‘sweet’ grassveld before it can burn. Foresters historically led the study of the ‘fuel properties’ of ecosystems mainly so that they could understand how to deal with fires that threatened forests.

Are fires good or bad? Fires are not uniformly bad. They’re needed to maintain healthy ecosystems and biodiversity in many parts of South Africa and elsewhere. But they can and do destroy crops and houses, and kill livestock and even people. Scientists need to understand very clearly where and under what conditions fires are desirable, and where and when they may not be. Given that fires are often inevitable, we also need to understand if and how we can prevent and contain them, and get them to burn under conditions that will bring maximum benefits and minimum costs. These are the questions that drive ‘fire science’.

What is fire science?

Above: A team ignites a prescribed fire in the Kruger National Park, using a road as a safe fuelbreak. Fires in such savanna vegetation are normally carried out in the dry winter months, at intervals of between two and six years. Photograph: B.W. van Wilgen Below: Igniting a prescribed burn in fynbos vegetation in the Western Cape. In this vegetation, fires are normally carried out in late summer or early autumn at intervals of between 12 and 15 years. Photograph: R.A. Haynes

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Fire science has essentially two branches – the physical study of the phenomenon of fire and the ecology of fire. The two fields of study complement each other, and the practice of fire management requires a basic understanding of both. On the physical side, we need to know what influences the spread and intensity of fires. This

means understanding ‘fuels’ (the spatial arrangement and chemistry of plant parts that make up fuel), the factors that influence fuel moisture, and the effects of weather and topography on the propagation and spread of fires. Scientists have developed intricate mathematical models to predict fire intensity and spread, to assess how fires will behave (for purposes of control), and to relate fire behaviour to the ways in which plants and animals respond. Physical fire scientists have developed a range of terms to describe fires. People often speak of ‘hot fires’ and ‘cool fires’, but orange flames all have roughly the same temperature (around 1 000°C), so all fires are in fact ‘hot’ (you’ll still burn yourself if you stick your finger into a ‘cool’ fire!). It is more correct to refer to the intensity of fires, which is significantly variable, and which depends on the amount of fuel available to burn and also on the conditions under which fires burn. Fire ecology is the study of plant and animal adaptations and responses to fires at various levels. The study of single species is needed to understand in detail how that species responds to fires. At a landscape level, ecologists try to understand how complex communities of species in fire-prone landscapes respond to repeated fires or to the exclusion of fire. Their work may include studies of ways in which firesensitive and fire-adapted communities coexist in fire-prone landscapes. Recently, scientists have become increasingly interested in the role of vegetation fires as sources of ‘greenhouse gases’ in the global atmosphere. Such understanding is needed for

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Right: Satellite picture of fires over southern Africa. Photograph: Courtesy of NASA – Goddard Space Flight Center Scientific Visualization Studio

Below left: A low-intensity fire burning in the grass layers of savanna vegetation. It releases energy at a low to moderate rate; one could approach such a fire on foot. Photograph: B.W. van Wilgen

Below right: A high-intensity fire burning in the crowns of a pine tree. Such fires release energy at a high rate, and it is impossible to approach such a fire on foot. Photograph: J.D. Goldammer

Measuring fire intensity

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‘Fireline intensity’ is the most widely used measure of fire intensity, and is normally strongly correlated with the impacts of fire on ecosystems. It is calculated as the product of three factors. ■ Heat yields are measured in joules per gram (J g1) of the fuel material: they are normally around 20 000 J g1 and vary so little (by about 10%) that they can be considered constant. ■ Fuel loads are measured in grams per square metre (g m2) and can vary in savannas from about 10 to 1 000 g m2. ■ Rates of spread are measured in metres per second (m s1) or metres per minute (m min1): they can vary from 0.1 to 100 m min1. By cancelling the units describing heat yields, fuel loads, and rates of spread when multiplying, one is left with units of joules per metre per second. One joule per second is equal to 1 watt, and because of the large numbers involved, kilowatts (kW) are normally used. The unit for fire intensity is therefore kW per metre (kW m1) and describes the rate of energy release in kW per metre of the fire front. The measure has a practical range from 10 to over 20 000 kW m1, primarily due to the large variation possible in spread rates.

developing global climate models that will help to predict the effects of global climate change. While such change is now known to be driven largely by the burning of fossil fuels, the contribution of vegetation fires needs to be factored in to gain a complete picture. The net contribution by fires of carbon dioxide (CO2) to the atmosphere is rapidly reabsorbed as the vegetation recovers after fires, but the same cannot be said for other gases. About 500 Gg (1 Gg = 1 billion [109] grams) of methane (CH4) and 450 Gg of nitrous oxide (N2O) find their way into the atmosphere each year as a result of fires in sub-Saharan Africa. Whether or not this represents an increase due to more fires started by ever-growing numbers of people is not clear, as we have no data on the frequency and intensity of fires before the start of the industrial revolution in the 1800s.

Why we need to study fires Scientists are interested in fires for many reasons. Obviously, we need to understand fires to be able to protect ourselves from their harmful effects. However, fires are also inevitable. Our combination of fire-prone vegetation and warm, dry climates means that fires have occurred for possibly millions of years and will continue to do so. Fires are also needed for healthy ecosystems to survive, and for maintaining the valuable services that these ecosystems provide. We have to learn to

live with fires, and for this we must study and know them better. Many standard ecological textbooks do not deal with fire ecology in much detail, if at all. This may be because the science of ecology seems to have been developed in parts of the world where fires are not common – in Europe and along the east coast of America – so the phenomenon did not attract serious attention from scholars in those regions. The situation is changing, however, as the global importance of fires becomes more apparent. Ecologists living and working in southern Africa (and other parts of the world as well) now know that fire is important and that we cannot interpret vegetation dynamics without referring to it.

What fire scientists and fire managers do Fire ecologists study the ways in which fires affect ecosystems. South Africa has a long, proud history of fire ecology, whose roots are in forestry and in pasture science (where researchers examined the effects of fire, combined with grazing, on the composition and quality of the veld). Pasture scientists pioneered the first burning experiments in South Africa in 1918, and forestry researchers were responsible for some of the most extensive burning experiments in the country. There are good examples of such experiments, where a range of different fire

Elements of a fire regime Ecologists use the term ‘fire regime’ to describe the typical combination of elements that characterize fires in a given region. Fire scientists need to understand what these fire regimes are, how they vary, if and how they are changing, and what the consequences of changes would be. Element of fire regime

What it measures



How often fires occur (i.e. the interval between fires on the same spot)

Fires occur every year in some infertile grasslands, less frequently in savannas and fynbos (every 3–15 years), and almost never in deserts and wet forests


The time of year at which fires occur

Many geographic regions have a warm, dry season when most fires can occur. In South Africa, hot, dry summers are the fire season in the Mediterranean climate regions of South Africa, while the dry winters provide these conditions in most other areas.


How fiercely fires burn (i.e. the rate at which energy is released by fires)

Fire intensity is the product of heat yield, the mass of fuel consumed, and the rate at which it is consumed. As a rule of thumb, flame lengths are good indicators of fire intensity.


What kind of fires occur

Fires can be headfires (burning with the wind) or backfires (burning against the wind). In addition, fires can be surface fires (burning in the understorey layers of forests) or crown fires (burning in the canopies of trees).


The area covered by the fires

Ecosystems usually experience many small fires and a few big ones, but typically it is the big ones that matter, as they burn up to 90% of the area.


How much successive fires in the same area vary in terms of frequency, season, type, and intensity

No two fires are the same, and variation in elements of the fire regime over successive fires often allows for species to coexist. All elements can and should vary. This is always difficult to measure and one of the biggest challenges for fire scientists.

regimes (called ‘treatments’) were applied to plots or larger areas of up to several hundred hectares. The results of these experiments have been used to formulate management guidelines for farming and conservation areas around the country. Researchers also try to understand the risks that fires pose. Fire danger rating systems have been developed, or adapted from elsewhere, to assist in the assessment of risk – that is, in the likelihood of fires, and the relative difficulty of controlling them, based on the prevailing conditions of fuel and weather. South Africa’s new Veld and Forest Fire Act, Act 101 of 1998, requires a national system of fire danger rating to be established. Once in place, this system will issue daily ratings of fire danger that will govern whether or not people will be allowed to ignite fires in the open air; it will also dictate the levels of preparedness of fire-fighting forces. Land managers use fire in different ways for different purposes. These include rejuvenating fire-prone vegetation for agricultural or conservation purposes, combating invasive alien plants, and preparing firebreaks. Managers are also often involved in fire suppression, where fires have to be extinguished or contained if they pose any threat to people or property. For all these purposes, fire managers rely on knowledge generated by researchers and supplemented by hands-on experience. Good fire managers normally have some scientific training and a good deal of practical experience.

