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ISSN 1729-830X ISSN 1729-830X

VOLUME 4 • NUMBER 4 • 2008 VOLUME 3 • NUMBER 2 • 2007 R29.95 R20


in South Africa Inva sive sp ec ie s A nt a rct ic sc ie nce Alie n r ept ile s


Their Dreams. Our Opportunity.

Member of the Anglo American plc group

Cover stories HIV in South Africa – 2008 The Desmond Tutu HIV Foundation is a key research facility in South Africa. Members of the Foundation discuss the epidemic in South Africa. 4


Taking the pain out of testing The Tutu Tester has been drawing the crowds around Cape Town – including members of the band Freshlyground.


HIV in South Africa – the numbers Landon Myer


Understanding the epidemiology of HIV infection in South Africa is a critical first step in any attempt to address the epidemic. Taking the medicine Catherine Orrell Antiretroviral treatment can transform an infected person’s life, but it must be taken for life.


Contents VOLUME 4 • NUMBER 4 • 2008

Features 26

The British Council Climate Change Champions are actively seeking solutions within their own local communities.

A double burden – HIV and TB Desmond Tutu HIV Foundation Current tuberculosis control measures are failing – mainly because of the epidemic of HIV.



South Africa is actively contributing to helping Mali conserve its important and ancient manuscripts.

With clinical trials of HIV currently stalled, the focus is now on all forms of prevention.


What can genes tell us about invasive species? Jaco Le Roux Genetics can help us to identify alien invasive plants accurately – which is crucial to their management. Antarctic science for the next generation

Regulars Fact files HIV vaccines (p. 16) • Antarctica (p. 33) • More on South African Reptiles (p. 39) 44


Organophosphates are common in the environment so it is important to avoid poisoning. 46

Diary of events


Books A Briefer History of Time. • The Story of Earth and Life. • Scatological Verse

Alien species – reptiles and amphibians Nicola van Wilgen South Africa does not yet have a problem with invasive alien species, but without the correct management this could change.

Viewpoint Bassie Marvey

David Hedding, Andrew Collier, Jennifer Lee and Brett Kuyper The Antarctic region is changing faster than anywhere else on the planet, so Antarctic science provides a sensitive indicator of environmental change in a unique environment.

Conserving the Timbuktu manuscripts Alexio Motsi and Mary Minicka

Prevention is key Surita Roux


Climate change – Taking the initiative


Subscription and survey form


Back page science • Mathematical puzzle

Quest 4(4) 2008 1


ISSN 1729-830X ISSN 1729-830X

VOLUME 4 • NUMBER 4 • 2008 VOLUME 3 • NUMBER 2 • 2007 R29.95 R20

HIV in South Africa Inva sive sp ec ie s A nt a rct ic sc ie nce Alie n r ept ile s


The Desmond Tutu HIV Foundation in action. Photographs: Desmond Tutu HIV Foundation


ISSN 1729-830X

Editor Dr. Bridget Farham Editorial Board Roseanne Diab (University of KwaZulu-Natal) (Chair) Michael Cherry (South African Journal of Science) Phil Charles (SAAO) Anusuya Chinsamy-Turan (University of Cape Town) George Ellis (University of Cape Town) Jonathan Jansen (Stanford University) Correspondence and The Editor enquiries PO Box 663, Noordhoek 7979 Tel.: (021) 789 2331 Fax: (021) 789 2233 e-mail: (For more information visit Advertising enquiries Barbara Spence Avenue Advertising PO Box 71308 Bryanston 2021 Tel.: (011) 463 7940 Fax: (011) 463 7939 Cell: 082 881 3454 e-mail:

Science in action I

n this, my first edition of QUEST, I am pleased to be able to highlight two of my greatest loves in science – medicine and biology. The series of articles featured on our cover deal exclusively with the issue of HIV and AIDS. This is particularly pertinent at this time of the year because 1 December is World AIDS Day and December has traditionally become a month in which the issue of HIV is highlighted. The HI virus has been with us for more than two decades. However, we are still far from on top of the hardship and death that results from infection with HIV. SubSaharan Africa bears the brunt of the epidemic and the series of articles that spotlight the work being done by the Desmond Tutu HIV Foundation at the University of Cape Town show just how much research is needed into controlling the effects of this devastating disease. And, more to the point, they show that the research that is done on our doorstep is world class. So too do the feature articles dealing with the problem of alien invasive species, both from Stellenbosch University. Reptiles are becoming increasingly popular as pets and the exotic or alien species often have more appeal than our local species. But what looks very pretty in a tank in your living room may cause untold havoc if the species is released into the wild, starts breeding and adversely affects the local fauna and flora. These adverse effects have been widely recognised in the problem of alien invasive plants, many from Australia, which were introduced into South Africa decades ago and which have, in some cases, totally taken over the indigenous flora. This article is particlularly interesting because it shows how important basic science is to our everyday lives. Without an understanding of the molecular genetics of these alien species we would have even more difficulty controlling them. So the seemingly esoteric pursuit of molecular genetics has plenty of application to important problems that affect us all. But above all, science is fun, interesting and exciting. I hope to continue to put this across in all forthcoming editions of QUEST and to show how we cannot live without science in our daily lives.

Subscription enquiries Angela Meyer and back issues Tel.: (012) 843 6484/81 e-mail: Copyright © 2008 Academy of Science of South Africa

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

Published by the Academy of Science of South Africa (ASSAf) PO Box 72135, Lynnwood Ridge 0040, South Africa (021) 789 2233 Permissions Fax: e-mail: Subscription rates (4 issues and postage) (For subscription form, other countries, see p. 56.)

South Africa • Individuals/Institutions – R100.00 • Students/schoolgoers – R50.00

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

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Write letters for our regular Letters column – e-mail or fax your letter to The Editor. (Write QUEST LETTER in the subject line.) ■ Ask science and technology (S&T) questions for specialist members of the Academy of Science to answer in our regular Questions and Answers column – e-mail or fax your questions to The Editor. (Write QUEST QUESTION in the subject line.) ■ Inform readers in our regular Diary of Events column about science and technology events that you may be 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, and make arrangements to tell us your story. To contact the Editor, send an e-mail to: or fax your communication to (021) 789 2233. Please give your full name and contact details. ■

All photographs in the HIV articles are courtesy of the Desmond Tutu HIV Foundation. These photographs are from the Foundation archives and represent the people and the communities the Foundation serves. The HIV status of the people features in these photograps is unknown, as in many instances are their names. No assumptions should be made regarding their appearance in this publication.

HIV in South Africa 2008

Members of the Desmond Tutu HIV Foundation – Masibambani Ngezandla – discuss the HIV epidemic in South Africa.


n estimated 33.3 million people worldwide were living with HIV in 2007. An estimated 2.5 million became newly infected with HIV and an estimated 2.1 million lost their lives to AIDS. Southern Africa remains the global epicentre of the epidemic. Almost one in three people infected with HIV globally lives in this subregion. About 43% (860 000) of all children (under the age of 15) living with HIV are in southern Africa, as are approximately 52% (6.8 million) of all women living with HIV. South Africa’s AIDS epidemic – one of the worst in the world – shows no sign of declining. An estimated 5.5 million people were living with HIV in 2005 – most of them without realising that they are infected. This estimate is based on extensive antenatal clinic surveillance and national surveys with HIV testing and mortality (death) data from the civil registration system. An estimated 18.8% of adults (15–49 years) were living with HIV in 2005. Almost one in three pregnant women attending public antenatal clinics were living with HIV in 2004 and trends over time show a gradual increase in HIV prevalence. Impact on households The impact on individuals and households is enormous. AIDS has been cited as the major cause of premature deaths, with mortality rates increasing by about 79% between 1997 and 2004. The increase was much higher among women than among men. Children are a particularly vulnerable group, with high rates of mother-to-child transmission. Children are also seriously affected by the ill-health and death of their parents. AIDS contributes to about 50% of the orphans in this country.

Close links to TB Closely linked to HIV/AIDS is the tuberculosis (TB) epidemic. The recent increase in the incidence of and mortality related to TB and the recent emergence of extremely resistant TB (XDR-TB) have been linked to the immune supression caused by HIV and AIDS. Poverty, overcrowding and a lack of specific interventions contribute to the impact of immune supression. The double stigma associated with dual infection with HIV and TB has become a deterrent to healthseeking behaviour among South Africans. The effective management of dual infections relies heavily on community-based interventions. ▲ ▲

Paediatric tragedy Children infected, via transmission from their mothers, and who survive the early mortality seen in HIV infection,

survive for an average of 16 years. In high income countries, antiretrovirals have been used to prevent mother-tochild transmission – virtually eliminating paediatric HIV. However, the ineffective and incomplete application of motherto-child prevention programmes means that South Africa will continue to have a needless and heartbreaking paediatric epidemic for the next 15–20 years at least.

Top: The Xoliswa family. Above: The Archbishop greets community members. Left: Archbishop Desmond Tutu gave his name to the research foundation. The Desmond Tutu HIV Foundation (DTHF) has been involved with the care and management of HIV-infected people for more than 10 years. They are linked to three antiretroviral clinics: Hannan Crusaid Treatment Centre in Guguletu; Desmond and Leah Tutu Treatment Centre in Masiphumelele; and Desmond Tutu HIV Centre in Cape Town.

Antenatal clinic surveillance Much of the data on HIV in South Africa comes from anonymous unlinked testing of pregnant women at antenatal clinics. The sample is barcoded and the information used to collect national data on the prevalence of HIV among pregnant women. The Department of Health then uses a mathematical model to extrapolate the data to the whole South African population. As you will learn in the article on current South African HIV statistics, there are some problems with using these data as a way of finding out how many South Africans are infected with HIV. One of the main problems is that the data are collected only from women of childbearing age – so there is nothing about people who are either too young or too old to have children. The data also come from pregnant women, so say nothing about women who are not sexually active, or who use condoms.

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The Desmond Tutu HIV Foundation (DTHF) has been involved with the care and management of HIV infected people for more than 10 years. Sizophila counsellors form part of a specific DTHF initiative to promote adherence to antiretrovirals – they operate out of the Hannan Crusaid Treatment Centre. The Foundation is involved in HIV prevention, adolescent sexual health and HIV prevention and HIV training. Their research activities include HIV treatment strategies that are appropriate for a resource-poor country, including developing novel drugs and new technologies. The increasing realisation that TB and HIV are

co-related epidemics has led to a unique TB and HIV interaction research programme in the community of Masiphumelele to investigate the interaction of TB and HIV, as well as formulating models to apply to other similar communities. The Foundation also evaluates a number of drugs, vaccine and microbicide products in international standard clinical trials. Psychosocial studies are integral to much of the Foundation’s work and include: the inolvement of youth in preventive research; adolescent sexual risk patterns; risk behaviours in men who have sex with men; drug vaccine adherence studies and efficacy of community education programmes.

Taking the pain out of testing Far left: Freshlyground band members Peter Cohen, Zolani Mahola and Simon Attwell wait to be tested aboard the Tutu Tester. Left: Evita says, ‘I never thought I would ever allow myself to be tested. But my grandchildren said: ‘Gogo, lead by example!’ So here I am! I invited the President to join me but he’s not in South Africa at the moment. Jacob Zuma was in the shower. So I will represent those who seem to also be scared. The Tutu Tester can only make one less fearful.’ Taking control

The Tutu Tester has been drawing the crowds around Cape Town.


or the past three months the Tutu Tester – a brightly painted red, green, blue and yellow mobile clinic for quick testing for hypertension, diabetes and HIV – has been seen at taxi ranks, church grounds and shopping centres in five township areas in Cape Town with a steady flow of people making use of the opportunity to check their status regarding these conditions free of charge. Launched at the end of May, the Tutu Tester combines quick fingertip HIV testing with screening for other

4 Quest 4(4) 2008

Above: All aboard the Tutu Tester.

common chronic diseases like diabetes and hypertension. The concept represents the DTHF’s vision that HIV should become viewed as a chronic treatable condition rather than one attached to stigma, discrimination and shame. As many as 45% of those making use of the opportunity were testing for the first time, indicating that the Tutu Tester

pilot project is achieving success in promoting awareness about the need for people to make regular testing part of their health maintenance programme. The results after three months show that of the 1706 people tested, 58% were men. Of those who tested positive for HIV, 59% were men. According to Dr Nienke van Schaik, who heads up the pilot testing project on behalf of DTHF, the results are not representative of HIV infection levels prevalent in society as a whole, as the majority of people tested were found to be HIV-negative. This is probably because people come in to test on the spur of the moment and not because they feel sick or suspect that they might be infected. She explains that the main purpose is to offer HIV testing outside of the traditional clinical setting to make it accessible to people who are otherwise difficult to reach. In this way the Tutu Tester promotes disease prevention as a self-initiated activity. ‘We work with each individual through a risk reduction questionnaire. Depending on their responses, they are given guidelines for an appropriate risk reduction programme of which regular annual testing forms a part.’ ■

HIV in South Africa – the numbers Landon Myer takes a look at the state of the HIV epidemic in South Africa.


nderstanding the epidemiology of HIV infection in South Africa – including the distribution of HIV in the country and the risk factors for HIV infection – is a critical first step in any attempt to address the epidemic. While a bewildering array of numbers and statistics have been presented on the state of the epidemic, these all point towards a number of unquestionable facts. First, the HIV epidemic is large, and touches on almost every aspect of South African society. Second, the epidemic is unevenly distributed in the population, with particular patterns of age, gender, socioeconomic status and geography that are important to understand to target prevention and treatment interventions. Third, the HIV epidemic is having a tremendous impact on morbidity (illness) and mortality in South Africa, and this will continue for the foreseeable future. Epidemiology is the study of the factors that affect the health and illness of populations. The information from these studies is used to guide interventions in public health and preventive medicine.

The HIV epidemic in South Africa

Trends in antenatal HIV seroprevalence The best data on the occurrence of HIV in the South African population as a whole come from annual surveys of HIV prevalence among pregnant women attending public sector antenatal care services at selected facilities across the country. These sentinel surveys (surveys conducted in a specific group for the purpose of surveillance) have been conducted since 1990, and provide a snapshot of how HIV has spread in the country, as well as the current geographic distribution of HIV. You can see from the table and the figures that the greatest burden of HIV infection is seen in the eastern parts of South Africa, particuarly KwaZuluNatal, which has been the province with the highest prevalence of HIV among antenatal clinic attenders since

in natural sciences and engineering and also in the social sciences. Economists use mathematical models extensively. In this instance, the models used are compartmental models. The mathematicians have a starting state, which in this case is the state of the population before HIV was present. In this starting state, they divided the population into different groups – men, women, age categories, HIV-negative, HIV-positive, alive and dead – these are the compartments. They started with no-one in the HIV compartment. The mathematicians then assigned what are called transition probabilities between the compartments. These transition probabilities are based on the probability that a man or a woman of different ages will become infected with HIV during a 12-month period. They then factor in the death rates for HIV-positive and HIV-negative people of different ages – these are people who are leaving the model. Births are factored in as people who enter the model. The model parameters, which are the numbers of people in the different compartments and the probabilities of moving (transitioning) between the different compartments, are updated each year. The updates are based on data obtained from, for example, antenatal surveys of HIV prevalence.

▲ ▲

Where the numbers come from There are two general sources of information on the state of the HIV epidemic in South Africa. First, the results of epidemiological research studies provide insights into the occurrence of HIV in certain populations. This includes studies of both HIV prevalence and HIV incidence (see the box for definitions of prevalence and incidence). While these studies are invaluable, they can be costly and complex to conduct on a large scale (such as at a provincial or national level). Smaller studies, such as a study measuring HIV prevalence in a certain community, are more common, and provide useful snapshots of how the HIV epidemic operates at a local level.

Second, mathematical models can be used to generate estimates of the distribution of HIV/ AIDS in the population, including the incidence and prevalence of HIV as well as AIDSrelated mortality. These kinds of models are particularly important in providing general TAC activist, Zackie Achmat speaks at an HIV awareness event. predictions on the future course of the HIV epidemic, including Definitions of prevalence and incidence how the future of the epidemic may vary with HIV prevalence = (the total number of HIV infections in a population) / (the total number of individuals in that different prevention and population) treatment scenarios. This is a measure of the proportion of individuals in a population who Mathematical models are HIV-infected. are valuable for HIV incidence = (the total number of ‘new’ HIV infections planning for health in a population) / (the total number of individuals in that and other services. population) x (the time period of observation) When viewed This is a measure of the rate of new HIV infections occurring in a population. together, the results of experimental research and mathematical modelling present a How mathematical models work clear picture of the dynamics of the HIV epidemic in South Africa, past, present A mathematical model uses mathematical language to describe a system. Mathematical models are used and future.

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Antenatal HIV seroprevalence in South Africa, 1990-2006


HIV prevalence (%)

30 25 20 15 10




















(a) Province

HIV prevalence

(b) Age group

HIV prevalence



Less than 20 years




20–24 years


Free State


25–29 years




30–34 years


North West


35–39 years


Eastern Cape


40 years or older




Northern Cape


Western Cape






Year Figure 1. Antenatal HIV seroprevalence in South Africa, 1990–2006.

the 1990s. Figure 1 shows the increase in national antenatal HIV seroprevalence from <1% in 1990 to 29.1% in 2006. Table 1a shows the 2006 antenatal HIV seroprevalence by province, with the highest prevalences in KwaZuluNatal and Mpumalanga. The lowest prevalences are in the Western Cape and Northern Cape. When the 2006 survey is analysed by age group (Table 1b), we see that the highest HIV prevalence is among women aged 25–34 years. All these data are obtained from the Department of Health of South Africa. Report: National HIV and Syphilis Prevalence Survey, South Africa, 2006. Pretoria: Department of Health, 2007. This antenatal HIV seroprevalence survey provides valuable insights into the dynamics of HIV across the country, but there are several notable problems with these data. First, the survey only samples women of childbearing age, and does not include men or women too young or too old to have children. Projected HIV prevalence by age group 35 Females

HIV prevalence (%)



25 20 15 10 5


55 to 59

50 to 54

45 to 49

40 to 44

35 to 39

30 to 34

25 to 29

20 to 24

15 to 19

2 to 14


Age groups Figure 2. HIV prevalence in a national survey of women and men, aged 2 years and older, during 2005.

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Table 1. HIV seroprevalence estimates among women attending antenatal clinics in South Africa, 2006, according to (a) province and (b) age group. All values are percentages (%).

Second, by selecting participants from individuals attending public health facilities, these surveys focus on women of lower socioeconomic status, on average, than the South African population as a whole (because women of higher socioeconomic status are more likely to attend private health facilities). Perhaps most significantly, by focusing on pregnant women these surveys exclude women who are not sexually active, and women who use contraception (including condoms) regularly. Taken together, this means that the prevalence of HIV from annual antenatal surveys is likely to overestimate the prevalence of HIV in the South African population as a whole. Nonetheless, the antenatal care surveys are a valuable tool for regular monitoring of the levels of HIV across the country. National HIV prevalence surveys There have not been many surveys that cover the entire South African population. This would be a survey that looked at the distribution of HIV infection among people of all ages, genders and backgrounds in South Africa. A national survey conducted in 2005 drew a representative sample of men and women two years of age and older; approximately 65% of those approached to participate agreed to be interviewed and provide specimens for HIV testing. This survey found the population HIV prevalence (across men and women of all ages) to be 10.8%. You can see the results of this survey in Figure 2. Again, the highest prevalence of HIV among women was seen in women 2534 years of age. However, the highest prevalence among men was seen in the age group 30–40 years. This pattern,

with the highest prevalences of HIV seen at younger ages among women compared with men, is an important feature of the South African HIV epidemic. This strongly suggests that younger women are engaging in highrisk sexual partnerships with older men. This increased risk conferred on younger women by having older male partners has been found in several studies. This information is taken from the publication: Shisana O, Rehle T, Simbayi LC, Parker W, Zuma K, Bhana A, Connolly C, Jooste S, Pillay V, et al. South African National HIV Prevalence, HIV Incidence, Behaviour and Communication Survey, 2005. Cape Town: HSRC Press, 2005. Local studies of HIV prevalence and incidence There have been hundreds of studies conducted over the past 15 years measuring the occurrence of HIV infection in specific populations within South Africa. Some of these studies have been based on individuals recruited at health facilities, such as those seeking treatment for sexually transmitted infections (STIs); others use populationbased samples from particular communities. Such studies have shown the particularly high risk of HIV faced by women sex workers, demonstrated the high prevalence of HIV among hospital inpatients, and confirmed the distinctive age-gender distribution of HIV in specific communities. Measuring the incidence of HIV is also important. This requires what are called cohort studies. These studies involve following individuals over a period of time to see how many become infected. This kind of study is particularly complex and so is

Projected number of deaths due to AIDS in South Africa


60 50

Total population


Total population (millions)



4 Total HIV+



Cumulative AIDS deaths




Total AIDS sick


0 2016













0 1990

Numbers of HIV-infected, AIDS sick and cumulative AIDS deaths (millions)

Tannie Evita speaks to a community worker by the Tutu Tester.


Impact of antiretroviral therapy on the HIV epidemic Antiretroviral therapy is now available in the public sector, although to a relatively

600 000

Effect of antiretroviral therapy (ART) on projected number of deaths due to AIDS

500 000


400 000 300 000

90% ART coverage

200 000 100 000









0 1999

The results of observational studies provide important insights into the past and present distribution of HIV in South Africa, but little insight into the possible future of the epidemic. In addition, there are important statistics that are difficult to measure directly on a national scale, such as the numbers of individuals who have developed AIDS. Mathematical models have played a critical role in these areas by helping us to understand the probable course of the epidemic. The most prominent of these models has been developed

limited extent. The latest models predicting the way that the epidemic will unfold include the impact of people taking regular antiretroviral therapy, and so not falling ill and dying from AIDSrelated diseases. Mathematical models are particularly valuable because they can provide insights into the impact that the largescale delivery of HIV care and treatment services, including antiretroviral therapy, may have on the course of the HIV epidemic. The ASSA-2003 model suggests that a dramatic reduction in the number of deaths due to AIDS can be achieved if the national antiretroviral therapy programme can treat approximately 90% of infected individuals requiring care (Figure 4). People who are taking antiretroviral


Future of the HIV epidemic

by the Actuarial Society of Southern Africa (ASSA), and is adjusted regularly to incorporate new experimental observations of the prevalence of HIV infection, the incidence of new infections, and the natural history of HIV/AIDS (with and without antiretroviral therapy). This model suggests that the numbers of new HIV infections in South Africa will continue to rise over the next decade, although at a lower rate, to a level of approximately six million infected individuals by 2016 see Fig.3). This assumes that the South African population will be approximately 50 million, i.e. with approximately 12% of the population infected. The number of individuals developing AIDS will continue to increase steadily during the same time, with an estimated five million AIDS deaths occurring by 2016. This number is important because it indicates the burden that HIV will place on our healthcare system, including the demand for antiretroviral therapy. This graph is taken from the publication: Dorrington RE, Johnson LF, Bradshaw D, Daniel T. The Demographic Impact of HIV/AIDS in South Africa. National and Provincial Indicators for 2006. Cape Town: Centre for Actuarial Science Research, South African Medical Research Council and Actuarial Society of South Africa.

▲ ▲

expensive to carry out. The long-term follow-up of one cohort of women sex workers in KwaZulu-Natal has shown a continued high incidence of HIV through time, with incidence rates of approximately 18 per 100 personyears. This is equivalent to 18 new infections seen among 100 women who were each followed for one year. Lower rates of new HIV infections have been seen in the general population, with HIV incidence rates in general population samples usually estimated as falling between one and six new infections per 100 person years. The highest incidence of HIV is usually seen among sexually active adolescents and young adults, but substantial rates of new infection can be found in older age groups as well. One cohort study from Khayelitsha, Cape Town, found an HIV incidence of two infections per 100 person-years among women age 35–65 years.


An actuary is a person who applies mathematical and statistical methods to assess risk in the insurance and finance industries. He or she studies actuarial science at university. This includes many different, but related, subjects such as probability and statistics, economics and finance. If you are interested in this career you need to be particularly good at maths.

Figure 3. Estimates from the ASSA-2003 model of the projected population, number of HIV-positive individuals, number of individuals with AIDS, and cumulative AIDS deaths, in South Africa for the period 1990–2016.

Deaths due to AIDS

What is an actuary?

Year Figure 4. Projected number of deaths due to AIDS in South Africa, comparing a scenario of 90% coverage of the national antiretroviral programme with a scenario with no antiretroviral therapy availability, 1995–2015.

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Sexually transmitted infections (STIs) HIV is actually quite difficult to catch from a single sexual encounter. But there are certain factors that increase the likelihood of this happening. One of the most important is already being infected with another sexually transmitted infection, such as gonorrhoea or any of the STIs that cause ulcers on the genitals. Sexually transmitted infections are common among people in South Africa, so the STI and HIV epidemics can be said to fuel each other.

therapy will not fall ill and die early – their lifespan will increase. From the point of view of the statistics of the HIV epidemic, this means that the population prevalence of HIV will actually increase as a result of more people taking antiretrovirals. This graph is taken from the publication: Dorrington RE, Johnson LF, Bradshaw D, Daniel T. The Demographic Impact of HIV/AIDS in South Africa. National and Provincial Indicators for 2006. Cape Town: Centre for Actuarial Science Research, South African Medical Research Council and Actuarial Society of South Africa. Factors influencing the HIV epidemic in South Africa Looking at the basic numbers helps us to understand the extent of the epidemic, but provides few insights into how HIV is spread and, in turn, why HIV is so common in South Africa. One general way of thinking about what causes the epidemic of HIV in South Africa is shown in Figure 5. Using this approach, the causes of the HIV epidemic can be understood as operating at several different levels of social and biological organization. The most immediate risk factors for HIV are biomedical conditions, such as the viral load of the infected partner, sexually transmitted infections or male circumcision. Another class of risk

factors operates through individual behaviours, such as sexual partner selection, condom use, and alcohol consumption. Causes of HIV can also be thought of in terms of conditions regarding the structure of society, such as poverty, the relationship between men and women in our society, and high levels of population migration. The HIV epidemic in South Africa appears to result from factors that operate at each of these levels – there is no single cause. Although HIV is the necessary cause of AIDS, the extent of the HIV/AIDS epidemic in South Africa is influenced by a range of biological, behavioural and societal factors.

Prevention activities may address determinants of the HIV epidemic at any of these levels

Structural factors & societal conditions including • Poverty & inequality in wealth • Population migration • Gender inequality • Healthcare infrastructure Individual behaviours including • Turnover of sexual partners • High-risk sexual partners • Levels of condom use • Drug & alcohol use around sex

Biomedical factors including • Sexually transmitted infections • Viral load of infected partner • Male circumcision • Genital mucosal trauma

Increased HIV transmission

Figure 5. A way of thinking about the factors that influence the spread of the HIV epidemic in South Africa.

8 Quest 4(4) 2008

Sexual behaviour Since most new infections in South Africa take place through sexual contact, individual sexual behaviour is very important in understanding the epidemic. One important factor is starting to have sexual intercourse at a young age. In South Africa the average age of first sexual intercourse – called sexual debut – is decreasing. Other important factors are: ■ Numbers of sexual partners. The more sexual partners a person has, the greater the probability that they will have sex with someone who is HIV-infected. ■ Condom use. Condoms can be highly effective in preventing the transmission of HIV during sex, but must be used consistently to afford protection. Levels of condom use vary widely across the country. Condom use is also influenced by a wide range of factors, including how easily available condoms are, perceived risk of HIV, and partner attitudes. Condom use is also greatly reduced when either partner uses alcohol or other drugs. An additional factor in the spread of HIV in South Africa is the role of coercion and violence in sexual relationships. While many studies assume that women and men freely choose who they have sex with, the high levels of rape in South Africa show that this often is not the case. Poverty and migration as drivers of the HIV epidemic South Africans move a lot – usually between rural and urban areas. This movement is generally driven by poverty and the need to find work. This movement separates stable partnerships and results in more people taking multiple sexual partners – men and women. Truck drivers are at particularly high risk of infection because they are away from home for long periods of

time, often in difficult and dangerous circumstances if they drive outside our borders. The highest prevalence of HIV is found in urban areas and along transport routes. The role of poverty in the South African HIV epidemic is controversial. As elsewhere in the world, poverty plays an important role in increasing vulnerability to HIV/AIDS. Individuals of lower socioeconomic status are often at increased risk of becoming infected with HIV, for example through their increased exposure to high-risk situations such as sexual partnerships where they are unable to negotiate condom use. Similarly, poverty may contribute to a worse prognosis for individuals who are already HIVinfected, for example by reducing access to appropriate healthcare services and good nutrition. In both cases, poverty is not actually a biological

cause of HIV or AIDS, but may be an important factor because it places people at an increased risk of infection and its consequences. Understanding the spread of HIV in South Africa and the current state of the epidemic is a critical first step in any attempt to reduce the impact of the virus. The extent of the HIV epidemic is massive, making it the single most important public health issue in South Africa, and the factors influencing the spread of HIV are complex and multifaceted. Insights into the distribution of HIV in the country and the factors that promote the spread of the virus play an important role in shaping interventions to prevent new infections as well as promoting the health of infected individuals. Acknowledgement: This chapter is based on the chapter on epidemiology of HIV in Handbook of HIV Medicine. Edited by

Taking the medicine HIV is a chronic disease. It leads to AIDS and eventually death unless the infected person takes antiretroviral therapy – for the rest of their lives. Catherine Orrell discusses the importance of adherence to treatment. – this suppression of the virus does not continue. Because suppression of the virus is the only way to prevent progression to AIDS, this makes sticking to treatment vital. In scientific terms this is referred to as adherence to therapy. If the infected person doesn’t adhere to their therapy – that is, they regularly miss doses – the virus may be only partially suppressed, which may allow it to develop resistance to the treatment. ▲ ▲

What does antiretroviral therapy do? Antiretroviral therapy acts in various different ways to stop HIV replication, thus reducing the damage HIV does to the immune system. Unfortunately it doesn’t cure the infection, but it does prevent the infected person from becoming ill. Antiretroviral therapy halts the progression of the disease. However, if the treatment isn’t taken correctly – and every day as prescribed

What are CD4 counts and viral loads? The CD4 count is the number of CD4 lymphocytes that are present in the blood of a person living with HIV. This count is regarded as the ‘gold standard’ to show the strength of the immune system. Once an infected person’s CD4 count starts to fall that means that the immune system is starting to suffer from the effects of HIV infection. A normal CD4 count is between 800 and 1000. In South Africa a person is usually started on antiretorival therapy when the CD4 count has fallen to below 350, but that figure is only a guide and other factors, such as the state of the person’s health, may mean that they start treatment sooner than this. The viral load is the actual number of viral particles present in the blood of an infected person. Once a person starts taking antiretroviral therapy his or her CD4 count should rise and the viral load fall. If these two things do not happen it means that treatment is failing for whatever reason.

Douglas Wilson, Mark Cotton, Linda-Gail Bekker, Tammy Meyer, Francois Venter and Gary Maartens. Published by Oxford University Press, 2008. ■ Landon Myer is an Associate Professor in the Infectious Diseases Epidemiology Unit, School of Public Health & Family Medicine, University of Cape Town. Further reading Department of Health of South Africa. 2007 Report: National HIV and syphilis prevalence survey, South Africa, 2006. Pretoria: Department of Health. Dorrington, R.E., Johnson, L.F., Bradshaw, D., Daniel, T. 2007. The demographic impact of HIV/AIDS in South Africa. National and Provincial indicators for 2006. Cape Town: Centre for Actuarial Science Research, South African Medical Research Council and Actuarial Society of South Africa. Gouws, E. ‘HIV incidence rates in South Africa. 2005’ In: HIV/AIDS in South Africa. SS Abdool Karim and Q Abdool Karim, eds. Cape Town: Cambridge University Press Southern Africa. Pages 67-78. Shisana, O., Rehle, T., Simbayi, L.C., Parker, W., Zuma, K., Bhana, A., Connolly, C., Jooste, S., Pillay, V., et al. 2005. South African National HIV prevalence, HIV incidence, behaviour and communication survey, 2005. Cape Town: HSRC Press.

What is antiretroviral therapy? Binding to receptor and co-receptors HIV in plasma

Fusion and virus entry 1

Uncoating 2 3 Viral DNA integrated into CD4 nucleus

Reverse transcription

Transcription and translation

Assembly 4 Budding 1 2 3 4 5

Maturation 5

There are two classes of entry inhibitors: fusion inhibitors and chemokine receptor antagonists. There are two classes of reverse transcriptase inhibitors: nucleosides and non-nucleosides. Integrase inhibitors. Protease inhibitors. Maturation inhibitors.

This diagram shows where antiretroviral drugs act in the cell and the way in which HIV replicates within a cell. There are three classes of antiretroviral drugs available in South Africa: nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), and protease inhibitors (PIs). ■ Nucleoside and nucleotide reverse transcriptase inhibitors (NRTI) inhibit reverse transcription by being incorporated into the newly synthesized viral DNA and preventing it growing. ■ Non-nucleoside reverse transcriptase inhibitors (nNRTI) inhibit reverse transcriptase directly by binding to the enzyme and interfering with its function. ■ Protease inhibitors (PIs) target viral assembly by inhibiting the activity of protease, an enzyme used by HIV to cleave proteins that are just starting to develop for final assembly of new viral particles. A combination of these drugs suppresses viral replication, allows the patient’s CD4 count to rise and so allows their immune system to keep HIV under control.