Fire science in the future

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Many exciting challenges face fire scientists. New ecological concepts of flux, as opposed to a ‘balance’ of nature, have led to the

formulation of new fire policies that promote flexibility and variability in many South African conservation areas. A range of policies has been proposed in several such areas, but none applies universally, so there’s much to be done in interpreting, understanding, and customizing fire policies. Global climate change also presents significant challenges for fire managers in the future, but there has been to date no analysis of the increased risks, if any. Higher temperatures or lower rainfall could increase the possibility of fire. In savannas, frequent fires strongly suppress tree saplings and thereby control tree dominance. Changes in atmospheric CO2 concentrations could influence tree cover in such metastable ecosystems by altering post-burn recovery rates. Lower CO2 concentrations would favour the spread of grasses (and fire) and lead to less tree cover. Predicted increases in CO2 concentrations will therefore lead to increases in woody vegetation (‘bush encroachment’), a trend that would have to be countered through the application of intense, frequent fires, rather than by striving to replicate ‘natural’ fire regimes. Invasion of natural ecosystems by alien plants threatens ecosystem integrity across the world.

Prescribed burns on experimental plots in the Kruger National Park. Above: Scientists sample smoke emissions from a low-intensity prescribed burn. Photograph: B.W. van Wilgen Below: A long-term study near Satara. In the middle is a firebreak between two plots. The plot on the right has been protected from fire for over 40 years, while that on the left has been burned every two years during that time, with profound influence on the vegetation. Photograph: W.S.W. Trollope

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Determining the rules for prescribed burns: an example from the fynbos The study of fire ecology can lead to the formulation of guidelines for managers wishing to practice prescribed burning. As shown below, management questions can be addressed by formulating rules based on ecological understanding. Management question

Basis for answering question

Examples of ecological knowledge that guides rule formulation


How often should I burn?

It depends upon • how frequent fires have to be to start eliminating species • how species are affected by long intervals without fire.

Proteas require at least 6–8 years to Burn at intervals between mature and to set seeds between fires. 10 and 15 years. Fires more frequent than this would eliminate them. On the other hand, long (>25 year) periods without fire result in senescence* and proteas disappear.

When should I burn?

It depends upon • the particular times of the year when plants and animals are more likely to survive fires.

Proteas and other plants show maximum Burn between mid-November and mid-April. seedling recruitment after summer Avoid winter or spring burns. or early autumn burns. Most species flower in winter and spring, and seeds only ripen in summer.

How intense should fires be? Fires must be intense enough to trigger biological responses, but not so intense that they become dangerous.

Flame length calculations are based on fuel and weather. The levels of intensity needed to stimulate seed germination need to be known.

Burn under warm, dry conditions, but avoid windy days that would increase flame lengths and make fires uncontrollable.

Where should I burn?

The age at which plants mature, and therefore will have seeds, determines the lower limit. The age at which plants begin to die (senesce) provides an upper limit. Accurate records of the date of the last burn are also useful, especially if stored on Geographic Information Systems (GIS).

Burn only in those areas where at least 50% of the slowest-maturing species have flowered for at least three successive seasons. Prioritize areas for burning where the vegetation is approaching senescence.

Areas that ‘need’ fire include those where fire has not occurred for a long time as well as those in which there is a risk of senescence*.

Such invasions can alter the fuel properties and fire regimes of ecosystems. In South Africa, the greatest threats come from the invasion of fynbos shrublands by alien trees and shrubs, which increase fuel loads and fire intensity, leading in turn to severe erosion and impoverished plant communities. Invasion of other ecosystems by alien grasses, and the consequent introduction of fire into previously fire-free areas, also pose large potential threats to the species-rich succulent Karoo (the world’s only arid biodiversity hotspot). Last but not least, growing human populations mean that the impacts of fires are increasingly felt. South Africa’s new Veld and Forest Fire Act includes the formation of fire protection associations (FPAs). The question of where the administration of the act should lie is currently being addressed (for example, if it is run by ‘disaster management’, the approach to fire management would be quite different to one adopted by the Department of Environmental Affairs and Tourism). More of the right people are needed to manage fires at the level of FPAs – and there’s work to be done to build and draw on a body of sound South African fire science. ■ Dr Brian van Wilgen is at the CSIR Division of Water, Environment and Forestry Technology in Stellenbosch. He has researched the ecology and management of fires in South African fynbos and savanna ecosystems for the past 30 years.

Proteas live only for about 25–30 years; then they senesce and die. Here, the dried flowers opened and released seeds into unburnt vegetation, where they will fail to germinate. Proteas need fires, which kill adult plants, but stimulate seed release and germination and are necessary in the life cycle of the plant. Photograph: B.W. van Wilgen For a broad overview of fire ecology read W.J. Bond and B.W. van Wilgen, Plants and Fire (London: Chapman & Hall, 1996) and W.J. Bond’s section “Fire”, in Vegetation of southern Africa, edited by R.M. Cowling, D.M. Richardson, and S.M. Pierce (Cambridge: Cambridge University Press, 1997). For studies concerning South African conservation, consult the following articles: W.J. Bond and S. Archibald, “Confronting complexity: Fire policy choices in South African savanna parks”, International Journal of Wildland Fire, vol. 12 (2003), pp.381–389; B.W. van Wilgen, H.C. Biggs, and A.L.F. Potgieter, “Fire management and research in the Kruger National Park, with suggestions on the detection of thresholds of potential concern”, Koedoe, vol. 41 (1998), pp.69–87; and B.W. van Wilgen, N. Govender, H.C. Biggs, D. Ntsala, and X.N. Funda, “Response of savanna fire regimes to changing fire management policies in a large African national park”, Conservation Biology, vol.18 (2004), pp.1533–1540. For interesting facts and figures about fires, as well as work opportunities in the field and satellite pictures of recent and current fire activity around the globe, go to the Global Fire Monitoring Center web site at www.fire.uni-freiburg.de

* Senescence is a term describing vegetation in which the majority of individual plants of a dominant plant species are dead or dying.

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The S&T tourist Q

Veld walk in the city Towns and cities around South Africa have protected areas where visitors can explore nature or geology or prehistoric remains. Johannesburg’s Melville Koppies Nature Reserve offers all three. ust seven kilometres from the city centre are the Melville Koppies, an unspoilt, peaceful, rural island of nature with panoramic views of Johannesburg, where you can walk and put at a distance the stresses, demands, and tension of city life. Covering just 160 ha, the site gives visitors a landscape of complex geology, with relics of human life from the Stone and Iron Ages, and a variety of indigenous plants, animals, and birds.


The geology

Top: Taking a walk on Melville Koppies West and looking east. The darker line running from left to right near the horizon is the geological fault that splits the quartzite ridges. Beyers Naudé Drive runs through this fault. Photograph: Maria Cabaco

Middle: One of the African Independent Church groups that gather on the Koppies each Sunday. Over 500 members of 20 church circles in the association meet on the Koppies. Photograph: Derek Davey

Below: A section of the 2.9-billion-yearold iron-stained quartzite ridge. Photograph: Maria Cabaco

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About 2 500 million years ago, the Melville Koppies area was part of a large inland sea or lake. Rivers that had flowed into it brought large amounts of eroded rock, which settled into various layers of mud and sand. With time, the centre of the lake gradually subsided, creating upturned edges like those of a saucer. The great weight of deposited material compacted the original mud, sand, and pebbles into hard rocks known as shale, quartzite, and thin bands (called ‘reefs’) of gold-bearing conglomerate, respectively. Visitors to the Koppies can clearly see the hard quartzite ridges with softer shale valleys. The quartzite forms the rocky ridges running from east to west along the reserve and is resistant to weathering and erosion. There is virtually no soil on the quartzite, and what there is is mildly acidic with few nutrients. Quartzite is a metamorphic rock originally derived from sandstone; it is the product of great heat and/or pressure. Normally white to pinkish in colour, it may also be brown on the surface as a result of iron oxide staining. The shale is a fine-grained sedimentary rock, caused by deposits of very fine particles at the

time when the Witwatersrand was still a lake. Shale is prone to weathering and we see it in the depressions between the quartzite ridges. Its colour varies from light grey, blue grey, and green to pink, pinkish brown, and deep brown. The soils that come from shale are more fertile than those developed from quartzite. Near the bottom of the Melville Koppies slope, the soil colour is distinctly red and clayey, formed from a rock called diorite. Higher up, however, the soil becomes lighter in colour because of sand from the quartzite.