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

In South Africa we have limited treatment options available because of the cost and availability of drugs in the public health service. Most people are started on one particular combination of drugs and if that fails, there is only one other combination available. This makes it particularly important that people adhere to their treatment because there are few options available if the treatment fails. How often is enough? Taking treatment, in the correct dosage, at the correct time every day is 100% adherence – and this is ‘enough’! Missing more than three doses of a drug that has to be taken twice a day over a 30-day period (less than 95% adherence) reduces the chances that the virus will be fully suppressed. If adherence drops to below 95% there is a progressive risk of failure of virological suppression. From information about how people take drugs for other chronic diseases, such as asthma or diabetes, we know that people seldom manage even 95% adherence. This makes hitting the

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target of 95–100% in HIV particularly challenging. How are adherence and resistance linked? This is not a simple straight line (linear) relationship. We know that patients who take very few of their drugs do not cause resistance in the virus because the lack of drugs means that the virus is not subject to any selection pressure from the drugs. Any drug-resistant mutants that do occur do not have any advantage over the non-resistant strains. Patients who have adherence of 95% or more suppress the replication of the virus completely and mutations do not occur. Resistance is selected for by patients who have moderate adherence. They are taking their drugs sufficiently often to stimulate mutations, but not often enough to suppress viral replication. So the resistant mutant strains have a selective advantage. While all antiretroviral drugs are susceptible to resistance, the degree of susceptibility varies. A single viral mutation results in complete resistance to the non-nucleoside reverse transcriptase inhibitors (NNRTIs), i.e. efavirenz and nevirapine. Similarly 3TC is made ineffective by a single mutation. In contrast, other nucleoside reverse transcriptase inhibitors (NRTIs) and the protease inhibitors (PIs) are more robust, requiring multiple viral mutations before resistance develops. Because resistant virus is only generated if there is enough drug pressure to drive the development of these mutations, different antiretroviral classes are vulnerable to resistant strains of HIV at different adherence rates. Resistance to a PI is found most often when adherence is between 80 and 95%, as high levels of drug are needed to create enough selective

pressure to allow a virus with multiple mutations to survive. Lower levels of drug do not create enough pressure and wild-type virus will remain the dominant virus. On the other hand, resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) is more likely at less than 80% than at 80–95% adherence. The single mutation that confers resistance to an NNRTI does not have an impact on the virus’s ability to replicate. Higher drug levels suppress the virus and do not allow generation of this mutation. Lower levels of NNRTIs commonly cause resistance. Despite these complexities, the message to an individual on antiretroviral therapy remains the same. Long term viral suppression will only be achieved with near perfect adherence (>95%). Measuring adherence There are a number of methods that are used to measure adherence. These are usually classified as objective (data recorded independently of the patient) or subjective (data provided by the patient). Objective assessments Objective adherence assessments include: ■ Pill counts: Counting returned medication in order to estimate the number of doses taken. This is often used. To calculate adherence you need four variables: • The number of tablets returned (for each medicine), e.g. 9 3TC tablets left in the bottle. • The number of tablets dispensed (for each medicine), e.g. 60 3TC tablets. • The number of days between the visits, e.g. 28 days. • The number of doses of the medicine per day, e.g. twice a day for 3TC. The adherence for this example would be: (no.tabs dispensed) – (no.tabs returned) (no.days between visits) x (doses per day) = =

(60) – (9) (28) x (2) 51 56

= 91%

Although valuable, this calculation can be time consuming in a busy clinic. The load can be shared by having the pills counted by a counsellor or pharmacy assistant

when the patient arrives, and the doctor or nurse simply completes the calculation. There is also a risk of people discarding their tablets to ‘improve’ their adherence, although this is not common. Surprise or unannounced pill counts at home may decrease the risk of pilldumping, but would require a dedicated team of counsellors to visit clients at home, and is not practical when monitoring adherence on a large scale. ■ Pharmacy refill data: Adherence that is assessed by pharmacy refill data has been shown to predict virological failure and survival in Zambian and South African studies. This is the simplest method of objectively recording adherence and is the best way to monitor adherence in large antiretroviral programmes. The number of times a patient receives medication over a fixed period, e.g. a calendar year, is expressed as a percentage of the number of times they should have collected medication, e.g. patient collected medication 11 times out of an expected 12 in the previous year = 92%. ■ Electronic monitoring: The use of electronic devices that record each time a bottle is opened is rare outside the research environment. These devices are expensive and need computers and software for downloading the information when the bottle is returned. This method is, however, accepted as one of the best means of objectively assessing adherence in the developed world. ■ Therapeutic drug monitoring: Measuring plasma concentrations of antiretrovirals is useful in selected patient subsets, for example patients whose viral load is rising in spite of the fact that they are taking their treatment correctly. These people may be absorbing the drugs poorly for some reason. But this is not a useful tool for general measurements of adherence. Patients also adhere best around their clinic visit, so-called ‘white coat adherence’, so measuring drug concentrations tends to overestimate adherence.

Risk factors for poor adherence Factors that may have either a positive or a negative impact on an individual’s pill-taking behaviour may be divided into three categories: patient-related, regimen-related and disease-related. These are shown in the table on p.12. With the simple regimens available as first-line therapy, the major impact on adherence lies with the individuals on therapy and their interactions with their families, communities and their health carers. The more favourable these relationships, the more likely an individual is to remain adherent over time. The value of an individual accepting their HIV status and being properly prepared for therapy should not be underestimated. Many people simply forget to take their medication. The use of devices such as pill boxes and diaries to remind them to take their antiretroviral therapy can be beneficial. Interestingly, educational level and gender seem to have no effect on levels of adherence, although younger people may be slightly less adherent than older.

A pill box that can be used both to remind someone which drugs to take when and to measure whether or not the person has been taking medication.

▲ ▲

Subjective assessments Subjective adherence methods are notoriously insensitive, but better results are obtained by adopting non-

judgmental attitudes and gaining the patient’s trust. Subjective assessments include: ■ Recall questionnaires: These are the most widely used tools to collect adherence data, usually asking the patient to recall doses missed over the past three days. Adherence percentage would be calculated based on the answer, for example missing one dose out of the six doses that should have been taken in the last three days means that five of six doses were taken; 83%. Many people will not admit to missing a dose when asked by their healthcare team, and so a recall questionnaire often results in an over-inflated estimate of individual adherence. This method may be more useful as a research tool as more open, accurate responses might be expected when results are not reported to the clinical team. ■ A 30-day visual analogue scale (VAS) of doses taken may be a faster and more efficient means of obtaining similar information to the recall questionnaire. Measurements of adherence are always approximate. But they do give us information that can be used to concentrate on particular people who need more help with adherence.

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Factors that influence adherence

Patient factors

Promoting adherence

Reducing adherence

• Comfortable with HIV-positive status • Motivated patient with a good sense of self-worth • Good understanding of HIV disease and therapy pre-treatment • Good understanding of importance of adherence • Education given in a patient’s home language prior to and during therapy • Use of diaries, pill boxes, etc. as reminders to take antiretrovirals

• Fear of disclosure of HIV status (to close family/friends) • Substance abuse, including alcoholism • Depression (or other mental disorder) • Anxieties or suspicions about the disease or therapy • Disorganised or disrupted daily routine, e.g. shift workers, truck drivers

Disease factors • Late or symptomatic HIV disease

• Still healthy with no symptoms

Therapy factors • Simple regimen with a small number of • Large numbers of tablets or complicated therapy tablets per day • Having to purchase therapy (financial • Easy access to free therapy constraints) • Noting positive heath benefits of • Severe or ongoing minor adverse events/ therapy with few adverse events reduced quality of life on treatment

Of these factors, disclosure and support by a treatment partner or peer counsellor have been shown to have a great impact on adherence. What can be done to improve adherence? Pre-treatment interventions People starting treatment need to be well prepared. Everyone should be provided with a standard set of information to ensure that they have a basic understanding of HIV and antiretroviral therapy before they start treatment. Caregivers, particularly of children and adults with a mental illness, also need this information. A ‘treatment buddy’ should be identified by the patient if possible and also educated about HIV and antiretroviral therapy. Education can be individual or in groups. Groups are more efficient and also allow a person to meet other HIVpositive people to help them overcome the stigma associated with the disease. Pre-treatment education should cover: ■ A simple explanation of HIV, including what would be expected

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in each stage of the illness from stage 1 to 4. ■ Details of symptoms that would be of concern (e.g. loss of weight, cough for more than two weeks). ■ Advice on living healthily with HIV (including nutritional advice) and how to prevent spread to other adults (e.g. safe sex and condom use) and from mother to child. ■ A short explanation of viral load and CD4 count. ■ An explanation of antiretroviral therapy, including the expected decrease in viral load and increase in CD4 count. ■ A discussion on the importance of adherence to therapy, explaining that treatment is lifelong. ■ Details of the actual antiretroviral therapy to be taken including names of the medications, colour and number of tablets per day, dosing (e.g.12-hourly not twice a day), and what to do if a dose is missed. ■ Explanation of common or severe adverse effects and what to do or who to call if these occur. This information can be given by a peer educator or counsellor over multiple group sessions, during the week or two weeks before starting therapy. Patients also need written material that they can take away and read at their leisure. Before antiretroviral therapy is started, the individual’s understanding should be checked with a few simple questions, e.g. how many different tablets must you take/what is a CD4 cell/how long must you take this treatment for? If knowledge is poor, provided the patient is not too ill, he/she should be encouraged to

repeat the sessions before treatment starts. Although not ideal, if antiretroviral therapy is needed urgently, for example for prevention of mother-to-child transmission or very late stage disease, education can be repeated during the first month on therapy. Interventions during treatment Most ‘treatment-ready’ people (80-90%) who start therapy take their medication correctly and might be expected to have very few viral particles in their blood by six months. However, some people never manage to take their pills correctly, and others tire over time and begin to miss doses due to pill-fatigue. These less adherent people need to be identified and targeted to receive more intensive adherence input. Identifying those at risk means that the adherence must be monitored using at least one of the measures described above throughout an individual’s time on antiretroviral therapy. Anyone who has an adherence approaching 80% or less, or who has a viral load that is not suppressed at any time after baseline, should receive attention from the healthcare staff. Step-up interventions are effective; more than 50% of those whose viral load starts to rise manage to achieve viral load suppression again. A stepped-up adherence intervention might include: ■ Time with a counsellor to discuss and resolve issues that may be leading to non-adherence or failure, e.g. non-disclosure, substance abuse, chaotic lifestyle. ■ Time with a doctor or a nurse to discuss and resolve issues that may be leading to non-adherence or failure, e.g. wrong dosing or timing of doses, adverse events. ■ Repetition of the initial treatment information, with an emphasis on the importance of adherence. ■ Use of a pill-box or dosing diary. ■ A home visit by an adherence counsellor to assess home circumstances, where possible. ■ Dispensing medication and monitoring adherence monthly until adherence back above 80% or again virologically suppressed. Expanding access to antiretroviral therapy across the resource-poor areas of the world remains a daunting prospect and there remains an anxiety that the clinical and political pressure to enroll large numbers of people onto antiretroviral programmes may adversely influence the quality of

the service rendered. Both new and existing antiretroviral programmes need to maintain a focus on adherence and create systems and structures that withstand the process of expansion. Acknowledgement: This chapter is based on the chapter on adherence in Handbook of HIV Medicine. Edited by Douglas Wilson, Mark Cotton, Linda-Gail Bekker, Tammy Meyer, Francois Venter and Gary Maartens. Published by Oxford University Press, 2008. ■ Catherine Orrell is a senior researcher at the Desmond Tutu HIV Foundation at the University of Cape Town.

Further reading Antiretroviral Treatment Protocol. Provincial Administration of the Western Cape, South Africa. Version 2, April 2004. Available: or http://www. 04.PDF Bangsberg, D.R., Acosta, E.P., Gupta, R., et al. 2006. Adherence-resistance relationships for protease and non-nucleoside reverse transcriptase inhibitors explained by virological fitness. AIDS; 20(2): 223–31. Mills, E.J., Nachega, J.B., Bangsberg, D.R,. et al. 2006. Adherence to HAART: a systematic review of developed and developing nation patient-reported barriers and facilitators. PLoS Medicine; 3(11): e438. Mills, E.J., Nachega, J.B., Buchan, I., et al. 2006. Adherence to antiretroviral therapy in subSaharan Africa and North America: a meta-analysis. Journal of the American Medical Association; 296(6):679–90.

A double burden – HIV and TB HIV and TB have become co-epidemics across southern Africa and in August 2005, the World Health Organisation declared the TB epidemic in Africa to be a regional emergency. Researchers at the Desmond Tutu HIV Foundation are investigating different approaches to this problem.

TB in Africa The annual incidence of TB has risen two to three times in many countries in subSaharan Africa since 1990. Africa contains only 11% of the world’s population, but carries 27% of the global burden of TB and 30% of TB-related deaths. There are 2.4 million new TB cases every year in Africa and 540 000 TB-related deaths in Africa every year.

Treating TB TB is treated using a combination of different drugs. The full course of treatment takes six to eight months and the drugs have to be taken exactly as prescribed for this full period. The intensive phase is when four different drugs in tablet DOTS workers form a close relationship with patients. form are given for five days a week, for two to three months. The second phase is the continuation phase, in which two drugs are given for five days a week, for four to five months. First-time TB patients must be treated for six months, while patients who have had TB before must take TB medicine for eight months. If there are side effects from the medication, the patient must return to the clinic. Sputum tests are taken again after two months on treatment to check for progress, and at five or seven months to confirm whether the patient is cured. Children with TB are given different medicines and treated for four months only. The Department of Health in South Africa has adopted the World Health Organisation’s DOTS (directly observed treatment short course) method to ensure that patients stay on treatment. An important element of the strategy is the support and encouragement offered to TB patients for the entire six- to eight-month treatment period, where people are directly observed taking their medication at the clinic. At community level, DOTS is undertaken by non-governmental organisations (NGOs) using volunteers as ‘treatment supporters’. TB NGOs recruit, train and supervise members of communities to function as treatment supporters for TB clients. Supporters refer TB patients to the clinic when necessary. TB drugs are not easy to take. They can cause unpleasant side-effects, such as nausea and skin rashes.


being infected with TB. In fact TB is the most common opportunistic infection found in people who are infected with HIV. In areas where the prevalence of HIV is high, the DOTS programme is simply not working. Researchers from the Desmond Tutu HIV Foundation in Cape Town are studying the interaction between TB and HIV in various communities in ▲ ▲

The drugs that are used to treat both TB and HIV can be difficult to take.

s Stephen Lawn and his coworkers point out, current tuberculsosis (TB) control measures are failing – mainly because of the epidemic of HIV. Why is TB increasing? The simple answer is because of the numbers of people who are living with HIV in Africa. People who are infected with HIV have an increased chance of

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HIV progressively destroys the immune system. This means that, even if the numbers of HIV infections are not rising, the rates of infection with TB will continue to rise.

Table 1. TB notifications and the prevalence of HIV infection in a Town between 1996 and 2004 Year No of TB Population TB notification notifications size rate, cases/ 100 000 persons 1996 32 5518 580 1997 42 6429 653 1998 67 7339 913 1999 74 8250 897 2000 90 9161 982 2001 142 10 071 1410 2002 150 10 982 1366 2003 175 11 892 1472 2004 188 12 803 1468

community close to Cape TB re-treatment rate (%) 3 21 7 20 17 15 18 22 24

Estimated prevalence of HIV infection (%) 6.3 8.9 11.6 14.2 16.5 18.4 19.9 21.1 21.9

Source: Lawn, S.D., Bekker, L-G., Middelkoop, K., Myer, L and Wood, R. Impact of HIV infection on the epidemiology of tuberculsosis in a peri-urban community in South Africa: the need for age-specific interventions. Clinical Infectious Diseases 2006; 42: 1040–7

Top: TB notification rates used to be higher among older people. Above: TB services need to be extended within communities.

the Western Cape. TB is a notifiable disease and the table above shows the numbers of TB notifications and the prevalence of HIV in a community in greater Cape Town. You can see that the TB notification rate rose steadily over this time period,

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as did the prevalence of HIV infection. However, an important aspect of the rising number of TB cases in this community is the fact that the ages of people who are falling ill with TB are changing. Historically, TB notification rates in this particular community were higher in people over the age of 60. But, by 2003 to 2004, the rates were highest among the 30–49-year age group. This is exactly the age group who are working – who are economically active and who have the most dependents. A particularly worrying aspect of the research was that TB rates are rising among adolescents – especially girls – with TB rates among 10–19-year-olds reaching 436 cases per 100 000 persons in 2004. According to Stephen Lawn and his co-researchers, this mirrors the prevalence of HIV among men and women in this age group. Because of the nature of the two infections, the risk of TB increases as

Intervention strategies The WHO DOTS TB control strategy is central to TB control, but is clearly no longer working in areas where HIV is common. Additional measures are needed. This research suggests that different strategies need to be aimed at different age groups – children, adolescents, those aged 20 to 49 years and those aged more than 50 years. Many of the children who developed TB in 2004 were infected with HIV. So interventions to reduce the transmission of HIV from mother to child need to be strengthened. Pregnant women need voluntary counselling and testing for HIV and those who are infected need access to antiretroviral treatment. TB diagnostic and prevention services for adolescents and teachers need to be introduced into schools. Working people need TB and HIV intervention in healthcare facilities and in the workplace. People in this age group are often diagnosed with HIV only after they have been found to suffer from TB. This means that strategies are needed to diagnose HIV before the person gets TB – which in itself will reduce the incidence of TB infection. Role of antiretroviral therapy in preventing TB Antiretroviral therapy reduces the risk of TB by 70–90% in someone who is infected with HIV, according to research. So anyone who is found to have TB should be offered voluntary counselling and testing for HIV and, if positive, be offered antiretroviral treatment. ■ Recurrent TB TB is an infection that you can get over and over again. In areas such as South Africa, where TB is very common, almost everyone has been exposed to TB. Most people’s immune systems prevent the disease from taking hold – the Mycobacteria is not killed, but it is stored harmlessly in the body. If a person develops a disease such as HIV that depresses the immune system, then TB becomes active – and can be spread from person to person through the air. Someone who has already had TB may have inactive focuses of disease in his or her body. All it takes is immune system supression for the disease to re-occur.

Prevention is key The Emavundleni centre started as a vaccine trial centre. But, as Surita Roux explained to QUEST, the focus is now on all forms of prevention.


linical trials of HIV vaccines started in Cape Town under the direction of the Desmond Tutu HIV Foundation (DTHF) in 2005. The first two clinical trials were run out of the University of Cape Town and Guguletu Community Health Centre. But this meant limited space, and in 2006 work started on a state of the art vaccine centre at Crossroads, about 5 km from the temporary vaccine site. By 2007 the building was finished – the Emavundleni Vaccine Centre. The building was designed specifically as a trials site, with a laboratory and a well-equipped pharmacy on site. However, as Dr Surita Roux explains, a vaccine is only one possible way to prevent HIV transmission. Which is just as well, because all vaccine trials, everywhere in the world, have stopped. The original trials Researchers working from the Emavundleni centre were concentrating on two vaccine trials – the Phambili trial , which was using the Merck Clade B vaccine and another study named HVTN204. There were a total of 166 people enrolled in the Phambili trial and 80 in the HV10204 trial. Why did the vaccine trials stop? Trials of the Merck product stopped in November 2007, when investigators found that the vaccine simply did not work. It did not prevent HIV infection and it did not reduce the amount of HI virus in the study participants who became HIV positive during the trial. More important than this was the suggestion that those people who had been vaccinated might in fact have been infected with HIV more easily after exposure to HIV. This increased susceptibility to infection is thought to be associated with the adenovirus type 5 (Ad5) – the common cold virus – that was used as part of the vaccine. People who carried immunity to the

The Emavundleni Vaccine Centre.

Emavundleni centre – the interior.

Ad5 virus – and there are lots of them because the common cold is, well, common – appeared to be at greater risk of HIV infection after being exposed to the virus. Where to now? Obviously there was global disappointment and concern over the results of the failed vaccine trials. Scientists are now back to the drawing board – quite literally – as they start basic laboratory immunological work to see what went wrong and where to go next. But in the Crossroads community the vaccine trial participants were quite

accepting of the results. This shows just how well the trial staff had done their job of education and community advocacy. People were told that this was an experiment – and they understood that it might not work. However, the focus of the Emavundleni centre was not just vaccines. Prevention is a broad issue. Staff from the clinic are involved in all forms of prevention and this starts with education. Educated people are empowered and can make decisions. The clinic also offers voluntary testing and counselling services and refers those who test positive to one of the many antiretroviral treatment centres in the community. In November and December 2008, the centre will start trials looking at the acceptability of microbicides –a vaginal preparation that can prevent HIV transmission. The first trial will not involve a specific microbicide, but will examine how prepared women in the community are for the concept, by looking at how well they accept a vaginal ring that will be used to deliver the microbicide. Although there are many scientists who believe that HIV will not be controlled until an effective vaccine is available, staff at the Emavundleni centre see prevention as a broad intervention, with education as the key to unlocking the potential of medical prevention techniques. ■

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Fact file Q HIV vaccines – the facts HIV vaccines may not work like other vaccines

We still don’t know exactly how an HIV vaccine will work but it is very likely that the mechanism will not be like that of other vaccines. An HIV vaccine may totally prevent infection – called sterilising immunity. This may work in 100% of the population or it may work in only certain sections of the population. Another possibility is that an HIV vaccine will not prevent the initial infection, but will prevent the transmission of the virus from an infected individual to another person. Another possibility is that an HIV vaccine will simply slow the progress of infection – delaying the onset of the infections related to HIV infection. This is a list of the ways that scientists think that an HIV vaccine might work: ■ Sterilising immunity • complete protection from HIV infection • no detectable HIV at any time • no transmission of HIV to others ■ Transient infection • infection occurs, but the immune system is able to detect and kill off infected cells • disease process does not advance, because the immune system is able to control the infection • no detectable HIV Page at later est2 ad 2008 10/14/08 11:27 AM 1 times (6–12 months after infection)

• seroconversion (becoming HIV+) may or may not occur • transmission to others might occur within a brief window of time, or might be completely prevented ■ Long-term controlled infection • undetectable or very low viral load throughout life • no harmful drop in CD4 cells • no immunodeficiency disease progression (HIV does not advance to AIDS) • seroconversion likely • transmission to others prevented or greatly diminished ■ Altruistic vaccine • little benefit to vaccinated individuals; however, the vaccine could help to prevent transmission of infection to others • viral load in mucosal secretions would remain low, so the vaccinated individual may remain healthy for a longer period of time

Different HIV vaccine strategies Unlike other viral vaccines, it is not possible to use attenuated or even dead HIV particles. Even though the risk of infection is tiny, in this disease that risk cannot be taken. So there is a different approach. Scientists take small parts of the HI virus and alter them in a laboratory to create synthetic copies. The experimental vaccines do not use whole or live HIV. The vaccines cannot cause HIV or AIDS. The vaccines C





being tested should produce either antibodies or cytotoxic T cells (CTLs) to fight infection.

Types of experimental HIV vaccines ■ Peptide vaccine: made of tiny pieces of proteins from the HI virus. ■ Recombinant subunit protein vaccine: made of bigger pieces of proteins that are on the surface of the HI virus. Examples of a recombinant subunit protein are gp120, gp140 or gp160 produced by genetic engineering. ■ Live vector vaccine: non-HI viruses engineered to carry genes encoding HIV proteins. The genes are inserted into another vector, which carries them into the body’s cells. The genes in turn produce proteins that are normally found on the surface of the HI virus. This type of vaccine most resembles the HI virus but is not harmful. Many vaccines used today, like the smallpox vaccine, use this approach. ■ DNA vaccine: uses copies of a small number of HIV genes which are inserted into pieces of DNA called plasmids. The HIV genes will produce proteins very similar to the ones from real HIV. ■ Vaccine combination: uses any two vaccines, one after another, to create a stronger immune response. Often referred to as ‘prime-boost strategy’. ■ Virus-like particle vaccine (pseudovirion vaccine): a non-infectious HIV look-alike that has one or more, but not all, HIV proteins.




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V I S I T O U R W E B S I T E AT W W W. U J . A C . Z A / S C I E N C E O R C O N TA C T U S O N 0 1 1 5 5 9 2 4 5 9

Q Science in action

‘Acacia paradoxa’ (Kangaroo wattle) in Table Mountain National Park.

‘Acacia cyclops’ (Rooikrans) tree.

This weed is currently only found in one moderately invasive population on the slopes of Table Mountain and may represent an incipient weed that is emerging from a lag phase.

’Acacia saligna’ (Port Jackson) tree. Photosgraphs: John Wilson

What can genes tell us about INVASIVE SPECIES? Identifying alien plant species accurately is crucial to their management in the South African environment. Jaco Le Roux from the Centre for Invasion Biology at Stellenbosch University tells how molecular genetics can be used. It was nevertheless estimated in 2001 that South Africa loses up to R21 billion annually as a result of losses of ecosystem services and environmental impacts caused by invasive species. Given the difficulty of quantifying such monetary values and the extensive number of invasive species in South Africa, this is likely to be a very conservative figure. The South African government realises the urgency of these ‘natural’ capital losses and has established programmes specifically aimed at reducing and countering the impacts of weeds and pests. The current and projected extent of invasive species and their impacts in South Africa call for integrating all possible management approaches. Maintaining appropriate levels of invasive species management and protecting South Africa’s natural resources over the long term will require increased resources. More importantly, management programmes will have to be innovative and will have to come up with novel approaches to keep pace with the anticipated increases in the numbers of introduced species in the future. To date, most molecular genetics ▲ ▲

Invasive species in South Africa If he was still around, Charles Darwin may not have been surprised by the extent and impact of alien invasive species around the globe today, as he noted in his 1859 publication The Origin of Species, the ease by which non-indigenous species naturalise in their new non-native environments. Invasive species are those species that occur, as a result of unnatural dispersal and movement, beyond their accepted and historical normal distribution and which threaten valued environmental, agricultural or other social resources. South Africa is home to an estimated 9000 alien plant species, some of which contribute to R30 billion in annual losses in the agricultural industry. It is difficult to obtain similar estimates that accurately reflect damages and losses of ‘natural’ capital. For example, what is the economic value attached to the reduction of species biodiversity or the alteration of ecosystem functions? A single ecosystem can supply numerous services. For example, a wetland can offer fishing, act as a biofiltration system for human-produced wastes, be home to diverse groups of species or protect surrounding areas from flooding.

Students and a professor (John Hoffmann) discussing biological control of Acacia longifolia. A gall-forming wasp, intentionally introduced from Australia, has greatly reduced seed production of this invasive tree, thus reducing its invasive capacity. Photograph: Dave Richardson.

A water management programme As an example, the Working for Water (WfW) programme was started in 1995 to conduct and coordinate alien plant management throughout South Africa. WfW is a multidisciplinary initiative with a primary focus on social upliftment and job creation throughout the country. Hailed both locally and internationally for its socio-economic achievements, the programme has also proved highly successful at managing certain invasive species that are threatening South Africa’s natural resources, particularly fresh water. WfW is currently one of the single largest conservation efforts in the world and since its inception has cleared more than one million hectares of invasive alien plants, providing jobs and training more than 30 000 people annually.

Quest 4(4) 2008 17

Invasive species management – a genetic approach A novel approach to enhance the efficiency by which invasive species is managed involves the use of molecular genetics and DNA technology. Charles Darwin would have been impressed and maybe even surprised by the scientific progress that stands firmly on the foundations laid by his 1859 publication. A mere century later James Watson and Francis Crick published the double helix structure of deoxyribonucleic acid (DNA), an achievement that gave a name and description to the variation that was invisible to Darwin and won them the Nobel prize. This variation is what underlies every single biological feature that we know. Today, little over half a century after the momentous discovery of DNA, research and technology have reached horizons stretching far beyond the imagination of any of these pioneering naturalists and scholars at the time of their discoveries. Biotechnologists now rearrange many biological features of different species in a copy-and-paste fashion of DNA. Genes for freeze tolerance copied from the deep sea flounder have been pasted into strawberries, creating frost-resistant varieties. Genes sensitive to low levels of nitrogen dioxide have been inserted into plants, creating transgenic plant species that are capable of ‘sniffing’ out unexploded landmines! The double helix structure of DNA

research, especially biotechnology, has been aimed at improving food supply (agriculture) and human health (e.g. pharmaceuticals and cancer research) with comparably fewer efforts focused on the wellbeing of natural ecosystems and resources. But this is slowly changing as research programmes around the world are now also applying advances in The basic steps that occur during biological invasions

Establishment lag period













Ecological and human impact


Abundance of invader Native elsewhere Successful transport


Establish in new areas


Is invasiveness correlated with life history traits? What are the genetic differences between native and introduced populations?

Lag period Spread (exponential growth) Ecological impact Human impact

What factors influence propagule pressure and how does this influence establishment? What environmental conditions facilitate establishment? Which life history stages are more suited for management? What is causing lag? Genetic or population factors or both? How does dispersal mode and reproductive system influence spread? What are the genetic consequences (structure) of spread? How do landscape characteristics influence spread?

What are biodivserity impacts and how are these measured? What properties determine the extent of the impact? What are the economic lessons associated with invasions?

This figure shows the basic steps during biological invasions. Species are transported deliberately or accidentally into their new environment. Species then need to establish or form self-sustained populations. Following establishment many species often remain in low numbers without spread into their new environment. This may reflect genetic constraints on local adaptation or the consequences of absolute population growth rates. This lag phase is normally followed by an exponential growth phase, rapid dispersal and spread into favourable habitat. Growth reaches a saturation point (asymptote) that represents the point when most available and suitable habitat has been occupied. A series of questions related to management at these steps where molecular genetics may aid is shown. This figure has been modified from Sakai et al. 2001.

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molecular genetics in a way that allows us to better understand biodiversity, global climate change, impacts of invasive species and the conservation of rare and endangered species. Effective management of invasive plant species requires knowledge of basic biological processes that were, prior to the recent advances in molecular genetics, hard to clarify or quantify under field conditions. For example: How far do seeds disperse and how do populations move and disperse into particular environments? How long does seed survive in seed banks and what are the sizes of seed banks? What landscape and environmental characteristics make invasions easier? A better understanding of these processes will not only help in identifying the best integrated approaches to combat invasive species but will also assist in strategic and policy-making decisions for programmes such as WfW.

An agreement between WfW and Stellenbosch University’s DST-NRF Centre of Excellence for Invasion Biology (C·I·B) has set the platform for a comprehensive research programme in South Africa to investigate the molecular ecology of plant invasions. Taxonomy and the native origins of weeds Many organisms, in particular plants, create unique taxonomic obstacles that make fast and reliable species identification difficult. Many plant species show great morphological variability within and among species, implying that it is not always easy and sometimes actually impossible to distinguish between closely related species on the basis of morphology alone. This becomes particularly problematic when we know that there are variants that occur below the species level, such as subspecies (see p.33). For example, Port Jackson (Acacia saligna), a widespread noxious weed in South Africa, has at least four known subspecies in its native Australia. These subspecies are genetically distinct and are not easily distinguished in the field. It is currently not known how many of these are present and invasive in South Africa. The genetic distinctness shown by subspecies will lead to distinctness for various adaptations such as habitat preference, physiological requirements and interactions and associations with other organisms. Species that

Part of a long-term collaborative research agreement that was signed between WfW and the DST-NRF C·I·B aims at improving the effectiveness of the alien plant management using genetic approaches. In terms of the agreement DST-NRF C·I·B will establish a research group to investigate the molecular ecology of various Australian Acacia species such as Rooikrans (A. cyclops), Black Wattle (A. mearnsii) and Port Jackson (A. saligna) that are invasive in South Africa. More specifically, it was agreed that the DST-NRF C·I·B will: 1. Develop capacity in South Africa to undertake coordinated work on the genetics of invasive plants. 2. Improve the success rate of biological control programmes by identifying the source populations of invasive alien plant species in their native range. 3. Improve strategic weed management decisions by understanding regional variations in weed populations in South Africa, in particular by identifying hybrids and new mutations. 4. Quantify the invasion risk posed by introducing new genotypes of non-native species by exploring the role of genetics in the lag phase of invasions and the link to climate. 5. Establish a plant material library for use in future research. 6. Quantify the risks of local invasion pathways by examining regional patterns of spread. 7. Identify possible mechanisms and sources of the spread of invasive plants at a local scale by determining the provenance of invasive populations. 8. Analyse the genetic consequences of biological control programmes on the agents released and compare the source of the agents released with the source of the plants. For further details go to:

Q Science in action The science of classification Taxonomy is the science of classifying organisms, i.e. naming living things. Biologists use the Linnaean taxonomic system, named after Swedish biologist Carolus Linnaeus (1707–1778), that breaks down organisms into seven major divisions, called taxa. The divisions are: Kingdom, Phylum, Class, Order, Family, Genus and Species, becoming more specific as you progress from kingdom to species so that many organisms belong to the same kingdom, fewer belong to the same phylum, and so on, with species being the most specific classification. These classifications also tell us something about the degree of relationship between different organisms. For example, two animals that belong to the same family and genus are more closely related than two animals that simply belong to the same family. The most widely accepted definition for a species was proposed by the biologist Ernst Mayr. It defines a species as a group of genetically distinct, interbreeding organisms. However, this definition would not include organisms that reproduce asexually such as most fungi, some plants, some insects and so on. In addition, morphology has been one of the most important taxonomic tools for centuries. However, biologists often do not know whether two morphologically similar groups of organisms can ‘potentially’ interbreed and thus whether they represent a single or multiple species. Recent genetic data reveal that genetically distinct populations may appear very similar morphologically while large morphological divergences may be found within the same population of a single species. Furthermore, there is considerable variation in the degree to which different species can outcross, especially plants. Taxonomy is thus complicated by numerous biological processes and not always straightforward.

A forest of invasive trees, with Acacia saligna (Port Jackson willow) in the foreground, and Eucalyptus species in the background. Dense stands like this totally transform natural fynbos communities by radically changing nutrient cycling regimes and other processes. Photograph: Dave Richardson.

How do subspecies arise? Subspecies normally result from geographic isolation over historical time, whereby populations of the same species become isolated so that in the absence of interbreeding, they become genetically distinct.

A lone shrub of ‘Hakea sericea’ in the fynbos in the Slanghoek Valley in the Western Cape. This species often forms extremely dense stands that supress the natural fynbos. Photograph: Dave Richardson.