Early human occupants Archaeological remains in the upper terrace of the central section of the Melville Koppies (by the lecture hut) show that people lived there throughout prehistory. • Hand axes of the Earlier Stone Age have been discovered, and these may date back as far as 100 000 years ago. • At a depth of one metre a Middle Stone Age camp was found (perhaps 40 000 years old). • The remains of a Late Stone Age camp indicate a place where ancient hunters (probably bushmen) left their stone weapons and stone tools as well as very small knives and skinscrapers. They would have belonged to a group of people who hunted all over Gauteng and beyond until a few centuries ago. • At 30 cm below the surface of the ground lies an Iron Age floor (possibly 1 000 years old), and a 600-year-old Iron Age furnace is on display under glass. Perhaps as early as at the beginning of the first millennium A.D., warriors from the north, armed with metal weapons, invaded and occupied the




Clockwise (from left): 1. Low-walled reconstructed ruin in the Central section (probably a cattle kraal); smaller circular sections perhaps for smaller domestic animals. 2. A shaped Stone Age axe used for general purposes. 3. On the left, part of a woman's tool for hoeing crops such as sorghum; on the right, the haft of this iron spear head would be inserted vertically through a hole drilled into a short stick, fixed with a gummy root juice, and bound with leather for a good hand grip. 4. A grinding stone for crushing sorghum, millet, and mealies; the powder was used to make porridge or beer. 5. A mountain fern nestling between rocks is protected from fire. 6. Sharp thorns on the Acacia robusta deter grazers. 7. A member of the large Asteraceae family: the central disc florets are fertile, and the infertile outer ray florets are colourful to attract pollinators. 8. A profusion of pompom-like flowers on the Acacia robusta. Other acacias have catkin-like flowers. Photographs: Maria Cabaco

entire region. It was rich in iron ore, and these Iron Age people built thousands of villages, opened many iron, copper, and tin mines and started the first farming communities. To forge iron for their spears, knives, hoes, and blades, they built smelting furnaces, two of which have been excavated. The iron workers left hundreds of fragments of charcoal, slag, raw iron, and broken blowpipes on the furnace floors, and charcoal samples have been dated to around the year 1400. The remains of the Iron Age settlements at Melville Koppies have a similar layout and structure to many hundreds of ruins of kraals, villages, and even towns found in the area from Lydenburg to Marico. In a low-walled reconstructed ruin south of the ancient Melville furnace we can see what was probably a cattle kraal, and smaller circular sections for domestic animals like sheep or goats: one could have been a communal reserve granary hut to supply visitors. The world of these cultures was torn to pieces when the Zulu impis of Mzilikazi swept through the Magaliesberg and Witwatersrand area in 1823. After that came the first European prospectors, farmers, and traders.

The bush The typical highveld landscape of the Koppies is largely grassland, with trees and shrubs on the northern slopes where there is shelter from the frost and, among the rocks, shelter from fires. Here, you can walk on grassy slopes – rich in pre-rain flora in spring and with aloes flowering in winter – through well-wooded areas, and along natural terraces higher up on the quartzite ridges. A wide variety of species has been recorded at the Melville Koppies: • 13 mammal species • over 200 species of birdlife • 12 species of snake, as well as many lizards and tortoises • some 60 insect species, as well as arachnids (such as spiders and scorpions) • 548 species of flora (62 trees, 16 shrubs, 59 grasses, 411 herbs): two are on the world’s Red Data List and vulnerable to extinction. ■ For more information about the Melville Koppies, the research undertaken there, what visitors can see and do, and what’s happening in Gauteng conservancies, visit www.veld.org.za; as you walk, consult the excellent Melville Koppies Nature Reserve Guidebook (revised 2002).

General information The three sections of the Melville Koppies Nature Reserve are open to visitors (if you plan to walk, wear strong shoes and carry drinking water). ■ The Western section (overlooking the Westpark Cemetery) covers 100 ha and is 3 km long. It is always open to the public and to dogs. For access and parking go to the cul-de-sac in Arundel Road, Westdene. You’ll find hiking trail maps in the little red postbox in 3rd Avenue, Westdene. Alternatively, join a guided tour on the 1st Saturday of each month at 07:30 or book at other times. For tours to services of the African Independent Churches contact Deanna at 083 266 9949; for abseiling contact Derek at 082 606 3563. ■ The Eastern section covers about 10 ha and is nearly 1 km long. It is always open to people and to dogs. Access it from streets leading off 7th Avenue, Melville or from Zambezi Road, Emmarentia. ■ The Central section (about 50 ha), with its Iron Age furnace, is a fencedoff national heritage site and nature reserve. No dogs are allowed and the public has access during specified periods on the first three Sundays of each month (1st and 3rd Sundays of each month September–April from 15:00 to 18:00 and May–August from 14:00 to 17:00; 2nd Sunday of each month all year round from 08:30 to 11:30). For group tours at other times contact Wendy Carstens at (011) 482 4797; for hands-on courses for schools (grades 4 and 7) contact Di Beeton at (011) 888 4831 or arrange other school group visits. There is a paved trail suitable for wheelchairs (book access in advance). Park at the Marks Park Sports Club in Judith Road, Emmarentia. Join a Melville Koppies work party on the last weekend of each month. The Koppies are managed and maintained by volunteers on behalf of Johannesburg City Parks, so assistance is welcome.




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Viewpoint Q

Why bother with What’s the use of physics in a developing country like South Africa? We start 2005, the International Year of Physics, with comments from the country’s senior physicist Frank Nabarro and his colleague Robert de Mello Koch.

What difference can the International Year of Physics make to South Africa? Frank Nabarro (FN): It’s an opportunity to emphasize the importance of physics. We all get stomach ache so we’re aware of the importance of medicine. The influence of physics is indirect, so we don’t recognize it straight away. It could help if the public knows more about it. And alerting politicians to what physics is and does in this country could tip the balance. It might, for instance, goad the Department of Education into somehow improving the teaching of science in schools. What is the importance of physics? FN: It underlies almost all technologies. Virtually every industry employs engineers trained by physicists. To discover what things do, you have to know that they react to forces. The study of forces is physics: its many applications require other expertise to be superimposed. Although it might be an overstatement to say that the future of technological development is where the physicists are, physics is terribly important – even in developments in molecular biology, for instance, which are swamping the whole of the physical sciences. Look at the Nobel laureates: Sidney Brenner has a very deep understanding of physics; Francis Crick was a physicist. The number of physicists in western countries seems to be shrinking. What are the implications? FN: China and Japan will take over. I believe that physics is growing in those countries and they’ve got the more dictatorial structures to be able to do what needs to be done. In a

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need is to improve old materials – making better ones (taking account of the local climate, raw materials, and so on) and making cheaper ones. As southern Africa develops, South Africa is in a wonderful position to grow economically by doing the technology that underpins this development.

Frank Nabarro

Robert de Mello Koch

totally random view of an issue of Scripta Materialia of last November, for instance – a research journal in just one branch of physics, materials science – seven out of twelve articles were either partly or completely written by oriental scientists. Robert de Mello Koch (RK): Shrinking numbers have implications for society as a whole, particularly for developing new technologies. You can get new technology by finding new ways to apply existing technology: for this, you need to understand the available technology well, as engineers do. But to invent genuinely new technology you need to understand basic science, including physics. What can your sort of physics do for South Africa? FN: My interest is in materials. Government likes new materials, but I believe that in southern Africa the real

Which old materials are worth improving or making cheaper? FN: All of them. For example, consider concrete, which is a very complicated material. It’s normally made from calcium carbonate. In South Africa we have dolomite, which is calcium magnesium carbonate. Materials scientist Nico Stutterheim worked out how to make decent cement out of this local raw material, which people can now do in local conditions. That is really important. An underlying set of physical principles forms the basis of this kind of thinking. If they’re ingrained in us, we’ve got opportunities. Why do physics in South Africa instead of just focusing on applications? FN: I’d say we can’t have contact with the big world of physics without some leading-edge physicists. You’ll only keep the people who are determined to do leading-edge physics if you let them do it. Sir Basil Schonland argued that, in choosing the expensive projects, one should choose those where there is a natural advantage, or need, or local expertise that you want to keep. He himself went from work on lightning to work on rock physics because that was needed. In addition, we must keep the bright people. If we can afford it, they should be given all the resources they need. If we can’t, then we should, say, invite them to spend a few weeks here every year at our expense.

Q Viewpoint

RK: We need physics to develop those things from which countries get value. When we trade in high tech applications – such as developing software – we sell knowledge. But for such sophisticated products we need physicists and other experts engaging with basic science to support the work of engineers and train the next generation for high-level inventiveness. We must maintain and develop the science behind innovation in South Africa and think beyond the short term.

imagining a situation in which it could be tested, once the means to do so were found. FN: There can be very good physics in applying new knowledge, and in the fields of applied physics (as distinct from engineering) there’s work that’s socially and financially rewarding though less obviously glamorous. Many young scientists want to work at the frontiers but we need good people at the rock face. For example, a local group is exploring ways to make grinding materials that are stronger and cheaper than diamonds by asking what might happen if we put certain elements together to form a crystal and what would be its properties. That kind of research is very important. We have to strike a balance: most of the jobs are in the latter type of work. RK: It’s partly a problem of education. Students registering for physics are conditioned into expecting to do things like string theory or astrophysics, while everything else fades into the background.

Nevertheless, there’s money in it, so people who’ve done it all along now say, “Look, we’re in the forefront.” Some exciting things will come of nano, such as new medicines and new communications, but will this really be the Nano Age? It’s new to the extent that the surface properties of matter differ from the bulk properties. And when [because of the tiny size of the nano scale] half the atoms in a particle lie close to the surface you really do have a different material. There are two branches of nano: nanoscience (the making of small particles) and nanomechanics (nanomachining). The machinery is very expensive, and I doubt if South Africa can compete in nanomechanics.