A flowering branch of Acacia podalyriifolia (Queensland Silver Wattle). Queensland Silver Wattle is among the most widely cultivated wattle species due to its attractive flowers and fast growth rate.

Taxonomy and the management of invasive species So how can all of these taxonomic obscurities be linked to or contribute to the management of invasive species in general? The short answer is that sound taxonomy is the very first step towards making appropriate management decisions that may drastically influence the outcome of particular management strategies. For example, biological control is currently the most efficient and effective way to control weeds that are widespread in natural ecosystems. ▲ ▲

Photograph: Dave Richardson.

are genetically quite distinct but which cannot be distinguished on morphology alone are also known as cryptic species. On the flipside of the coin, genetic distinctness in noncryptic species is normally shown by the fact that these species do look different, thus making reliable identification on morphology alone straightforward. Some plant species also frequently interbreed with closely related species or subspecies, a process known as hybridisation. The occurrence of hybridisation can, in some instances, readily be seen when offspring are morphologically ‘intermediate’ between their parental species or lineages. However, in many cases hybrids remain undetected because they look like their parent species.

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Biological control Biological control makes use of natural enemies (control agents) such as fungi or herbivorous insects that parasitize or feed on the target species (hosts). Control agents are selected and collected from native range areas of the host plant. For example, exploration for control agents against invasive acacias in South Africa would thus be done in Australia. This is because the associations and interactions between host plants and natural enemies evolved over historical time.

The evolution of tightly knit interactions such as mutualisms, antagonisms or commensalisms is known as co-evolution, and has important implications for the success of biological control programmes. In native ranges, geographic and reproductive isolation will, in a way similar to the way that subspecies arise (discussed earlier), influence the underlying genetic signature of coevolutionary processes so that genetic signatures for co-evolved organisms become distinct. In other words, an insect species that is specialised to exist on only certain subspecies of a particular Acacia species would show genetic distinctness that mirrors that of their host subspecies. Historic geographical isolation that led to subspeciation in the host plant would have led to reproductive isolation among the insect species specialised for each subspecies. This would imply that host-enemy relationships will become genetically distinct with the potential of being cryptic and thus left unnoticed in the field. This clearly illustrates the need for sound taxonomy when dealing with biological control as a management approach. For example, a particular insect variant may have evolved to recognise one particular Port Jackson subspecies that it is associated with more easily than to recognise other subspecies. Such preferential associations between control agents and host species is know as host-specificity. Hostspecificity is not only an important factor that will influence the effectiveness of potential control. It will also influence the likelihood that control agents will have harmful and damaging effects on beneficial plants, a phenomenon known as non-target impacts. For example, South Africa is home to numerous indigenous Acacia species, which means that to find the most host-specific control Mutualism â&#x20AC;&#x201C; a symbiotic relationship in which both species benefit from the association. Antagonism â&#x20AC;&#x201C; a symbiotic relationship where one species benefits while the other is harmed. Commensalism â&#x20AC;&#x201C; a symbiotic relationship in which one species benefits from a relationshiop, while the other species neither benefits nor is harmed.

20 Quest 4(4) 2008

agents for Australian acacias we need to eliminate potential non-target impacts on these indigenous species. We can do this by looking for coevolutionary relationships using a phylogenetic comparison of DNA sequence data for both the host plant and the natural enemy of interest in their native ranges and matching that to genetic information (DNA) of

invasive populations. Phylogenetics is the study of evolutionary relationships between organisms based on genealogy, that is, their shared characteristics due to common ancestry. The rust fungus Uromycladium tepperianum was deliberately introduced to South Africa from Australia as a biological control agent

Q Science in action against Port Jackson. This fungus is known to have different genetic variants. But because at the time of introduction, we lacked current molecular technologies, we don’t know whether the best suited variant against Port Jackson was released in South Africa. Extensive host-specificity trials did show that the released strain was specific to Acacia saligna only, with no non-target effects. But, we still don’t know how many different strains of Port Jackson exist in South Africa. However, now that we can reconstruct phylogenetic relationships between A. saligna variants from Australia and those found in South Africa we can determine the number of subspecies present in South Africa. These data will also show us the geographical origins of South African variant(s) within Australia. It is these Australian regions that would be most likely to provide us with host-specific (co-evolved) and more damaging natural enemies of A. saligna. Phylogenetic analysis for all Uromycladium tepperianum variants associated with native Port Jackson variants will also confirm whether intraspecific variants are found in association only with certain Port Jackson subspecies. Research to show these relationships is currently underway at the DST-NRF C·I·B and will contribute to untangling coevolutionary relationships and improve biological control programmes against Port Jackson in South Africa. Hybridisation and managing invasive aliens Hybridisation also has important consequences for the management of invasive species. Making crosses between closely related species and invasives (outcrossing) can lead to offspring that have characteristics of both parents that can potentially lead to higher invasiveness, a process that leads to hybrid vigour. Hybridisation normally also inflates genetic variation in hybrids, enhancing their ability to adapt to new environments. Genetic approaches are the fastest and most reliable way to accurately identify such events, especially when offspring show

morphological characteristics that show that they come from one line of parents but not the other. In most plant species particular genetic regions are only inherited from one of the parents. Chloroplast DNA (found in the cell’s cytoplasm) is usually inherited from the mother as it is absent in pollen, while nuclear DNA (found in the cell’s nucleus) is inherited from both parents. DNA sequencing from nuclear and cytoplasmic regions will, in hybrids, lead to dissimilar evolutionary relationships. Chloroplast and nuclear gene regions in nonhybridising species leave the same genetic signature so that, when individually analysed, they show the same relationships within and between different species. Placing hybrid species in an evolutionary line using chloroplast genes will show relationships similar to the maternal parent’s relationships to other species. On the other hand, evolutionary relationships based on nuclear genetic information will be derived from both parents as a result of introgression. The genetic signatures of differently

Leaves and a woody follicle of the highly invasive shrub Hakea serica, an Australian member of the protea family. The absence of natural enemies of this species in South Africa results in it producing vast numbers of seeds, which enhances its ability to spread. Photograph: Dave Richardson.

inherited genes, when considered separately, will thus be different; showing that hybrids came from different genetic lines (species). For invasive species management such data can be valuable because it shows us the areas that need to be eradicated first because hybridisation has already occurred or where different parental species are likely to outcross. This needs a sound understanding of what pollinators are visiting plants and how far pollen is likely to move and how far and by what mechanism(s) do seeds disperse. Some Australian acacias that are invasive in South Africa such as the Black Wattle (A. mearnsii), Cootamundra Wattle (A. baileyana) and Silver Wattle (A. dealbata) are known to hybridise under plantation conditions, and that this may potentially also occur under field conditions. Novel morphological variants of Black Wattle have been observed in wild invasive populations in South Africa, raising the question of whether these are the result of hybridisation or whether they are new genetic variants as a result of mutation.

▲ ▲

Hybrid vigour is the superiority of a hybrid that is produced by crossing two different types of parent species that have one or more inferior characteristics compared to their offspring.

Introgressive hybridisation is the spread of genes from one species into the germ plasma of another species by hybridisation.

Quest 4(4) 2008 21

Spread and dispersal of weeds To better understand biological invasions and how to manage them, we need to understand landscape processes and the way in which they shape weed dispersal. For animals the direction, frequency and distance of dispersal are relatively easy to measure by mark-and-recapture studies that are carried out over long periods of time. For sessile terrestrial plants the situation is more complicated because movement is through the dispersal of seeds or vegetative plant parts. It is hard to quantify seed dispersal, and so the frequency, direction and distance of spread, in the field. There are three major types of seed dispersal: diffusive, long-distance and stratified. During diffusive dispersal, populations expand in a concentric fashion over short distances with movement into suitable habitats next to the currently occupied range, in the same way that an army advances across a front. Jump dispersal, as the name indicates, involves occasional long jumps from source

22 Quest 4(4) 2008

populations into the new environment, with new populations being established whenever suitable habitats are encountered. Stratified dispersal is a combination of diffusive and jump dispersal so that the initial (source) and distant (outlier) populations that result from long-distance jumps expand in a concentric fashion. Each of these patterns has implications for invasive species management. Each dispersal pattern also has characteristic genetic consequences that can easily be differentiated from one another using molecular genetic approaches. Dispersed seeds take all the genetic information derived from their source population along with them. The spatial and temporal distribution of numerous unlinked genes, also known as genetic structure, should thus give a good substitute for seed dispersal. A diffusive dispersal pattern would result in genetic structure that shows a gradient in genetic similarity when measured from the core of the source population to its border. Such a genetic pattern, also known as

isolation by distance, would show a strong correlation between geographic distance and genetic similarity, so that neighbouring populations are more genetically similar than geographically distant populations. Long-distance dispersal, on the other hand, would be characterised by a genetic signature indicating high similarities over much larger landscape areas (between source and outlier populations for instance). Seed movement and thus gene flow over such large temporal scales stop the formation of a strong population genetic structure. Spatial distribution of genetic diversity (the genetic structure) can be related to various environmental conditions such as rainfall, temperature, altitude, and vegetation to identify those habitats suitable for establishment and at highest risk of being invaded based on dispersal. Knowledge of dispersal would help conservationists in identifying areas for management prioritisation, defining the appropriate size of areas to be surveyed for the presence of outlying foci, and in determining the risk of re-colonisation from neighbouring populations following removal of given stands. Looking at dispersal distances would also identify how connected different populations are and so would help to identify â&#x20AC;&#x2DC;unitsâ&#x20AC;&#x2122; where simultaneous removal efforts would yield the best results. This would minimise recolonisation risks. Dispersal distances are also interesting from a biological control point of view. Those invasive species that disperse over long distances would need a control agent capable of dispersing over equally long distances in order to keep up with its target host. Genetic diversity Evolutionary theory predicts that populations with high levels of genetic diversity and correspondingly high levels of phenotypic variation are better equipped for adaptation to new environments. This is because higher levels of diversity will, by chance alone, increase the likelihood of harbouring individuals with traits that are better suited for survival in any particular environment. Indeed, various weedy species show high genetic diversities that have contributed to their success in their new environments. Molecular genetics can now be used to assess the amount and distribution of genetic diversity within and among invasive populations. Characterisation of gene diversity will allow the

Q Science in action identification of populations with high genetic diversity that should be the initial focus of eradication programmes. This will lead to a decline of gene diversity over time and higher levels of inbreeding that may hamper the species’ ability to spread and adapt. If genetic changes, and thus evolution, are common during biological invasions then it is important to understand the role of genetic diversity, and evolutionary analyses may need to be a major focus of work on invasive species biology. For example, studies of genetic variation may help to predict the potential for populations of invasive species to evolve in response to management practices such as resistance to herbicides or biological control agents. Genetically poor populations of invaders would be easier to manage since their chances of evolving resistance against management practices are lower. The importance of genetic diversity also cautions against multiple introductions and subsequent genetic augmentation of exotic species. Many species that are not currently invasive, such as escaped ornamentals, may be considered ‘safe’. Invasions can generally be depicted by a logistic growth curve so that, initially, species go through a lag phase followed by exponential growth. Lag phases may reflect the consequences of genetic constraints such as inbreeding, low genetic diversity and adaptive ability. Many species have only become serious weeds after a long lag phase and after genetic augmentation via separate, multiple introductions, which increase their genetic diversity, and thus their ability to adapt to their new environment. On the other hand, the consequences of genetic diversity can guide biological control programmes to evaluate the genetic diversity present in the control agents’ native populations. Such estimates should give insight into the minimum number of individuals (known as the effective population size) that need to be introduced to sustain sufficient levels of genetic diversity in order to avoid inbreeding. This will insure maximum adaptive potential for control agents in their new environment and thus effectiveness against their target hosts. What does the future hold? The age of functional genomics, the study of gene expression throughout whole genomes, is a new and rapidly

expanding field of enquiry in molecular genetics research. Whole genome sequences are becoming available for well-studied model organisms. Soon, major invasive weeds may be added to the list of species for which full-genome sequences are available; this will give researchers insight into the sub-cellular processes associated with biological invasions. This would allow for gene expression levels to be estimated under certain environmental conditions so that candidate genes for ‘invasiveness’ can be identified. For example, comparing genome-wide gene expression in invasive and native populations of weeds may lead to the identification of genes whose expression is associated with invasiveness. In the near future such genes could potentially be used as ‘invasiveness barcodes’ to screen closely related species for their potential to become invasive. Similarly, comparing different levels of gene expression between ‘more’ host-specific and ‘less’ host-specific variants of potential biological control agents may lead to the identification of important functional genes. Functional genes that directly influence host specificity, host recognition, confer virulence or pathogenicity, for example, can be valuable tools in novel and future approaches to controlling invasive species. Just as biotechnologists rearrange traits by copying and pasting their underlying genetic information between different organisms, next generation biological control agents may include transgenic pathogens or arthropods with enhanced virulence and host-specificity genes cloned into them. Such transgenic biological control agents may emerge soon as research using genome-wide gene expression to identifying virulence and pathogenicity associated genes is currently being done in laboratories around the world. Genetically inferior populations of plants, i.e. those harbouring traits that are detrimental or that significantly lower population fitness, can be created through classic artificial selection experiments and inbreeding. These populations can then be used to ‘swamp’ gene pools of invasive populations, allowing introgression of inferior traits to the detriment of invasive populations. Traits such as terminator seeds (seed incapable of germinating) have been introduced into agricultural transgenic varieties and may also prove useful against plant invaders; transgenic

Top: Echinopsis spachiana (torch cactus) is a species of cactus native to South America. It is commonly cultivated as a pot- or rockery plant in many parts of the world, including South Africa, where the species has spread from plantings in many areas and is classified as a major invader. The picture shows the species invading in semi-arid savanna near Kimberly. Photograph: Dave Richardson Above: The attractive Dutchman’s pipe (Aristolochia elegans) is widely used as an ornamental plant in many parts of the world. It was first recorded in the Kruger National Park in 1950. It was grown in at least six rest camps and has now spread into natural vegetation. Photograph: Dave Richardson

plants fertilise invasive plants to create terminator seeds, lowering propagule pressure and invasive ability. Analogous approaches have been used to combat some invasive insects whereby millions of sterile males are released into invasive populations to allow competition with wild males to fertilise females. This approach has been successfully applied to eradicate highly invasive Mediterranean fruit flies (Ceratitis capitata) in California in the USA. As global trade and travel increase every year, so does the number of potentially invasive species hitching a free ride. Genetic approaches will play an increasingly important role in solving problems associated with invasions and in finding improved and novel ways to deal with them. ■ Further reading Sakai A.K., Weller S.G., Allendorf F.W., Holt J.S., Lodge D.M., Molofsky J. With K.A., Baughman S., Cabin R.J., Cohen J.E., Ellstrand N.C., McCauley D.E., O’Neil P, Parker I.M., Thompson J.N. (2001) The population biology of invasive species. Annual Review of Ecology and Systematics, 32, 305–32.

Quest 4(4) 2008 23

The South African government is offering generous tax incentives to encourage the private sector to invest in research and development

Apply for Research

and Development Tax Incentives

The South African government is offering generous tax incentives to encourage the private sector to invest in research and development (R&D) activities in the country, in terms of section 11(D) of the Income Tax Act No. 58 of 1962.

Private sector enterprises in all economic sectors and individuals are eligible. To claim for the R&D Tax Incentives, taxpayers must do the following:

The R& D Tax Incentives are being administered by the Department of Science and Technology (DST) to encourage innovation and advanced scientific or technological research in the country. It has been in operation for a year, and received first applications in November 2007. The incentive consists of a deduction of 150% in respect of expenditure on eligible scientific or technological R&D undertaken by enterprises or individuals within the Republic; and an accelerated depreciation of assets used for purposes of scientific and technological R&D over three years at the rate of 50:30:20, starting from the year of assessment in which the asset is brought into use.

n Complete and submit information to the Department of Science and Technology as prescribed in the R&D Tax Incentives Form. This form is available on request and can be downloaded from the DST website: The forms must be submitted to the DST within six months of the taxpayerâ&#x20AC;&#x2122;s financial year end. It will be possible to submit these forms online in the near future. n Complete the relevant entries in the Income Tax Return Forms as prescribed by South African Revenue Services (SARS).

For more information about the R&D tax incentives, contact: Ms Dimakatso Mokone, Manager: R&D Tax Incentives, Department of Science and Technology on (27) 12 843 6560 or email:

Training champions – getting started.

Taking the initiative Through International Climate Change Champions, the British Council is encouraging young people to engage with issues of climate change. QUEST found out exactly what four of these young people are doing.


he International Climate Change Champions is an international project that falls under the British Council’s Low Carbon Futures Programme. The project manager is Chris Griffith, who outlined the project as a programme that targets learners and teachers, providing support for the climate change section of the South African school curriculum. This is being carried out in close cooperation with the

The Kobe Challenge To tackle climate change, we must recognise the challenge, accept responsibility and respond with integrity. ■ Integrate climate change into all education systems and demonstrate practical solutions to every community. ■ Introduce a strict international carbon-cap-and-trade system to limit emissions. ■ Provide technology and funding for those worst hit by the inevitable effects of climate change.