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What about the current state of physics? FN: It worries me and others that the exciting physics is in elementary particle theory and cosmology, string and brane theory, and, at the other What has South Africa end, biophysics, in which this country contributed, given limited is very weak. But industry needs resources and distance from traditional physics, which now seems other physicists? dull – because we know so much of FN: Schonland on lightning was a it through work done in the early world leader. Astronomers have done 20th century – unless you get well – double stars was once a big involved in the nature of space and thing, and that work has been very time and mass and force by asking important. The first sensible orbit of philosophical questions, which is no Sputnik was determined in South longer really physics. Africa at Hartebeesthoek, as I RK: We need to pay less attention to remember, by people using rather fashions and fads and assess each simple means, while elsewhere more area on its scientific merit – just The study of sophisticated groups were still because something is new working on it! There were the forces is physics: its doesn’t mean it’s valid. Every technologies, of course, like the so often, some field emerges as many applications require tellurometer and the Scheffel exciting and new – past bogie. Leading work on analysis other expertise examples include quantum of rock bursts in mines has been computing and string theory. done here. Jack Gledhill and the Nanotechnology seems to be in radio noise from one of the moons of fashion right now. Often, after some Jupiter was important. I think South progress is made, a few practitioners FN: There’s great satisfaction for a Africa has played a big part in oversell and make wild claims that physicist when your work gets back Antarctic research. R.W. James, in one might never be realized. This is the to society in some tangible way. All master’s class, had two future Nobel wrong way to promote a field. I also sorts of applications in the electronic laureates: Aaron Klug and Allan believe it’s unhealthy for any one field, nuclear energy, and things like Cormack. The cosmic ray work at field to dominate. A democracy of artificial isotopes and nuclear Potchefstroom is world class. They fields is better, where each competes medicine have been important. were doing work on cosmic rays 40 for students and for funding. It’s And there’s nano, of course, where or 50 years ago. It’s grown and detrimental for fields that are not there’s a technical point of confusion. they’ve supported their good people. popular to be deprived of support, We live in three dimensions. If a thing and for fields that are currently How could the Department of is small in all three dimensions, that’s popular not to be sufficiently Education improve the teaching certainly a nanoparticle. If it’s small in challenged. of physics in schools? two dimensions (a wire or a little In string theory, for instance, it’s FN: They could designate a few tube, for example) then we accept difficult at present to make direct universities to have strong centres of that as nano. If a thing is small in one contact with experiment, so in such a science education and give tied dimension it’s a surface layer, and field we need to work to higher bursaries for undergraduates, who surface layer science dates back to standards because it lacks the would then be well paid if they the year dot. The nano people have discipline of experiment. It’s hard stayed in teaching and who’d have to tried to incorporate that, and those when you’re working at the very repay their bursaries if they left. working on surface layers are willing edge of physics, but studying a For attracting children, lorry to be incorporated, but there’s still a problem means asking ‘Is this demonstrations are useful. We’d need confusion of ideas. solution in principle testable?’ and several to cover South Africa. Another

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Q Viewpoint

thing would be to make a cheap physics kit available to schools, for the whole class to use with their very own hands instead of just reading about experiments in text books. It would come with variants to accommodate different energy sources – one for schools whose only source is paraffin, for example, and another for those who have bottled gas but not electricity. RK: Our teachers should be paid better – their current pay reflects the fact that teaching is insufficiently respected. Taiwan is different, for instance: with good money in teaching there’s competition, and so many apply that the authorities can select and employ those who are really best for the job. What should government spend on science? FN: Statistics show a strong correlation between growth of the GNP and government expenditure on research. So we scientists say, “See? Spend more money on research and your GNP grows.” Cynics say, “With a growing GNP we can afford to spend more money on science.” RK: I think the cynics are wrong! FN: If South Africa can afford expensive projects for physics, then the Southern African Large Telescope (SALT) and the Square Kilometre Array (SKA) bid are well chosen because they use our geographical advantages. The synchrotron is not a geographical choice but it’s an important tool. An essential factor will be to determine if South Africa has the scientists qualified to use it. RK: Theoretical physics is cheap, which should be factored into decisions because it’s easier to be internationally competitive in this area. With the worldwide web, I hardly need to travel any more. Conference slides appear on the web together with the audio file, and I can ask questions myself by e-mail. The web brings us closer than was ever possible before. We aren’t eliminated from the world community of theoretical physicists just because we live and work a continent away. Research papers are posted on an electronic bulletin board before their formal publication, so you have early access to work that will be published. These changes in communication,

especially for theoreticians, make geographical location far less of an issue than in the past. How can government use the Year of Physics to uplift this very important discipline? FN: They should seriously try to prioritize the large number of desirable developments in the latest report, Shaping the Future of Physics in South Africa. Invite bids. Make each proposal include a cost-benefit analysis and a realistic estimate of the qualified people available. The inclination is to present hypothetical benefits. Government should try to address feasibility too and then prioritize.

The web brings us closer than was ever possible before. We aren’t eliminated from world theoretical physics just because we work a continent away. RK: There’s been countrywide collaboration to prepare a national facility in theoretical physics, with a few full-time research appointments as well as postdocs. This facility would be cheap, compared with iThemba LABS in the Cape, for instance, and we’d increase the community of theoretical physicists in the country by about 15% or more. That’s incredible value for money. Does South Africa have enough physicists? FN: It’s hard to get good staff. In terms of pay, there’s no reason for a good physicist to leave Europe or the USA. For the long term, I don’t think South Africa has the resources to keep the very top people, but it ought to be able to develop its own Ph.D.s. Postdocs should travel to experience something else. But what’s to attract them when they return? The Oppenheimer scheme offered financial incentives for them to return for a certain number of years. Some then settled back. But it’s very difficult: if they’re white, they may feel there’s a glass ceiling; if they’re black, they feel pressure to take on

senior administrative positions rather than to make their reputations as scientists. [Director-General of the Department of Science and Technology] Rob Adam, though, has the clever idea that leading international institutes should be encouraged to set up their headquarters in African countries. RK: We don’t have enough physicists. Subsidy cuts at universities and the rising average age of researchers are a worry. Good departments that attract and retain good staff take decades to build: they must be maintained as assets and not be allowed to shrink. Then we’ll build an environment in South African physics in which a new generation of people, whose disadvantaged backgrounds kept them back in the past, can get good teaching and can flourish. FN: There’s a fantastic gap between what scientists think is the need for physics in industry and what in fact are the practical demands. Perhaps, to answer the question ‘Is it better in post-apartheid South Africa to invest in primary education than in tertiary education?’ we have to nurture universities as a longer-term investment that will help us to build a new environment for science in the country – including physics. ■ Professor Frank Nabarro FRS was head of the Physics department at the University of the Witwatersrand from 1953 to 1977 and then founded the Solid State Physics Research Unit, which he fostered and headed till 1984. He remains active in physics at Wits as an Honorary Research Professorial Fellow. Professor Robert de Mello Koch, also at the Wits School of Physics, wrote an article selected in late 2001 by the ISI Essential Science Indicators as a ‘fast breaking paper’ (that is, among the 1% of the most highly cited international papers in his field in that bimonthly period). Visit the South African Institute of Physics web site at www.saip.org.za for the report, Shaping the Future of Physics in South Africa, and for local information about the International Year of Physics; for world physics visit the Institute of Physics at www.iop.org; for a mirror of the famous arXiv bulletin boards, maintained and administered by the Wits Centre for Theoretical Physics, go to http://za.arXiv.org/ Discover interesting South African science projects by visiting the SALT telescope web site at www.salt.ac.za, the SKA site at www.ska.ac.za, and the Stellenbosch Institute for Advanced Study at http://academic.sun.ac.za/stias/; for UCT’s role in an international project to detect the quark-gluon plasma go to http://hep.phy.uct.ac.za/~cleymans/uct-alice For physics education projects visit the African Institute for Mathematical Science at http://aims.ac.za/english/ and the South African National Astrophysics and Space Science Programme at www.star.ac.za; for the international view go to http://education.iop.org

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Books Q

Fire goby (Nemateleotris magnifica)

Sixstripe wrasse (Pseudocheilinus hexataenia)

Pineapplefish (Monocentris japonica)

Coastal Fishes of Southern Africa. Royal angelfish (Pygoplites diacanthus)

By Phil and Elaine Heemstra (Grahamstown: National Inquiry Service Centre and the South African Institute for Aquatic Biodiversity, 2004). ISBN 1 920033 01 7

his easy-to-use and easy-to-carryaround fish guide covers the shallow water coastal fishes in the southern African region from Namibia through South Africa into Mozambique, and includes some deep-sea or pelagic species of interest to those who fish for sport or commercial purposes. It’s a must for identifying fish around this coastline and indispensable for divers, aquarists, researchers, ichthyologists, anglers, and fish-watchers alike. The southern African coast is one of Earth’s richest, most biologically diverse, and oceanographically complex marine environments. Its 1 800 species (excluding fishes occupying ocean depths below 200 m) represent about 80% of the world’s shallow water marine fish families. This great range and number of species is due partly to the range of temperature in the region (from tropical to cool-temperate) and partly to the variety of habitats – coral reefs, estuaries, sandy beaches, rocky shores, mud flats, mangroves, kelp beds, and ocean depths of more than 5 km. A high proportion (about 16%) of our coastal fish species are endemic, known only from southern Africa. Phil Heemstra has been an ichthyologist for 40 years. “Early in my career I got hooked on fish taxonomy,” he explains, “and on questions like ‘How do you tell