26 Quest 4(4) 2008

Department of Education. The ‘Champions’ are young people who are either in senior school or at university, who are selected to spread the word about climate change in their schools, universities and communities – and to get others involved. As part of the global programme, three schools in the Western Cape – the Cape Academy of Maths, Science and Technology (CAMST), Herzlia High School and DF Malan High School – were chosen to take part. City Varsity, Cape Town and the University of the Western Cape were also involved. The Western Cape pilot is overseen by mentors Gillion Bosman and Asanda Dodi. Zanelle van Zyl who will shortly matriculate from DF Malan High School, described how students were selected to take part in the programme,

through a competition that looked for innovation, creativeness and a youthfriendly approach to designing a media campaign to stimulate awareness of climate change. She elected to design a web site – – which is full of information on climate change, the carbon dioxide problem and what you – as an individual – can do about it. She has also started recycling intiatives at her school and takes her passion about climate change issues out into the wider community by talking to local community groups and newspapers about the issues involved. Zaid Philander is a second-year environmental science student at the University of the Western Cape, who was chosen as a Champion after he produced an innovative dress made of recycled material and asked a

Q Climate change

Offsetting emissions Each time Zanelle, Emma, Zaid and Albertus stepped into an aircraft and flew to their meetings they were adding to greenhouse gas emissions in the atmosphere. They were, of course, aware of this and the International Climate Change Champions project uses emissions offsets to mitigate the effects of their air travel. To do this, the project supports the Malavalli Biomass Power Project in Southern India. The project uses industrial waste to make electricity and heat and has created at least 500 jobs. Farmers also make extra money by selling their waste to the project. This is done through PURE (, a charity that gives funds to the Malavalli Project.

friend to stand in prominent places to stimulate questions and discussion. Zaid’s community outreach programmes include inviting local school children to the nature reserve on the Belville campus of the university and discussing issues around nature conservation and climate change. Students are encouraged to propagate indigenous plants at their schools and homes – a practice that he hopes to spread through the community. Emma Doubell, about to matriculate from Herzlia High School, has also started recycling initiatives at her school, concentrating on the enormous amount of paper produced for classroom materials. One positive result of this is that the amount of paper produced has decreased. Herzlia school notice boards are now full of posters about climate change and tips on how individuals can reduce their carbon footprint. Albertus Duba is unusual among these four because he is not a science student. He studies sound engineering at the City Varsity, Cape Town. Albertus is concentrating on local city radio stations – persuading them to introduce climate change into talk shows, jingles – anything that will raise awareness and attract attention. During this time, the Climate Change Champions have also met with scientists, industry leaders and government departments to broaden their understanding of climate change and to learn about current best practices. London, Kobe and Nairobi In March this year Zanelle, Emma and Zaid went to a meeting of the G8

Environment Ministers, where they gave presentations and had the opportunity to challenge the ministers on their country’s approach to climate change. In Kobe, Japan, in May this challenge was formalised into three statements and called the Kobe Challenge: Albertus did not travel quite as far afield. He attended the Tunza Africa Youth Environment Network (AYEN) conference in Nairobi last September. The conference was arranged under the United Nations Environmental Programme’s Regional Office for Africa (UNEP-ROA) with the theme: African Youth for a Sustainable Future. This conference provides a platform for young environmentalists from around the continent to meet and exchange ideas of better ways of conserving the environment. It is seen as a movement of young people around the continent to put together a pool of resources and information, in a regional effort to reverse climate change and to mitigate its effects. One of the biggest issues, according to Albertus, was that of sustainable development in a continent that desperately needs technology in order to grow its economy. These and other challenges have become a way of life for the Climate Change Champions, who now network with other young people as far away as India. The future Early in October, an extension to the current pilot programme in the Western Cape was announced in Johanesburg. Seven other provinces are

Top: Zaid with his creation. Above: Two South African Champions meet the UK Environment Secretary, Hilary Benn, at Number 10, Downing Street, London.

to be included in the programme and Climate Change Champions are to be recruited in each province. Although climate change will affect the whole region, each province faces different challenges and so will need different approaches. And it is these innovative approaches to climate change that the Champions will be tackling. ■

Quest 4(4) 2008 27

Figure 2. The SANAE-IV station on the Antarctic continent. Photograph: D.W. Hedding

Ant arct ic science for The Antarctic is an exciting and varied place to study science. David Hedding, Andrew Collier, Jennifer Lee and Brett Kuyper illustrate this during a recent Antarctic winter science school.

Figure 1. Manned South African bases on Antarctica, and Gough and Marion islands.

28 Quest 4(4) 2008

Antarctic science Antarctica is an integral component of the Earth system and it provides an exceptional archive of historical changes in the Earthâ&#x20AC;&#x2122;s environment. However, the Antarctic region is now changing more rapidly than any other region on the planet, primarily through climate change. The region is thus recognised as an extremely sensitive indicator of environmental change and provides a unique vantage point to study many terrestrial, oceanographic and cosmic phenomena. This makes Antarctic science crucial to understanding our planet and our impact on it. Unfortunately, even in this era of free information, much of the important work that is being conducted in the Antarctic does not filter through to the general public. The third International Polar Year (IPY; 2007â&#x20AC;&#x201C;2009) provides an opportunity to correct this. As one of the most ambitious coordinated science programmes ever attempted, the programme hopes to bring Antarctic science into the public consciousness. Involving thousands of scientists from over 60 nations, the IPY has inspired a wealth of interdisciplinary research in both the Arctic and Antarctic, and hopes to encourage future generations of natural

and social scientists and stimulate the development of new technologies. South African research in the Antarctic region South Africa has a long history of conducting research in the Antarctic and was one of the original signatories of the Antarctic Treaty in 1959. Originally, South African research in Antarctica focused on earth sciences (geology) and upper atmospheric physics (geophysics) but, at present, research is being conducted in space physics, biology, geodesy (measurement and representation of the Earth and its gravitational field), earth sciences (geomorphology) and even engineering. South African Antarctic research is conducted by manned bases in the Antarctic and on subAntarctic Islands (Figure 1). The world-class research station, SANAE-IV, is located on the Vesleskarvet nunatak, a rocky outcrop approximately 160 km inland from the coast, in Western Dronning Maud Land on the Antarctic continent (Figure 2). SANAE-IV is complemented by the bases on Marion Island (Figure 3) and Gough Island. Researchers on Marion Island, in particular, have produced a substantial body of scientific work. It is one of the Prince Edward Islands,

Figure 4. S.A. Agulhas making its way through icebergs on route to the ice-shelf of the Antarctic Continent. Photograph: J.K. Davies

t he nex t generat ion

â&#x2013;˛ â&#x2013;˛

which represent a tiny South African territory in the Southern Ocean. The Prince Edward Islands have been a South African possession since 1948 when they were annexed from Great Britain. Marion Island has been permanently inhabited since then and the construction of a new research base on the island is nearing completion (Figure 3). When completed, this research facility will be one of the best in the subAntarctic and promises to provide a great base from which to conduct research. Through the numerous voyages, mostly aboard the S.A. Agulhas, to and from these islands and the Antarctic much information has also been gathered from the Southern Ocean (Figure 4). Antarctic science winter school Typically, most of the research done at the South African bases is done in collaboration with students but, unfortunately, many students remain unaware of the exciting and challenging opportunities available in Antarctic science. Consequently, an Antarctic Science Winter School (ASWS) was arranged to expose Honours level students from across South Africa to some of the worldclass research which is being conducted and provide information

Figure 3. The base on Marion Island.

Photograph: B. Kuyper

Quest 4(4) 2008 29

Figure 6. Magnetic loop antenna recording very low frequency (VLF) radio waves at SANAE-IV, Antarctica. Photograph: A.B. Collier.

on how they could become involved. The school was held at the Hermanus Magnetic Observatory (HMO) from 14 to 18 July 2008 and was funded by the National Research Foundation (NRF) through a South African National Antarctic Programme (SANAP) Development Grant (Figure 5). While at the school, students were exposed to all the key areas of Antarctic science including space physics, biology, oceanography, climatology, earth sciences, engineering, and even social sciences and humanities. Although all these areas of Antarctic science were touched on, the focus of the school was to highlight disciplines in which there is current research in the Southern Ocean, Antarctica and the sub-Antarctic Prince Edward Islands, as well as to foster the idea of collaboration and interdisciplinary work. The school took place over four days, each focusing on a specific discipline, preceded by an initial introductory day. Space physics

Top: Figure 5. Students participating in a debate discussing the ethics of entering Lake Vostok. Photograph: D.W. Hedding Above: Figure 8. Hunting for invertebrates on a remote Antarctic nunatak. Photograph: D.W. Hedding Middle: Figure 9. Preparing to conduct a field survey on Marion Island. Photograph: J.D. Shaw

30 Quest 4(4) 2008

Space physics in the Antarctic and sub-Antarctic encompasses magnetospheric, ionospheric and neutral-atmosphere research. Ultimately the driver for these systems is the Sun which, through electromagnetic radiation, the solar wind and the interplanetary magnetic field exerts a profound influence on the plasma dynamics and chemistry in the Earth’s upper atmosphere. The Antarctic is a prime location for space physics research since it is an environment with very low levels of electromagnetic noise and it is located at the convergence of the Earth’s magnetic field lines, thereby

providing a window into a vast region of near-Earth space. Not only does the magnetosphere act as a natural plasma laboratory on a scale unattainable on Earth, but it is also the medium in which communication, weather, military and other satellites operate (Figures 6, 7). Biology

Biological research in the Antarctic covers a range sub-disciplines including ecology, entomology and genetics, which all add to the global understanding of biological processes. The Antarctic region encompasses a range of habitats from small exposed mountain peaks and large dry valleys surrounded by ice, to the highly variable Southern Ocean islands, which have a considerable range of sizes and geological histories. Some ice-free areas of the Antarctic are devoid of anything except microbial life, while others support bryophytes, lichens, nematodes, arthropods and, occasionally, breeding seabirds. The Southern Ocean islands range from those covered by glaciers to others that have lush, vegetated landscapes at their lower elevations, riddled by the burrows of breeding seabirds and home to large colonies of penguins, albatrosses and seals. Their biota varies substantially, reflecting the diverse locations and origins of the islands. The range of climatic conditions experienced by the flora and fauna of the Antarctic region also varies greatly. Climates range from wet and relatively mild sub-Antarctic islands to the polar desert of continental Antarctica where temperatures can plummet to –50°C and wind speeds can exceed 200 km/h. Remarkably, some insects are

Figure 7. Astrid 2 microsatellite ground station at SANAE-IV.

Figure 11. Sorted circles (patterned ground) on Marion Island. Photograph: D.W. Hedding.

Photograph: A.B. Collier.

able to survive such extremes and employ a wide range of physiological adaptations to achieve this. Cold tolerant arthropods are divided into those that are freeze tolerant, which can survive freezing of a portion of their body fluids, and those that are freeze avoiding and survive by lowering the temperature at which their body fluids freeze. Many of the species found in the Antarctic represent the limit of distribution within their taxa. Understanding their physiological tolerances is fundamental to understanding what limits speciesâ&#x20AC;&#x2122; geographic ranges, which is of particular relevance in the context of global climate change (Figures 8, 9). Earth sciences (geomorphology)


Oceanography in the Southern Ocean looks at physical, biological and chemical processes and how these may have an influence on local climate and climate change. The Southern Ocean is the largest uninterrupted ocean in the world and forms the southern part of the Atlantic, Pacific and Indian Oceans. There are a number of oceanographic fronts that divide the Southern Ocean. These fronts play a role in the formation of new water masses and the transport of heat and salt into and out of the Antarctic and between the oceans. Climatological forces drive these fronts, causing them to move and change over time. Exploring the movement of these water masses, the mechanisms of frontal development, the dynamics of the fronts and their implications

Figure 10. Measuring the physical characteristics of patterned ground (circles) at Vesleskarvet, Antarctica. Photograph: J.E. Lee.

will lead to an understanding of how the system may be changing and what this might mean in terms of global climate change. Importantly, physical oceanic and atmospheric forces limit and control the cycles of phytoplankton and the food web in the Southern Ocean. Chemical analyses are used to identify and quantify the nutrients found in seawater upon which microscopic organisms called plankton depend. Phytoplankton forms the base of the food web. Primary production â&#x2013;˛ â&#x2013;˛

Geomorphology is the study of landforms and landscapes (assemblages of landforms) and the processes that shape them. The Antarctic region provides an interesting range of glacial and periglacial environments to study geomorphological processes and their responses to climate change as well as landform and landscape development. Periglacial environments (cold but not glaciated regions dominated by frost processes) range from the ice-free areas of the Antarctic continent to the wet and relatively mild sub-Antarctic islands. Geomorphological research in the Antarctic typically investigates weathering, frost processes as well as glacial and periglacial landform development. Weathering is the precursor to landform development. Understanding weathering processes is, therefore, fundamental to understanding landform development

and the interpretation of landscapes in cold environments. Frost processes, generated through the repeated freezing and thawing of the ground, generate distinct landforms and are also particularly important in terms of landscape development in Antarctica and on the sub-Antarctic islands. However, climate change will have a significant impact on the efficacy of frost processes. Any warming may prevent the ground from freezing while cooling would prevent the ground from thawing. This will, in turn, affect landform development and maintenance. The influence of frost processes on plant colonisation on recently deglaciated areas is also significant and highlights an opportunity for interdisciplinary research in biology and geomorphology (Figures 10, 11).

Quest 4(4) 2008 31

Figure 12. An Honours student performing a chemical analysis while aboard the S.A. Agulhas.

Figure 13. Deployment of the Conductivity Temperature Depth (CTD) profiler aboard the S.A. Agulhas as part of the SOCAB study. Photograph: J. Howard.

Photograph: B. Kuyper.

occurs in cycles and it is constrained to fronts and eddies in the ocean by the same forces that drive the cycles. CO2 and nutrients are used by phytoplankton in much the same way as trees on land would use them. It is thus hypothesised that phytoplankton may play a significant role in global climate change (Figures 12, 13). Guest lectures and workshops

In addition to talks on each of the Antarctic Science disciplines, a series of guest lectures and evening activities were offered, exposing students to a wide variety of topical issues such as governance, conservation and the wide-reaching impacts of climate change. The school also presented a series of workshops which allowed students to learn some new skills such as Geographic Information Systems (GIS) and data analysis (Figure 14) as well as refine those which they already had such as writing, publishing and presentation. Debates and quizzes

Top: Figure 14. Dr A.B. Collier guiding students through the data analysis workshops. Photograph: D.W. Hedding. Above: Figure 15. 2008 Antarctic Science Winter School group.

32 Quest 4(4) 2008

All the material presented at the ASWS was made available online to the students on the HMO Modular ObjectOrientated Dynamic Learning Environment (MOODLE). The MOODLE provided a userfriendly web-based interface for the presentation of learning material

online. Students used this facility to prepare for their debates, which were arranged as an evening activity to stimulate discussion of topical issues in Antarctic Science. The MOODLE was also used to conduct an online quiz before the start of the school and after its completion. There was a marked improvement in the quiz scores with the mean score being 40% before the school and 68% afterward, demonstrating that in just one week students had substantially expanded their knowledge of Antarctic systems. Essentially, the ASWS offered a broad picture of current research in the Antarctic as well as specific options available for postgraduate research. It also provided the opportunity for students to gain insight into techniques and approaches employed in other disciplines and should foster future interdisciplinary collaborations. It is hoped that the ASWS will increase the uptake of postgraduate studies in Antarctic science, thereby engaging students in high-quality research and building capacity in this field. Enthusing young South Africans with a passion for science and equipping them with the necessary skills to be successful in Antarctic science will keep South Africa at the forefront of science in the Antarctic (Figure 15). â&#x2013; David Hedding is at the Department of Geography, UNISA, Andrew Collier is at the Hermanus Magnetic Observatory, Jennifer Lee is at the DST-NRF Centre of Excellence for Invasion Biology at the Stellenbosch University, and Brett Kuyper is at the Department of Oceanography at the University of Cape Town. Reference:

Q Fact file

Ant arct ica

Antarctic ice shelf. Photograph: D.W. Hedding

■ Antarctica is the best place in the world to find meteorites. Dark meteorites show up against the white expanse of ice and snow and don’t get covered by vegetation. In some places, the way the ice flows concentrates meteorites. The ice makes them gather in one place. ■ One of the biggest icebergs ever (possibly the biggest iceberg ever) broke free from the Ross ice shelf in Antarctica in 2000. It was 295 km long and 37 km wide, with a surface area of 11 000 sq km above water – and 10 times bigger below. It’s similar in size to Gambia, Qatar, The Bahamas, or Connecticut. ■ A domestic deep freeze runs at about –20°C. The mean summer temperature on the East Antarctic ice cap is about –30°CGeochemical, and the Metallogenic mean winter temperature is around –60°C – • Geological, Geotechnical, and Marine mapping • Geoscience Museum • Minerals Development • National Core Library a lot colder than your freezer! • Construction Materials and Agricultural Minerals • Water-Resource Assessment and Protection ■ The Antarctic ice cap contains 29 millionCOUNCIL cubic millimetres of FOR GEOSCIENCE MISSION:To provide expert • Environmental Geoscience information and services to improve the management of ice. This is 90% of all the ice on the planet and between 60% • Engineering Geology and Physical Geohazards natural resources and the environment for the benefit of the • Palaeontology and 70% of the world’s fresh water. society. • Laboratory Services • Geophysics ■ Samples of ice called ice cores are regularly drilled through 280 Pretoria Street, Silverton, PRETORIA • Seismology the ice in Antarctica by scientists. They are removed as• Private a long Courtship of Wandering Bag X112, PRETORIA, 0001 • Geographic Information Systems (GIS) +27 (0)12 841-1911 • Fax: +27 (0)12Albatrosses 841-1221 • Information Databases on Marion Island. cylinder of ice that gives an indication of the past,Tel:going back • National Geoscience Library Photograph: D.W. Hedding tens of thousands of years. The properties of the ice, of dust trapped in the ice, and even of air bubbles trapped in the ice give valuable information about the Earth’s climate at various times in the past. ■ The Antarctic is a desert. The region averages less than 4 mm of precipitation monthly, about the same as the Sahara Desert. ■ The population of scientists in the Antarctic can reach 4000 in the peak summer research months. Tourist visits can double that number in the summer. ■ Dogs have been banned from the Antarctic since April 1994 to protect the native seal populations from distemper. ■ The cold and dry conditions in the ‘Dry Valleys’ region of Antarctica are so close to those on Mars that NASA have conducted testing there for the Viking mission. It has not King penguin colony at rained in the dry valleys for at least 2 million years. Kildalkey Bay, Marion Island.