Blue and yellow rockcod (Epinephelus flavocaeruleus)

Ragged-tooth shark (Carcharias taurus)

Short alfonsino (Centroberyx spinosus) Pictures: Elaine Heemstra

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one species from another? How do you separate males from females, or juveniles from adults of the same species? How do you recognize related species?’ “ Discoveries in this scientific field are growing fast and, in the past decade alone, more than 100 new species have been discovered. With Margaret Smith, Heemstra co-edited the comprehensive 1 047-page Smiths’ Sea Fishes (1986), covering more than 2 000 species and used to identify marine fishes all over the world. But scientific natural history books cannot easily stay updated – nor can a large heavy volume be used on the beach – so the smaller, more portable Coastal Fishes was planned. The main species accounts were limited to 400 ‘common’ or particularly interesting species, Heemstra explains: “Complying was difficult, as some fish commonly seen by scuba-divers may rarely be caught by anglers and never seen in tide pools, and I wanted to include all the shallow water species in our area.” The introduction covers the anatomy and biology of fishes, details of the southern African marine environment, interaction of people and fishes, fish names and classification, and an illustrated guide to fish families in the book. Each main species account has colour paintings for easy identification and includes basics such as size at maturity, maximum size, diet, type of reproduction, habitat,

Q Books New books The Mammal Guide of Southern Africa. By Burger Cillié (Pretoria: Briza Publications, 2004). ISBN 1 875093 45 1

Bluebanded snapper (Lutjanus kasmira)

Knysna seahorse (Hippocampus capensis)

behaviour, distribution (worldwide and in southern Africa), edibility, suitability for the aquarium, and fishing restrictions. Readers can glimpse the astonishing variety of life among coastal fishes – in their reproduction habits, for instance. “Most fish are oviparous and release their eggs into the water when they are spawning or deposit the eggs on the bottom,” says Heemstra, “but some are viviparous (give birth to their young). In certain species (like the ragged-tooth shark) unborn pups practise intra-uterine cannibalism (with the largest pup feeding on eggs and its smaller siblings) in the later months of the 9–12-month gestation period, and the pups (one in each oviduct) are about one metre long at birth.” Phil and Elaine Heemstra wrote the text together, and all the paintings are hers. Illustrating fishes has its challenges, she explains, particularly when it comes to size and colour. “Ideally, I start each painting by looking at specimens. This

was not possible with larger sharks and I had to rely on good photographs. The South African Institute for Aquatic Biodiversity (SAIAB), where Phil and I work, has an excellent collection of southern African fishes – like a fish library (with the fish in bottles or bins). But when fish die they lose their exquisite colour, and the fish in the SAIAB collection are a symphony of brown and black, so an accurate colour source is essential.” Many common fishes had never been photographed in colour for the SAIAB image collection, but help came from students at Rhodes, who took or lent photographs and collected specimens. “With Phil’s encouragement I learnt to scuba-dive and seeing live fish under water was fascinating. On a field trip to the Comoros, soon after qualifying as a diver, I was drawing under water on my slate – so engrossed in trying to capture details as I floated near the reef that before I knew it I was seasick under water. Never again! Now I just make abbreviated colour notes under water and rough sketches of details to jog my memory later.” For both Phil and Elaine Heemstra, Coastal Fishes was “a labour of love, fun, and a lot of hard work.” Their beautiful book will encourage its readers to find out more about fishes, their wonderful diversity, and the extraordinary world beneath the surface of the sea. ■

Having first appeared in 1985, this book is now fully revised and updated. It is written for game watchers, hikers, and everyone who wants to identify easily and quickly the 120 or so of the region's most common land mammals. The easily portable volume uses colour photographs, diagrams, maps, and identification symbols to describe each animal at a glance. The mammals are grouped as ungulates (animals whose last joint of the toes is covered with a horn-like hoof, including antelope, pig, zebra, and giraffe), very large mammals (browsers with bare greyish skin and large feet: elephant, rhino, and hippopotamus), and carnivores (cat- and dog-like animals that hunt their prey or are scavengers, such as lion, hyaena, jackal, and mongoose), and a new section for small mammals covers small browsers, omnivores, and insectivores. Each description gives the animal's conservation status, size, food, life expectancy, enemies, habits, voice, and breeding characteristics, as well as habitat and the area in which it is found, spoor, and habits. It's a book worth having and using again and again.

Evolving Eden: An Illustrated Guide to the Evolution of the African LargeMammal Fauna. By Alan Turner and Mauricio Antón (New York: Columbia University Press, 2004). ). ISBN 0 231 11944 5 Covering some 35 million years of evolution, Turner presents – and Antón beautifully illustrates – the drama of continental drift and climate change, physical alterations in Africa's landscapes, and the biological evolution of its mammals, including our human ancestors. The notion of Africa as the cradle of humankind implies an African Eden, with warm climate, rich vegetation, and variety of animal species. Hominids evolved here in the context of other mammalian communities with all kinds of fellow travellers in different localities. This book draws on meticulous fossil reconstruction, based on detailed anatomical research and new dating, and it compares fossil forms and species living today. It introduces clearly and accessibly the thorny issues and debates in modern evolutionary theory. It will be welcomed by everyone – specialist and general reader alike – who takes a serious interest in human origins. QUEST readers can order Rebirth of Science in Africa: A Shared Vision for Life and Environmental Sciences (edited by Himansu Baijnath and Yashica Singh) direct from the publisher at a special price of R130 (incl. p&p). Contact Umdaus Press, PO Box 11059, Hatfield 0028; tel. (011) 880 0273; fax (011) 788 1498.

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Letters Q

Letters to Environmental costs and benefits wish to take issue with George Ellis’s Viewpoint portrayal last year of ‘environmental absolutism’ (QUEST, vol. 1, no. 1). I agree with concerns about fundamentalism of whatever kind, but we need to understand that at the heart of the three issues he raises lie the problem of the costs and benefits of alternatives and the question ‘who pays and who benefits?’ Commenting on the Pebble Bed Modular Reactor (PBMR), Ellis presents a limited, supply-side analysis of the energy debate. He compares the PBMR to other sources of energy, but nowhere does he mention demand management. I once demonstrated that it was possible to reduce by as much as 60% the use of energy by visitors to the Kruger National Park. Although such savings would be impossible across the country, the facts indicate that our efforts at conserving energy are still in their infancy. Strong focus on energy conservation could postpone controversial choices about augmenting our energy supply. We also need more aggressively to explore the use of escalating block-rate tariffs and peak-demand tariffs. A comprehensive resource–economic assessment of demand-management and supply-side alternatives, which factors in all externalities, would show that the best returns on investment come from a focus on demand-management options. This approach would also have greater benefits for poorer and small-scale users, whereas the supplyside options subsidize (predominantly rich) big users. In the matter of genetically modified (GM) crops, there are well-founded concerns about our understanding of the full consequences of the choices we face – such as, for example, irreversibility and potential invasiveness. Again the concern is around


‘who pays and who benefits’ in a field where the powerful companies can wield control over farmers – especially over resource-poor farmers. The development of GM organisms is driven by profit-orientated interests that can seriously compromise the integrity for which Ellis argues. I am sure that experts in previous decades (who were paid by industry) were confident about their chemical practices in agriculture, yet clearly did not anticipate their subsequent development of super-pests. While GM organisms perhaps do get disproportionate adverse attention (relative to bigger issues such as climate change and invasive aliens), it is perhaps dogmatic to dismiss genuine concerns as ‘environmental absolutism’. Finally, in writing of the battle against invasive alien species, Ellis seems to confuse ‘alien’ and ‘invasive alien’ species. Many alien species are very beneficial in terms of food, fibre, building materials, objects of beauty, for instance. It’s the invasive alien species – those that swamp indigenous species – which are and need to be the object of attention. The problem of invasives is so great that we cannot (and do not) waste money on ‘controlling’ alien species that are not invasive and do no harm. To state that “fynbos was in its own time an alien invader” shows little understanding. It is also factually wrong to say that felling gums and pines in Newlands Forest will “result in suburban flooding from time to time”. The converse is true. Fynbos and Afro-montane forest are far better at regulating water flows than are stands of invasive alien plants. With regard to the invasive pines at Silvermine in the Table Mountain National Park, it might have been tactical for the

authorities to have left some of them for a period of time until alternative species had established themselves. But the funding was available to do the work in one (cheaper) contract. Furthermore, the trees could then be harvested after the fire, which reduced the danger of trees shedding branches or falling down because the collective protection against wind was lowered. We also needed to consider the additional seed pollution had we allowed some of the invasives to remain for a time – although there is the counter-argument that a truly massive seed-bank of cluster pines and other invasives exists in the area already. Contrary to what Ellis implies, South African National Parks has been sensitive in maintaining vast tracks of land containing invasive alien plants in what I would call ‘sacrificial zones’. Similarly, the policy of the Working for Water programme and its partners is indeed to acknowledge the cultural value of certain invasive alien plants. In Cape Town, only those oak trees invading in the indigenous forests are cleared. The rest (diseased as they are, ironically, by other invasive species) are left alone. In Pretoria, it is accepted that jacarandas should be left as street and garden trees (but cleared where they invade river systems). Working for Water even maintains woodlot stands in areas where the invasives are a critical source of biomass for local poor people. To dismiss as ‘absolutism’ the nuanced responses of the authorities to the problems posed by invasive alien species smacks of absolutism itself: “My trees, right or wrong”. Guy Preston, Hout Bay, Cape Town (Letter shortened – Editor)

W h a t ’s i n a n a m e ? urther to Valdon Smith’s fine articles on South Africa’s Prince Edward Islands (QUEST, vol. 1, no. 2), here are additional details about how the islands received their present names. On 13 January 1772, the two French frigates Le Mascarin and Marquis de


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Castries (captained by Marc Marion du Fresne and Julien Crozet, respectively) found the islands in their current position of 46°55’S. Du Fresne named the smaller one (now Prince Edward) Ile de la Caverne, for its large cave visible from the sea. Without landing, he sailed east to

discover what is now named the Crozet Island group. On 12 December 1776, Captain James Cook in the Resolution and Discovery on his third voyage of discovery reached the islands. He had heard of them (and of the Crozet Islands) previously from Captain

Q News Space mission extraordinary Address your letters to The Editor and fax them to (011) 673 3683 or e-mail them to editor.quest@iafrica.com (Please keep letters as short as possible. We reserve the right to edit for length and clarity.)

Crozet, who had given him a chart when they had earlier met by chance in Cape Town’s Table Bay. Crozet’s chart did not name the islands, so Cook called them Prince Edward’s Islands after the British king’s fourth son (the father of Queen Victoria). Cook did not give the two islands individual names nor did he land. He sailed east and gave to what are now known as the Crozet Islands the names ‘Marion’s and Crozet’s Islands’ after their 1772 discoverers. How or when the names Marion and Prince Edward became used for the individual Prince Edward Islands is not known, but they most likely became adopted sometime in the first half or the middle of the 19th century by sealers, who were notoriously vague and secretive about naming the islands they visited. Since then no other names have been used for the Prince Edward Islands. The existing names are well entrenched in the scientific and popular literature, as well as on maps and charts and in maritime pilots. John Cooper, Avian Demography Unit, Department of Statistical Sciences, University of Cape Town, Rondebosch 7701 Visit http://web.uct.ac.za/depts/stats/adu/ princeedwardnames and read J. Cooper and R.K. Headland, “A history of South African involvement in Antarctica and at the Prince Edward Islands”, South African Journal of Antarctic Research, vol. 21 (1991), pp.77–91.

lan Rice’s article on diamonds (QUEST, vol. 1, no. 2) was very interesting, with its fascinating picture of a diamond crystal still embedded in its matrix. I have always enjoyed the irony of the fact that from the lowly carob tree sprang the word ‘carat’, the unit of weight used for diamonds and now inextricably part of the dazzling world of diamonds and glitz. It came into the English language via Arabic, from the old practice of comparing the weight of a diamond to that of a seed or seeds from the pod of the carob tree – a good shade tree often planted in gardens, and whose pods are used by farmers as fodder for livestock. The weight of a carat is now standardized as 200 milligrams. A large diamond for a ring might weigh two carats or more, and a small one half a carat. Liesel Smith, Pretoria


Cassini reports from Saturn The Cassini-Huygens mission to Saturn and Titan is a cooperative project of NASA, the European Space Agency, and the Italian Space Agency. The Cassini spacecraft went into orbit around Saturn in July 2004, and it is sending back spectacular pictures of the planet and its moons as it travels. Here are three of them.

Images from left to right: 31 January 2005 – Sun-striped Saturn. In a dazzling and dramatic portrait painted by the Sun, the long thin shadows of Saturn's rings sweep across the planet's northern latitudes. Within the shadows, bright bands represent areas where the ring material is less dense, while dark strips and wave patterns reveal areas of denser material. The globe of Saturn's moon, Mimas (398 km across), comes into view near the bottom of the frame. (The picture was taken at a distance of 1.4 million km from Saturn.) 1 February 2005 – Impact Central. This view of the trailing hemisphere of Saturn's moon Rhea shows the region's bright wispy markings, but also shows off the moon's craters in great detail. Of particular interest to imaging scientists is the distribution and orientation of the many craters with polygonal rims. These are craters with rough, angular shapes rather than smooth, circular ones. Rhea is 1 528 km across. (This picture was taken at a distance of about 500 000 km from Rhea.) 3 February 2005 – January's moon. The month of January is named after the mythical Roman god Janus, who guarded the gates of heaven. Cassini spied the heavily cratered, irregularly shaped moon of Saturn as it glided along in its orbit, about 11 000 km beyond the bright core of the narrow F ring. Janus is 181 km across. Follow Cassini's voyage of discovery yourself. Visit http://Saturn.jpl.nasa.gov and view the pictures on http://ciclops.org Images: Courtesy of NASA/JPL/Space Science Institute

Huygens reports from Titan In January 2005 the European probe Huygens was launched from Cassini and entered the upper atmosphere of Saturn's big moon, Titan. It floated down by parachute for two-and-a-half hours, then survived a hard landing to return a 'wish you were here' view of a truly alien world, reports Richard A. Kerr in Science (21 January 2005). The mission was a brilliant engineering feat, for the first time revealing the moon's surface previously hidden by surrounding haze. It has canyons, riverbeds, plains, rocks, mud, and possibly lakes and seas. With its rock-hard ice, organic goo, and liquefied natural gas, it appears to investigators much like Earth's Mojave desert and others on Mars. The Huygens images show, on a flat plain, 'rocks' constituted possibly of water ice. Powerful currents seem to have carved Titan's surface and imaging specialist Martin Tomasko (University of Arizona, Tucson) has observed what look like "drainage channels", with signs of seepage from canyon walls that we recognize from Earth

and Mars. So far, Huygens has found no obvious sign of standing fluids. John Zarnecki (University of Kent, UK), responsible for analysing the surface, reports that the 'penetrometer' encountered a thin crust before passing through 15 cm of something the consistency of wet sand, or clay, or, he suggests imaginatively, crème brûlée. The atmosphere's methane and photochemically produced ethane (analogous to Earth's water vapour) condense into hydrocarbon clouds. These perhaps rain onto the moon surface to erode the channels in some way. Spreading across the plains, the hydrocarbon rivers would deposit heavy sediment. Evaporating fluids would leave organic goo behind in much the same way that water on Earth leaves salts on flat surfaces. Some fluid might soak into the plain, becoming "ground hydrocarbons". To icy-satellite geologist Robert Pappalardo (University of Colorado, Boulder) there are parallels with desert environments on Earth, where eroding rain may be infrequent but can be torrential.

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Q News

Q Q UEST crossword You’ll find many of the answers in our pages, so it helps to read the magazine before doing the puzzle. 1




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44s smother Earth Off-road 44 driving destroys fragile desert surfaces and releases clouds of fine dust particles, reports Andrew Goudie (Oxford University). It contributes to a tenfold increase in dust storms around the globe, and could have severe consequences for human health, coral reefs, and climate change. What Goudie calls 'Toyotarisation' (damage caused by four-wheel-drive vehicles) creates atmospheric dust and pollution. In the Middle East, nomads now tend their flocks in 44 vehicles and in the USA dune buggies are all the rage. Scientists estimate that 3 000 million tonnes of dust are being whipped thousands of kilometres around the world, generating storms across Africa, China, the Middle East, and the USA. Already, parts of North Africa have experienced a 10-fold rise of dust production in the past 50 years and environmentalists warn that dust storms could jeopardize the future of African rural areas in the same way that the Dust Bowl of the 1930s destroyed the prairie lands of the American West. Reported in The Guardian and The Times, London, August 2004.