Photograph: D.W. Hedding

LEADING EARTH-SCIENCE SOLUTIONS • Geological, Geotechnical, Geochemical, Metallogenic and Marine mapping • Minerals Development • Construction Materials and Agricultural Minerals • Water-Resource Assessment and Protection • Environmental Geoscience • Engineering Geology and Physical Geohazards • Palaeontology • Laboratory Services • Geophysics • Seismology • Geographic Information Systems (GIS) • Information Databases • National Geoscience Library • Geoscience Museum • National Core Library

COUNCIL FOR GEOSCIENCE MISSION: To provide expert information and services to improve the management of natural resources and the environment for the benefit of the society.

280 Pretoria Street, Silverton, PRETORIA • Private Bag X112, PRETORIA, 0001 Tel: +27 (0)12 841-1911 • Fax: +27 (0)12 841-1221


QUEST spoke to Nicola van Wilgen about managing the potential problem of invasive alien reptiles and amphibians in South Africa.


A sign advertising the sale of alien reptiles.

Alien reptiles and amphibians (herpetofauna) Reptiles and amphibians are collectively known as herpetofauna. This is not a natural grouping, meaning that these groups are not classified together on the basis of a close evolutionary relationship.

Tortoises and the albino and normal colour morphs of the Burmese python at Tygerberg Zoo.

34 Quest 4(4) 2008

ot all aliens come from outerspace. Within our planet we refer to alien species as species which have been moved by humans from the area where they occur naturally to a new area. Often, such species do not survive in the new area because environmental conditions are not suitable. However, some species do survive and a few manage to perform even better than the species which are native to the area. They outcompete indigenous species because they have no natural enemies in the new area. If these species spread and start to cause problems, including displacement of natural species, destruction of the environment or impacts on society, then they are known as invasive alien species. Biological invasions are a growing problem in South Africa. Over the past few centuries, many alien species have been introduced for many different reasons. The most notorious alien species are plants, which colonize and take over indigenous landscapes, often choking river systems. For example, the Australian Black Wattle (Acacia mearnsii) which is estimated to have cost R8550 million in South Africa before 1998 through reducing stream flow. When people first started moving plants and animals around the world, no-one thought that this could possibly cause problems, because the impact of invasive aliens on indigenous environments was not understood. Many of the species were actually beneficial, being used for food and timber. We are in fact reliant on many alien species which are not invasive â&#x20AC;&#x201C; nearly all of the foods which we buy in the shops (vegetables and meat) which are grown or bred in South Africa, are alien species. However, some species

are not useful as food sources and provide little other benefit; in fact, they may have detrimental effects if they are introduced and spread. Just as there are some plants which have caused large ecological and economic damage, animals too can cause problems. In South Africa, the Argentine ant (Linepithema humile) and the black rat (Rattus rattus) are examples of alien pest animals which were introduced accidentally via ship cargo. However, there are some species which are introduced intentionally as pets that may have unwanted side-effects. Two groups of animals which are being kept by more and more people as pets are reptiles and amphibians. Because more of these and other species are arriving in South Africa now than ever before, we need to understand what is driving these introductions, so that we can start to develop a management strategy to deal with them. When these animals escape or are released they may cause problems. Right now, invasive alien reptiles and amphibians are not a problem in South Africa, but their increasing popularity as exotic pets means that they may become one in the future. Invasions in other parts of the world show us that herpetofauna can cause some problems. Understanding how these problems arose and how they are being dealt with will allow us to develop a management strategy in South Africa and prevent the problem before it starts. Why can alien animals be a problem? Alien species pose a problem as they may bring foreign diseases against which our local species have no natural defences. This is something which also happened to people, when long-distance travel first started. For example, the first Europeans in

Collecting the data

Table 1. Alien reptile and amphibian species in South Africa recorded from permit data and CITES lists Province

Number of reptile species

Number of Total Source and notes amphibian alien species species in province

Eastern Cape




N. Bam. (Dept. of Economic Affairs, Environment & Tourism, EC)

Free State




(Dept. of Tourism, Environment and Economic Affairs) Import permits only


No data



Limpopo Province

Several extralimital African species as well as aliens similar to those in other provinces

V. Egan. Loop hole in law around permits, therefore limited data


Only CITES trade data available and no electronic records

B. Swart (Mpumalanga Parks Board)

Northern Cape



D. Paulse. (Department of Tourism, Environment and Conservation, NC)


D. Hignett. (Fauna and Flora permits, Cape Nature, WC) Captivity Permits

There are several pathways by which alien herpetofauna have arrived in other parts of the world, including accidental imports with ship cargo, the pet trade and even as food for humans. For example, the American Bullfrog (Lithobates catebeianus) is traded extensively as a source of frog legs – popular in French cuisine. However, in South Africa, nearly all species are imported for the pet trade or for display in zoos and private parks. It is now illegal to import alien amphibians into South Africa, in order to minimise the likelihood of spreading amphibian diseases, so most research is concentrated on the pet trade and reptiles. Researchers at the Centre for Invasion Biology at Stellenbosch University have compiled a list of species that have been imported into South Africa. These data have been collected using records from permits, pet store inventories, zoo species lists and by communicating with people involved in the trade. Most of the nine South African provinces issue permits for the import or captive keeping of amphibians and reptiles. However, many provincial records are not complete and people often do not apply for a permit because the application process can be drawn out. So information from permits is an underestimate of the true number of these species in South Africa. Zoos across the country provided another source of information as they often receive unwanted animals. Websites advertising pet sales can also be useful to collect data. CITES (the Convention on International Trade in Endangered Species of Wild Fauna and Flora) is an organization which governs the international agreement between governments seeking to ensure that the survival of species (both animals and plants) is not threatened by international trade. This organisation therefore monitors trade of a large number of species. Data on legal imports of alien reptiles over the past 30 years are available from the CITES website.

L. Lötter (Dept. of Agriculture, Conservation & Environment, Gauteng) Captivity permits not required, therefore no data available 7



S. Hughes. (KZN Wildlife Permits Office) Import permits only

North-West Province No data available Western Cape



sites. Carnivorous alien species may feed on native species, which will have damaging effects especially if the native species do not have defences against these new predators. What do people import and from where? A total of 275 species of alien reptiles and 14 amphibians have been documented in South Africa. According to the records, most are in KwaZulu-Natal, but there are likely to be as many or more species in Gauteng, where no permit data were available (see Table 1). Snakes were the most popular reptile class and 167 species were imported. The class with the next most species imported was lizards (77) (Figure 1). The number of animals imported each year has increased substantially since 1976, peaking in 2000 (Figure 2). Some of the most numerous species

▲ ▲

America unintentionally took diseases like smallpox with them. Because the people already living there had no immunity against the diseases, many people died. Because most animals cannot move such long distances on their own, it is particularly problematic when people start moving them around. A South African frog species, Xenopus laevis (the platanna) is thought to have spread a particularly damaging disease chytridiomycosis (caused by the Batrachochytrium fungus) to amphibians in many other parts of the world, where it has been transported for laboratory use. The release of pets into the wild is also of concern, as these animals could also have negative effects on the species already living there. Disease is not the only fear. Alien species may also negatively impact on native species in other ways, including competition for nesting and breeding

Nicola with John Spence, the owner of Tygerberg Zoo.

Quest 4(4) 2008 35

Iguanas at the National Zoological Gardens, Pretoria.

Blue tongued skinks (Tiliqua spp), which are native to Australia.

Species imported per class 180

Number of species imported

160 140 120 100 80 60 40 20



de an




tle Tu r

ds ar


ak es









Figure 1. The number of species in four different classes of reptile (crocodiles, snakes, lizards and turtles) and two classes of amphibians (frogs and salamanders) which have been imported into South Africa.

CITES species imported per year Number of individuals of species imported

2100 1950 1800 1650

documented by CITES include day geckos (Phelsuma) from Madagascar (305 individuals), the green iguana (Iguana iguana) (1287 individuals) most of which came from El Salvador, the royal python (Python regius) (2136 individuals, imported from twelve different countries) and 1100 common tegus (a species of lizard, Tupinambis teguixin), which arrived in a single shipment from the USA. There were only seven countries which exported more than 1000 individuals of one or more CITESlisted species. These include five African countries: Botswana, Ghana, Kenya, Mozambique and Namibia as well as two extra-continental countries: the USA and El Salvador. Interestingly, most of these countries did not export many species but rather a large number of individuals of the same species. Though one is not allowed to collect indigenous species in South Africa, a number of South African species have also been recorded in the pet trade. Prominent examples include the leopard tortoise (Geochelone pardalis), the Nile

Leopard gecko (Eublepharis macularis) hatchlings.

crocodile (Crocodylus niloticus) which is commonly bred on ranches, and the olive and brown house snakes (Lamprophis inornatus and Lamprophis fuliginosus). Large numbers of crocodiles are also imported into South Africa for these ranches, making up a significant number of the imports (over 100 000 individuals imported over the last 10 years). Popular species and associated problems Some species are obviously more popular as pets than others, which will affect how many individuals are traded. This is important for two reasons. Firstly, a large number of individuals of a single species in

1500 1350 1200 1050 900 750 600 450 300 150 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002 2004 2006


Year Figure 2. The number of individuals of species listed by CITES that were imported into South Africa every year between 1976 and 2005.

36 Quest 4(4) 2008

The American Alligator, kept on some crocodile ranches.

You, the law and alien herpetofauna Two sets of regulations govern the environment in South Africa: The National Environmental Management

Act (NEMA) (No 107 of 1998) and the National Environmental Management: Biodiversity Act (No 10 of 2004) (NEMBA). The Acts promote conservation and aim to ensure an environment where sustainable development can take place for the benefit of all South Africans. One of the aims of NEMBA is to prevent the introduction and/or spread of alien species. The Act requires all activities involving an alien species to be regulated by a permit. Certain economically important alien species do not require permits (‘permitted species’, often species used for food) other species are banned altogether (‘prohibited species’). The Act also recommends that ‘independent risk assessment or expert evidence’ is conducted/consulted before permits are issued. Experts are currently (September 2008) compiling the lists of permitted or prohibited species. So, if you want to keep or breed any alien species (reptile, amphibian or other), you will need to get a permit. This does not mean that you will be able to get a permit for any species. Some species, like amphibians, have been banned. Risk assessment is used to help decision making regarding which alien species should be banned and which can be allowed. How can risk assessment help decisions? Risk assessment looks at two things: the likelihood of an event occurring and the consequences of the event if it does occur. In this case, this means looking at how likely it is that a species will be able to establish populations in South Africa and what the effects of any established populations will be. Part of our current research is developing models estimate the likelihood of species establishing themselves in South Africa. How is this done? Firstly, some species are more likely to be imported than others. Remember propagule pressure –more individuals, more chance of establishing a population. However, if the climate and habitat are completely unsuitable, then a species may not be able to establish, no matter how large a number of the species are brought in. So we also need to look at the suitability of climate and habitat in areas where species are to be introduced. There are a number of

different ways of doing this. Usually, data from the climate in the species’ native range are used to build models, which assess the overlap in certain environmental variables such as rainfall and temperature averages, minima and maxima. The green iguana is a species which occurs in tropical climates (Figure 3). Our models show that the iguana should be able to survive in most tropical areas in the world, but that most of South Africa probably has unsuitable climate for this species (Figure 3). A third factor used in predicting whether or not a species may become established involves analysing characteristics unique to the specific species. People generally look at traits such as the number of offspring an ▲ ▲

one place gives the species a greater chance of becoming invasive. Secondly, if a species is very popular and there are not enough individuals to meet trade demand, people will catch individuals from the wild, which could threaten the long-term survival of the species. Local people may also start to catch these species as an extra source of income, which can have devastating effects on natural populations. The number of individuals of an alien species introduced to a region is called ‘propagule pressure’. Propagule pressure has been a significant predictor of whether an alien species will be able to establish in a new region for a number of different organisms (e.g. birds, fish, insects and mammals). This has also been important in the establishment of some reptiles. In Florida, for example, many reptile species were able to establish populations following a large hurricane which resulted in the unintentional release of a large number of individuals at the same time. So far in South Africa we do not have any established alien herpetofaunal species. This may be due to low propagule pressure because large numbers of individuals are not often released, or don’t escape simultaneously. But alien species have been seen outside of captivity on a number of occasions. Sightings include a kingsnake (Lampropeltis alterna) in a garden in the Strand, an alligator snapper turtle (Macroclemys temmincki) in a pond at a crocodile farm in George, a Burmese python (Python molurus bivittatus) and a yellow ratsnake (Elaphe obsoleta quadrivittata) in Cape Town, western diamond-backed rattlesnakes (Crotalus atrox) and a green iguana (Iguana iguana) in Gauteng province, several corn snakes (Elaphe guttata), a grey rat snake (Elaphe obsoleta spiloides), and a northern pine snake (Pituophis melanoleucus melanoleucus) in Durban. Most of these animals were successfully recaptured, but incidences like these could have severe consequences and care needs to be taken in regulating the number of species traded.

Reptiles are becoming popular in the pet trade.

Quest 4(4) 2008 37

Worldwide climatic suitability

The Green Iguana Iguana iguana Suitability 0 1

Figure 3. The results of climate suitability modelling show that nearly all equatorial climates are suitable for the green iguana (left). This species occurs naturally in northern South America and Central America (top right in green). The photograph on the right shows someone holding a baby green iguana. Further reading Brooke, R.K., Lloyd, P.H. & de Villiers, A.L. (1986) Alien and translocated terrestrial vertebrates in South Africa. The ecology and management of biological invasions in southern Africa (ed. by I.A.W. Macdonald, F.J. Kruger and A.A. Ferrar), pp. 63–74. Oxford University Press, Cape Town. Duggan, I.C., Rixon, C.A.M. & MacIsaac, H.J. (2006) Popularity and propagule pressure: Determinants of introduction and establishment of aquarium fish. Biological Invasions, 8, 377–382. Kolar, C.S. & Lodge, D.M. (2002) Ecological predictions and risk assessment for alien fishes in North America. Science, 298, 1233–1236. Kraus, F. (2003) Invasion Pathways for Terrestrial Vertebrates. Invasive species: Vectors and management strategies (ed. by G. Ruiz and J. Carlton), pp. 292–349. Island Press, Washington D.C. Lowe, S., Browne, M., Boudjelas, S. & De Poorter, M. (2004) 100 of the World’s Worst Invasive Alien Species A selection from the Global Invasive Species Database. Invasive species specialist group, Auckland. Mack, R.N., Simberloff, D., Lonsdale, W.M., Evans, H., Clout, M. & Bazzaz, F.A. (2000) Biotic invasions: Causes, epidemiology, global consequences, and control. Ecological Applications, 10, 689–710. Meshaka, W.E.J., Butterfield, B.P. & Hauge, J.B. (2004) The Exotic Amphibians and Reptiles of Florida. Krieger Publishing Company, Malabar, Florida. Richardson, D.M., Cambray, J.A., Chapman, R.A., Dean, W.R.J., Griffiths, C.L., Le Maitre, D.C., Newton, D.J. & Winstanley, T.J. (2003) Vectors and pathways of biological invasions in South Africa – past, present and future. Invasive species: Vectors and management strategies (ed. by G. Ruiz and J. Carlton), pp. 292–349. Island Press, Washington, D.C. Van Wilgen, N.J., Richardson, D.M. & Baard, E.H.W. (2008) Alien reptiles and amphibians in South Africa: Towards a pragmatic management strategy. South African Journal of Science, 104, 13–20.