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1 Colour caused by iron oxide staining on hard quartzite (5) 4 Prefix meaning one thousand millionth (4) 6 Prongs of a fork or pitchfork (5) 7 Physics is the study of ------ (6) 9 Hard stones of nearly pure silica; used to make prehistoric tools or weapons (6) 11 Unit of heredity in an organism (4) 12 The Age in the classification of prehistoric periods based on the use of a ferro-magnetic metallic element (4) 14 -------- Koppies Nature Reserve; 7 km from Johannesburg city centre (8) 17 Predatory eight-legged arachnid (6) 20 Abundant nonmetallic element; symbol C (6) 22 English meaning of the oriental word 'tsu' (7) 25 Colour of flames that have roughly the same temperature of 1 000˚C (6) 27 Sir Basil Schonland carried out world class work on this type of physics (4) 28 Sheet of floating ice (4)

2 Brenner used this invertebrate as a model organism in his study of gene function (4) 3 The name by which the explosive trinitrotoluene is better known (3) 5 Units of electrical resistance (4) 6 Huge destructive wave caused by disturbance of the ocean floor (7) 7 Plant life (5) 8 The name of a 'hot' pachyderm (6) 10 The approximate number of microseconds by which days have been shortened by the impact of the Indonesian disaster of 2004 (5) 13 This hand tool, dating back 100 000 years, can be found at 14 Across (3) 15 The acronym of the laser technology used in speed traps (5) 16 Name of the scale for stating the strength of an earthquake (7) 17 Fine-grained sedimentary rock that splits easily (5) 18 T.H. Maiman built the first ever laser device, a crystal of which gem? (4) 19 A rigid layer of the earth's crust (5) 20 Surname of Marie and Pierre who were pioneers of the study of radioactivity (5) 21 Hydrocarbon compound of the paraffin series occurring in petrol (6) 23 Hard black mineral found below ground and used as fuel (4) 24 Acronym for the instrument that records the cardiac cycle (3) 26 A new approach to conservation is Global --- Analysis (3)

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By November 2004, the International Census of Marine Life – the first systematic global attempt to catalogue and map the Earth's oceans – had logged nearly a quarter of a million species. But perhaps ten times more still remain to be found. "Humans have explored less than 5% of the world's oceans," explains census director Frederick Grassle (Rutgers University, New Jersey). Now in year four of its 10-year projected life, the census consists of a network of projects in over 70 countries, with records from many sources, including current research and historical data. Nearly 50 new marine species are located each week, of which typically only two or three are fish. But, say researchers, most unknown species could be tiny algae floating in the ocean and nematode worms on the sea bed. The census database (the Ocean Biogeographic Information System) contains more than five million separate reports. The 40 000 species catalogued so far represent less than one-fifth of the number of described marine species, with more to be discovered, particularly in the deep oceans. Some 95% of the data comes from surveys of the ocean surface, but less than 0.1% from the bottom half of the water column. At the current rate of discovery, it could take 1 000 years to record everything, but the project is in an exponential growth phase, says Grassle. "The major obstacle wasn't technical. It was getting people to understand the value of making their databases publicly available." Reported in New Scientist (23 November 2004). For more, visit www.coml.org

Boozy tastes in the genes? People with taste buds that are dull to bitter flavours drink twice as much alcohol as those with more sensitive palates, suggests a US study. "For the person who tastes the most bitterness, it makes sense that you aren't going to want to drink as much alcohol," says researcher Valerie Duffy (University of Connecticut). But, she warns, people can override the demands of their taste buds by drinking sweetened beverages, or ignore them in some social situations, like student parties. People generally fall into three taste categories: supertasters (with acute sensitivity to bitter chemicals), nontasters (who sense bitterness only at higher concentrations), and medium tasters in between. The bitter chemical 6-n-propylthiouracil (PROP) is often used in taste tests. In 2003 a gene (TAS2R38) was discovered that influences the sensitivity to PROP. It codes for a taste bud receptor and has natural variations. Could the variations accurately predict sensitivity to bitterness and, in turn, influence alcohol consumption? The answer seems to be yes, according to Duffy's testing of 53 women and 31 men, all light-to-moderate drinkers, for their response to PROP, their TAS2R38 gene profile, their self-reported alcohol consumption, and the number of taste buds on each person's tongue. Says Dennis Drayna, whose team discovered TAS2R38, "That taste appears to be so clear a factor is very exciting. The finding may have a substantial impact on the worldwide problem of alcoholism." Reported in New Scientist (15 November 2004).

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Diary of events Q on the life, work, and times of Albert Einstein, from his miserable days as an unsuccessful student, to his annus mirabilis (1905) and his influence as one of the greatest scientists that ever lived. (Also on 19 & 22 March.) 18 March

Sasol SciFest 2005 (1820 Settlers National Monument, Fort Selwyn Drive, Grahamstown) In one week, the Sasol SciFest (the National Festival of Science, Engineering and Technology) features 600+ events including popular lectures, game drives, a laser show, workshops, robotics, competitions, ‘Science Olympics’, school quizzes, exhibitions, the PlayFair, field trips, 'Talkshops', films, and tours to the Makana Meadery. Here are some highlights.

■ Official opening by Mr Mosibudi Mangena, Minister of Science and Technology ■ Opening of South Africa's programme celebrating the International Year of Physics: "Looking for 'Earths' around other stars" – lecture by Gibor Basri (of the University of California, Berkeley and a co-investigator of the NASA Kepler Mission) about the search for other worlds and our quest to discover life elsewhere in our Galaxy. ■ "Unravelling the biology of dinosaurs and other extinct animals" – lecture by Anusuya Chinsamy-Turan (University of Cape Town) on the way in which – using bones, teeth, and geological setting – palaeontologists reconstruct the biology of ancient animals. ■ Sunset Show School: Science in Sport – presentations on science in sport by Wendy Sadler and Zbig Sobiesierski from Wales and graduates of the pre-Sasol SciFest School (where selected SciFriends train as festival presenters). (Also on 19 March.)

16 March ■ "Sharks like Maxine – wired for sound" – lecture by Malcolm Smale (Bayworld, Port Elizabeth) on studying sharks in the wild. They're large and live in a medium where visibility is poor. But ultrasonic telemetry allows signals sent out by tags on sharks to be picked up by receivers and analysed. Hear about Maxine, the ragged tooth shark. ■ "Music vs machine" – audio and visual presentation by Wendy Sadler (Cardiff University and Science Made Simple) about synthesizers, voice recognition systems, and the technology behind the music we listen to. 17 March ■ "Sex, hormones and drugs: a molecular view" – lecture by Janet Hapgood (University of Stellenbosch) about hormones and how they work in the body and inside the cell. Discover what this knowledge can do to help us design better drugs with fewer side effects. ■ "Imagining Einstein" – science theatre from David Muller (MTN ScienCentre)

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switched on in the brain during disease and injury and contributes to the damage. 20 March ■ "Engineering and the human genome" – lecture by Tom Bligh (Cambridge University) about the engineering involved in extracting DNA for sequencing. The Human Genome Project began in 1990 and is the largest scientific programme ever. Its goal is to map the location of all the genes on every chromosome, to determine each gene's chemical structure so as to understand its function in health and disease, and to determine the precise sequence of the 3.2 billion base pairs of the entire genome. The cost? More than the whole NASA Apollo moon-landing programme. ■ "Human evolution: past, present, and future" – lecture by Rebecca Rogers Ackermann (University of Cape Town) on the everyday evidence of human evolution (such as the shape of our spines and the distribution of our genes) and how we can use the present to understand the past – perhaps even the future? ■ "Perfection in motion" – a show featuring top gymnast, Christian Berzeanu. 21 March ■ "The search for a complete history of the Cosmos" – lecture by Neil Turok (Cambridge University, and a founder of the African Institute for Mathematical Sciences [AIMS] in Cape Town). He will speak about the beginning of the universe and where it could be going. Daily

19 March ■ "Modern motorbike design" – lecture by Pierre Terblanche (Ducati). He will present basic design method based on his own experience as designer of famous bikes such as the Supersport 900, the MHe900 Evoluzione, and the Ducati Multistrada (the fastest-selling Ducati in modern times). ■ "Tracking down killers in the brain" – lecture by Nancy Rothwell (University of Manchester) about molecules, produced by injured cells, that kill healthy cells around them. Her research led to the discovery that the protein IL-1 is

■ Sport 'n Science – link sport and science through outdoor education, map work, compass work, orientating and testing 'pioneering' skills. ■ Sunset Shows – end the day with the bangs of chemistry or physics shows and laugh at the unexpected. From 16–22 March 2005. For information tel. (046) 603 1106 or visit www.scifest.org.za Arrange special pre-festival teacher registration (giving free entry to evening lectures and observer status at workshops) through the Sasol SciFest Advance Booking Office at (046) 603 1106 by 12 March. Diary of Events welcomes news of science and technology events or happenings. Send full details under the heading QUEST DIARY to The Editor, tel./fax: (011) 673 3683 or e-mail: editor.quest@iafrica.com

Q ASSAf News

Science-for-Society Gold Medals 2004 The Academy of Science of South Africa (ASSAf) awards two gold medals annually for outstanding achievement in applying scientific thinking to the service of society. Last October, the 2004 awards were presented to Professor Hoosen Coovadia and Professor Brian Warner. Professor Coovadia holds the Victor Daitz Chair in HIV/AIDS research and is Director of Biomedical Science at the Centre for HIV/AIDS Networking at the Nelson R. Mandela School of Medicine, University of KwaZulu-Natal. As a leading paediatric immunologist, he has made significant contributions in paediatric diseases including those more specifically affecting black children. He has also championed justice and human rights and was a leader in the struggle for a democratic South Africa: he continues fearlessly to criticize policies that damage the life chances of the people he serves. More recently, he has received worldwide renown for his achievements in the field of HIV/AIDS, especially for his ground-breaking work on mother-to-child transmission. He chaired the XIIIth International Conference on AIDS in Durban in 2000, and remains a world authority in the field of paediatric HIV/AIDS, both as a researcher and as a powerful force in shaping policy with respect to the disease. Brian Warner, Distinguished Professor of Natural Philosophy at the University of Cape Town, has made his name as an astronomer in a remarkable career spanning over 40 years. He has published over 300 scientific papers and 11 books, of which the one on cataclysmic variable stars is considered the ‘bible’ of its field. He is one of the world’s experts on William and John Herschel. In 1997, he was one of the three astronomers chosen to address the General Assembly of the International Astronomical

Union in Kyoto, Japan. Further recognition came in 2003, when he took up office as one of the Union’s six vice-presidents. Besides his academic achievements, he has served on numerous bodies that integrate science with society, notably the Council of the South African Museum (now Iziko) and the South African Library.

ASSAf’s link with prestigious academic award The Harry Oppenheimer Award of up to US$100 000 is one of the country’s most prestigious academic grants. It is made annually by the Ernest Oppenheimer Memorial Trust to an established South African scholar for a year’s full-time research at the most advanced level. The Academy will in future co-sponsor public lectures in South Africa’s main centres by the holders of the award after completion of their year’s work.

Human sciences symposium ASSAf’s annual symposium, held in conjunction with its annual general meeting in 2004, dealt with the role of research in the humanities and social sciences in South Africa. An area of concern was a decline in ‘public sociology’: professional studies ought to be fed into policy-making and public awareness of key issues affecting society, but professional social scientists often fail to make their insights sufficiently available to the public. For the natural scientists at the symposium, the presentation of the human sciences came as a welcome and useful innovation, particularly in the area of socioeconomic development.

S&T publication In April 2001, the international InterAcademy Council invited member

Bright birds Some birds could be as intelligent as chimpanzees, say a consortium of 29 avian experts from six countries. They point to behaviour that seems odd in birds believed to have simple brains. African grey parrots talk, make up new words, and have a sense of humour, for instance. Crows make hooks and spears of small sticks to carry on foraging trips, and some have learned to put walnuts on roads for cars to crack. The scientists argue that avian brains are as complex, flexible, and inventive as those of mammals. Over seven years, the group has developed new, more accurate names for structures in both avian and mammalian brains, on the grounds that old terminology has hindered

academies to take part in a global advisory project, “Promoting Worldwide Science and Technology Capacities for the 21st Century”. In response, ASSAf set up a ‘think tank’ in August 2001, to probe locally in South Africa the issues to be examined internationally by the participating science academies. South Africa is a microcosm of the global situation in which, according to the IAC Prospectus, “90% of the world’s population lives in nations that contain only 5% of the scientists”. ASSAf launched a project, “Promoting South African S&T capacities for the 21st century”, to address the South African situation and to contribute to the international study. Three reports emerged: a background document, the proceedings of a consultative forum, and a synthesis report. ASSAf is now publishing these three documents in one as its contribution to ensuring adequate science and technology capacity for the future. The combined report acknowledges the many policies of the South African government to achieve a major enhancement of the country’s S&T capacity, and it points to short-term interventions that can support and accelerate the beneficial effect of these policies.

New ASSAf Council The new Council to govern the affairs of the Academy of Science of South Africa took office for two years from 29 October 2004. The members of the executive committee are: Professors Robin Crewe (President), Anusuya Chinsamy-Turan (Vice-President), Jonathan Jansen (VicePresident), Vivian de Klerk (Treasurer), and Dr Philemon Mjwara (General Secretary). The remaining Council members are Professors Solly Benatar, Manfred Hellberg, Colin Johnson, Benito Khotseng, N. Chabani Manganyi, Luigi Nassimbeni, Jennifer Thomson, and Jimmy Volmink.

Q News scientific thinking and progress. For example, the pallium is now the name they give to the bird's seat of intelligence, or higher brain. If birds are smart, how did they get that way? One view is that birds' brains make the same kind of internal connections as do mammalian brains and that intelligence in both groups arises from these connections. The other view is that bird intelligence evolved through expanding an old part of the mammal brain and using it in new ways, and the question is how developed might that intelligence be. Puzzles remain, but realizing that one can study mammal brains by using bird brains may be revolutionary. Reported from Nature Neuroscience Reviews in the New York Times, 1 February 2005.

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Back page science Q Classical music fights crime

Ig Nobel Prizes

A UK grocery store chain plays classical music outside its shops to stop youths from hanging around and intimidating customers. It seems to work well. Staff with a remote control "turn on the music if a situation starts developing and they need to disperse people," says Steve Broughton of Co-op. But the greatest use of aural policing is in the 30 underground train stations that pump out classical music to discourage vandals and loiterers. A spokesman for Transport of London says that the best deterrents are anything sung by Luciano Pavarotti or written by Mozart. Hospitals have caught on too. At the Royal Bolton hospital, classical music plays in the accident and emergency ward as well as in the eye ward and the main reception area. According to matron Janet Hackin, patients appear calmer. Could this be a strategy worth trying in South Africa? (From a report in The Economist, London, 8–14 January 2005.)

Since 1991, 10 annual Ig Nobel prizes have been awarded for "achievements that cannot or should not be reproduced". They celebrate the unusual, honour the imaginative, and make people chuckle. The winners receive their prizes from Nobel laureates in an elaborate ceremony at Harvard in September. The 2004 winners included the following (all from the USA): Medicine – Steven Stack and James Gundlach for their report, "The Effect of Country Music on Suicide" Public Health – Jillian Clarke for investigating the scientific validity of the Five-Second Rule about whether it's safe to eat food that's been dropped on the floor Physics – Ramesh Balasubramaniam and Michael Turvey for exploring and explaining the dynamics of hula-hooping, in "Coordination Modes in the Multisegmental Dynamics of Hula Hooping" Engineering – Donald J. Smith and his father, the late Frank J. Smith, for patenting the combover (US Patent #4 022 227), a method of concealing partial baldness by dividing a person's hair into three sections and carefully folding one section over another. For more, visit www.improbable.com

What physicists say ■ "E = mc2" (Energy = mass  the speed of light squared). Albert Einstein (1905) ■ "When a man sits with a pretty girl for an hour, it seems like a minute. But let him sit on a hot stove for a minute – and it's longer than any hour. That's relativity." Attributed to Einstein (1879–1955). ■ "A fact is a simple statement that everyone believes. It is innocent, unless found guilty. A hypothesis is a novel suggestion that no one wants to believe. It is guilty, until found effective." Edward Teller (1908–2003). ■ "An experiment is a question which science poses to Nature, and a measurement is the recording of Nature's answer." Max Planck, in Scientific Autobiography and Other Papers (1949). ■ "In physics, you don't have to go around making trouble for yourself – Nature does it for you." 2004 Nobel laureate Frank Wilczek (1951– ).

Chocolate muti for coughs? Chocolate may be better for coughs than you think. One of its constituents, theobromine, may be more effective than codeine, without the side effects of drowsiness and constipation. In a study led by Peter Barnes (Imperial College, London), volunteers took tablets containing theobromine, or codeine, or a placebo, then inhaled a gas containing capsaicin – derived from chilli peppers – that induces coughing and is used to test the effectiveness of cough medicines. Those given theobromine needed about onethird more capsaicin to produce coughing than

those who took codeine, and codeine was only marginally better than the placebo at preventing coughing. The volunteers received the equivalent of about two cups of cocoa, explains Barnes: "The next stage will be to look at different doses." The results could help lung disease sufferers who develop persistent coughs, but, warns Dame Helena Shovelton of the British Lung Foundation, patients should consult their doctor "before changing their medication or treating their cough with chocolate", however tempting that may be. (Reported in New Scientist [22 November 2004].)

Don't worry, be happy In a 10-year psychiatric study in The Netherlands led by Erik Giltay, people who described themselves as highly optimistic a decade ago had a 55% lower risk of death from all causes and 23% lower risk of death from heart failure than pessimists. The study was conducted in a group of 999 men and women who were 65 to 85 years old when the study began. "A predisposition toward optimism seemed to provide a survival benefit in elderly subjects with relatively short life expectancies otherwise," report the researchers. They note that pessimistic people may be more prone to developing habits and problems that cut life short, such as smoking, obesity, and hypertension. (Reported in the Archives of General Psychiatry [November 2004].)

Answers to Crossword (page 45) ACROSS: 1 Brown, 4 Nano, 6 Tines, 7 Forces, 9 Flints, 11 Gene, 12 Iron, 14 Melville, 17 Spider, 20 Carbon, 22 Harbour, 25 Orange, 27 Rock, 28 Floe. DOWN: 2 Worm, 3 TNT, 5 Ohms, 6 Tsunami, 7 Flora, 8 Kinkle, 10 Three, 13 Axe, 15 LIDAR, 16 Richter, 17 Shale, 18 Ruby, 19 Plate, 20 Curie, 21 Octane, 23 Coal, 24 ECG, 26 Gap.

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