38 Quest 4(4) 2008

animal can produce in one season, the number of times an individual may reproduce in one year and the type of habitat and food the species prefers. Potential biotic interactions also play a role: for example competition between individuals for food or space, or predator-prey interactions. Measuring all these factors allows us to estimate the likelihood that a species has of becoming established. If a species looks likely to become established easily, then it is normally not a good idea for it to be imported. In a few cases, species establish without any negative consequences, but this is extremely rare. A good example is the flowerpot snake (Ramphotyphlops braminus), which has been accidentally introduced to many parts of the world, including Cape Town, in soil used for potplants. Though it is actually a snake, this species resembles an earthworm and is not known to have any harmful effects in its introduced range. There are some herpetofaunal species that have caused dramatic effects on local environments. The best example is the brown tree snake (Boiga irregularis), which has invaded some Pacific Ocean islands. Species native to these islands previously had no predators and the introduction of this predatory snake has caused several bird, bat and reptile species to become extinct as a result. The snake also hunts along powerlines, where it often gets caught, resulting in massive power failures, which have cost the

region millions of dollars. Another example is the cane toad (Bufo marinus), which was introduced to many parts of the world, with the idea that it would eat sugar cane pests and save farmers money. The toad didn’t eat the targeted pests and has caused extensive damage to native species wherever it has spread. So, if you want to keep an alien reptile species as a pet, make sure that you get a permit for the species. You should also find out if the species is known to be invasive anywhere else and whether a risk assessment has been carried out to determine whether or not the species is likely to be invasive in South Africa. Most importantly, be sure that you are able to keep the species in a safe enclosure, so that it cannot escape. Make a point of finding out the requirements of keeping the species and be sure that you are prepared to see these through. You cannot simply release the animal into the wild if you are tired of keeping it. The animal will probably die if conditions are unsuitable, but there could be serious negative consequences. It could spread disease, or attack and kill native bird, mammal, invertebrate or herp species. Should the species establish a population, the consequences could be even worse. Remember – in South Africa we are very privileged to have very high biodiversity (lots of different species) and we would like to keep it that way for generations to come! ■

Q Fact file

More on South African reptiles Leopard tortoise (Geochelone pardalis)

Southern spiny agama (Agama hipida)

The leopard tortoise is widely distributed in South Africa. Photograph: A. de Villiers

This large, attractively marked tortoise is found throughout the savannas of Africa, from Sudan to the southern Cape. It feeds by grazing and favours semi-arid to thorny and grassland habitats. On average, this tortoise weighs between eight and 12 kg. However, it can grow a lot larger in the Eastern Cape, where adults weigh an average of 15â&#x20AC;&#x201C;20 kg and may be 700 mm long. Adults face few obstacles besides humans and wild fires. But the hatchlings have many predators, including rock monitors, storks, crows and small carnivores. Berg adder (Bitis atrapos)

Aurora house snake (Lamphrophis aurora)

The aurora house snake rarely attempts to bite. Photograph: A. de Villiers

These agamas live in tunnels, usually at the base of a bush. Photograph: A. de Villiers

Agamas are plump, short-bodied lizards with thin tails and triangular heads. They are active and diurnal and occupy a variety of habitats. The southern spiny agama is found in the western and northern Cape, extending into the south of Namibia. There is an isolated population in the north western Free State. They often use burrows dug by ground squirrels.

This attractive snake is found in the highveld of Gauteng and Free State, extending into KwaZulu-Natal and Eastern Cape. There are isolated records from the southern Cape and the western Cape escarpment. It eats nestling rodents. Giant ground gecko (Chondrodactylus angulifer)

Armadillo girdled lizard (Cordylus cataphractus)

The berg adder is found from the Cedarberg to Port Elizabeth. Photograph: A. de Villiers

This is a small adder that you may come across while hiking or climbing in the Cape mountains. It loves basking in the sun on rocks and ledges. The species preys on lizards and rodents, as well as amphibians. It is mildly venomous. The bite will cause symptoms in the nervous system such as drooping eyelids and loss of smell and taste. The symptoms resolve in one to two days.

A curled armadillo girdled lizard. Photograph: A. de Villiers

This attractive lizard is found from the succulent Karoo to the southern Richtersveld to Matjiesfontein. It is frequently illegally collected and is listed as vulnerable on the South African Red Data List. It lives in large cracks on low rock outcrops and feeds on insects.

Ground geckos are endemic to South Africa. Photograph: A. de Villiers

There are two subspecies of this gecko, C. a. angulifer and C. a. namibiensis. The species is nocturnal, spending the day in a short burrow, which is either freshly dug each night or stolen from a scorpion. They feed on a variety of insects as well as other small geckos.

Quest 4(4) 2008 39

Careers in S&T Q

C AR E E RS IN invasion biology & ecologic al management CITES

Zoo keeper Species biologist Vetenarian

IUCN TRAFFIC Environmental lawyers Policy makers Government officials

Zoos, pet stores, breeders

International organisations

Nature conservation agent Invasive species program manager



World climate data: Climatologist

Management Risk assessment for alien herp species Model building

Data creation: Abiotic data

Data creation: Biotic data Laboratory work

Mathematical statistician

Technical assistant Principal researcher

Species physiological data: Physiologist

Species life history traits: Species biologist


here are many different career options in science. Indeed science is a broad field. Here we will use the two articles on invasives as an example to illustrate the jobs available in these fields. Both are branches of science – specifically biology or Life Sciences. Though we focus on invasion biology here, careers in science may span many other fields too, including physics, mathematics, chemistry, geology, microbiology, genetics and conservation. Applied sciences may also make use of modellers and computer scientists. The qualifications that you need To pursue a career in science you need to start by taking the correct subjects at school. Most universities and technikons will require subjects like Life Sciences, Mathematics and Physical Sciences to qualify for registration for a science degree. There are a number of different types of degree you can do, depending on what you are particularly interested in. Your first degree – a BSc – is only a start. You can study further and do Honours, a Masters (MSc) or even a doctorate (PhD). Having a doctorate will enable you to gain a position at a university or research centre. You may even be able to run your own laboratory. The variety of people needed in conservation risk assessment Not all careers in science are purely research based. The project discussed in the article ‘Alien species – reptiles and amphibians’ can be used to illustrate the number of jobs and different skills that are required for just this one aspect of science. To begin with, basic

40 Quest 4(4) 2008

Nicola van Wilgen (holding a boa constrictor) works on building models to predict patterns in biological invasions. She started off with a BSc degree in Biodiversity & Ecology at Stellenbosch University, followed by Honours in Zoology. She decided to pursue a career in conservation biology and is now doing a PhD with the Centre for Invasion Biology at Stellenbosch University.

research needs to be done. This research is necessary to put together an accurate assessment of the way in which the species lives, where it lives and how it interacts with other species and the environment. For this, biologists, ecologists and physiologists who devote time to studying the species are needed. These are usually postgraduate students or senior researchers working for universities or research institutions. This work normally involves a large amount of time in the field or laboratory. Understanding species/environment interactions requires an understanding of abiotic factors (non-biological things such as climate and habitat that affect a species’ ability to survive and reproduce). For example, to understand the climate and temperature ranges that allow different species to survive, you need access to climatic data that span a long time period. This can be provided by climatologists. You may also need information on how species are related and how populations are structured. For this, genetic studies conducted in special laboratories are very useful. The next phase in risk assessment requires people who can collect data on species and compile models to predict whether species will be able to establish themselves in a particular environment and what impact this will have. These could be two separate jobs and could be carried out by people who have a mathematical, statistical or biological background. Once such models have been developed and tested, they need to be applied. This involves many different groups of people working together. Policy makers, environmental lawyers and government officials will interact with scientists to compile sensible regulations. Management of these regulations is also essential and people in nature conservation agencies, government officials and alien species programme managers need to work together on these issues. Finally, there are a number of other people who contribute to work like this, and who have very different jobs. These include people working at zoos, who need knowledge of the animals kept there. Vets can also play an important role at zoos, where a lot of research is also conducted. Many international organisations also work together to provide information, regulate trade to protect species and serve other conservation requirements (e.g. The World Conservation Union (IUCN), The Wildlife Trade Monitoring Network (TRAFFIC) and CITES). By pursuing a career in science, many job opportunities in these institutions are made available, providing opportunity to travel and work in many exciting overseas destinations. ■



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The town of Timbuktu, with the minaret of Sankore mosque in the background and nomads’ tents in the foreground. Photograph: Alexio Motsi and Mary Minicka for the Timbuktu Manuscripts Preservation Project

Conser ving t he Timbuk t u manu script s Timbuktu is a name that conjures up visions of shimmering buildings in a desert haze. But, as Alexio Motsi and Mary Minicka explain, conserving the city’s ancient manuscripts is a triumph for heritage conservation. Top right: Al-shifa bi ta’arif huquq al-Mustafa or The Rights of the Prophet, as this work is known, describes the life of Prophet Muhammad in detail, describing his high moral qualities, miracles and marvels. It includes a genealogy of the Prophet going back 21 generations. It is highly admired in the Muslim world and many commentaries have been written about it. It is even considered to have protective powers for the owner and his household. The author was a prominent scholar in the Maliki school of thought that is dominant in North and West Africa. This copy of a 12th century work has been made especially beautiful in order to reflect the glory of the subject. Decorated with gold illumination and written in Maghribi script, the praises of the Prophet are written in red. Some words in the text are explained in the marginal notes. Photograph: Alexio Motsi and Mary Minicka for the Timbuktu Manuscripts Preservation Project

Above: The entrance of the Ahmed Baba Institute in Timbuktu, a library housing thousands of manuscripts. Photograph: Alexio Motsi and Mary Minicka for the Timbuktu Manuscripts Preservation Project Ahmed Baba Institute (IHERI AB) library.

42 Quest 4(4) 2008


ention the word ‘conservation’ to most South Africans and they will think of things that crawl, run, fly, creep, swim, bite and claw. However, a significant portion of the preservation of humanity’s social environment is intimately connected with preserving the record of its existence. This record includes tangible heritage objects, such as paintings, pottery, personal ornament, books and documents, clothing, photographs and architecture; but it also extends to the intangible: ritual, thought, ideas, knowledge, memory… it’s a long list. This is the field of heritage conservation. One of the most significant heritage preservation projects on the African continent has been quietly underway since 2003. A small group of South African book and document conservators have been engaged in conservation repair and preservation, and the training of Malian conservators. The project was initiated after a visit to Timbuktu in Mali by President Thabo Mbeki in 2001. Mali, like many African countries, struggles to balance the pressing demands of social and economic development with the perceived ‘luxury’ of preserving an immensely significant heritage. In Mali’s case the preservation of the manuscripts in Timbuktu, and throughout the wider West and North African region, is an imperative. The manuscripts of Timbuktu once and for all put an end to the myth that Africa had no indigenous literary or scholarly activity before the

arrival of the colonial powers. Realising the immense importance of the manuscripts as a record of Africa’s intellectual history, President Mbeki pledged South African technical and material expertise to assist in the preservation of this valuable African heritage in order to make the manuscripts and their contents accessible to present and future generations for research and study. The Timbuktu Project is hailed as the first cultural initiative of Nepad – The New Partnership for Africa’s Development. Conservation repair is one of the most important aspects of the Timbuktu Manuscripts Preservation Project. Conservators are highly trained specialist professionals concerned with the actual physical repair of damage to – in this case – the paper and leather materials of which the Timbuktu manuscripts are composed. Conservators have a variety of treatment and repair techniques in their professional arsenal, aimed at halting further deterioration or decay of the manuscripts. These treatments can range from the fairly straightforward cleaning of surface dirt and grit from paper, to the careful immersion of paper in a variety of chemical baths to halt or delay the continuation of the chemical decay of paper. Conservation also seeks to look at the broader picture, to understand where and how damage occurs to books and documents, and, importantly, how to prevent that damage from happening in

Q Science in action This mosque was one of the major centres of Islamic learning in Timbuktu. Photograph: Lindsay Hooper for Iziko Museums of Cape Town

Left: A team of South African conservators have been training Malian conservators in preservation techniques. Photograph: Alexio Motsi and Mary Minicka for the Timbuktu Manuscripts Preservation Project

the first place. The individual treatment of damaged manuscripts, books and documents is an expensive, time-consuming and labour-intensive process. Here too, there are a variety of tools and methods at the conservator’s disposal. They range from ensuring that books and documents are stored in optimal conditions that do not accelerate the natural ageing process, to the construction of individualised protective boxes and assorted enclosures for manuscripts, books and documents to ensure that these items are further protected from the knocks and effects of their environment. In the case of Timbuktu’s manuscripts, you could almost say that just about every condition conducive to the deterioration of the manuscripts exists in the region – in the extreme. Temperatures rocket to the upperforty degrees (and beyond) in the summer heat, and can plummet to minus degrees in the winter nights; humidity will swing from the normal very, very dry, to flashes of high humidity during the rare spells of rain. Neglect and rough handling, termites, sand and dust, and inferior materials all work in concert to render the manuscripts damaged and fragile. Some manuscripts are beyond repair and others are little more than piles of debris. Timbuktu’s manuscripts and the extreme climatic conditions in Timbuktu have presented the conservation team with considerable and ongoing challenges. The challenge is not only to repair the often highly advanced levels of damage, but, more importantly, also to devise treatment and repair modifications that would work in Timbuktu’s extreme conditions. A number of manuscripts at the Ahmed Baba Institute bear reproachful witness to previous conservation intervention attempts, where otherwise sound conservation repair techniques not suited to the conditions in Timbuktu were applied without thought or consideration. A vital link in the long-term preservation of the Timbuktu manuscripts is the training of Malians in conservation repair. Five

Malians have been trained in South Africa for eight-week periods over a period of three years (2003–2005). The training was aimed at equipping the trainees with a broad range of basic skills, which included basic paper repairs, making specialised protective enclosures, leatherwork, exhibition mounting, cleaning and documentation. This aspect of the project has ensured the maintenance of a high standard of work through the regular monitoring of progress in Timbuktu by means of annual fieldwork trips. A new, purpose-built library building is currently under construction. It will house a conservation repair facility to allow the Malian conservator-trainees to work in a specialised conservation facility. More importantly, this new building to house and store the manuscripts will not only be a modern research facility for the many scholars journeying to Timbuktu, but will also provide the first and strong line of defence against the depredations of Timbuktu’s extreme climate. The Timbuktu Manuscripts Preservation Project is an immense and exciting opportunity for heritage conservation in Africa. It has the potential to assist in expanding the profession to beyond the more than (literally) handful of book and document conservators currently working in South Africa. Heritage conservation, in general, is an amazing opportunity for job creation growth in Africa. The potential for this is already being realised by the Malian conservator-trainees who are now engaged in training conservators in other centres of Mali. The manuscripts of Timbuktu have shown that there is no longer any question about an indigenous tradition of writing, literacy and scholarship in Africa. It exists, and is vast. Rather, the question is now how to respond to caring for and studying this gift from the past in a responsible way. The scope for the study of the manuscripts

extends beyond the obvious translation and analysis of texts by academics. West African Islamic manuscripts constitute a distinct sub-genre within the world’s historical Islamic book and manuscript heritage. Islamic manuscript- and book-making itself is considered to be one of the major bookbinding and artistic traditions of the world. It is also one of the most underdocumented and studied. The scope for understanding how European-manufactured paper came to be in Timbuktu, the inks and pigments used by scribes, the scribal industry, the economics of manuscript production, the leather-making craft, and calligraphy are an immense opportunity for current and future generations of conservators and scholars with a bibliophilic bent. ■ For more information on the project please consult the project website:

Above: A manuscript containing extracts in verse from the famous 11th century work on medicine by Ibn Sina, who is also known as Avicenna in the Western world. This famous scholar of Persian origin was from the Bukhara region of Central Asia. The work is encyclopaedic in that it covers all the medical knowledge that was available from ancient sources at this time, as well as Ibn Sina’s own advances in the fields of contagious diseases and the link between psychological and physical health. This copy contains his guide to healthy living, and advice for the treatment of various medical issues from broken bones to cleaning teeth. The script is eastern Arabic, written on paper that may be of Islamic manufacture. The tooled leather cover was probably made in Timbuktu. Photograph: Alexio Motsi and Mary Minicka for the Timbuktu Manuscripts Preservation Project

Quest 4(4) 2008 43

Viewpoint Q

Organophosphate insecticides – towards a toxin-free environment Organophosphates are common in the environment. Bassie Marvey explains how to avoid poisoning. Organophosphate insecticides: facts and trivia Organophosphate insecticides are the most widely available products used for pest control in homes, gardens, veterinary medicine and agriculture. They are commonly used on insects such as ants, cockroaches, termites, moths, spiders, fruitflies, fleas, locusts, caterpillars, ticks, lice and grubs, to name a few. Because they break down faster and have a shorter lifetime in the environment their use has since accelerated over that of organochlorine insecticides (DDT or dichloro- diphenyltrichloroethane, methoxychlor, lindane, and the cyclodienes: endrin, aldrin, chlordane, heptachlor, dieldrin, and toxaphene). However, in their breakdown process additional chemicals are produced which can be more toxic than the original chemical and longer lasting in the environment. They are easily absorbed by inhalation, ingestion, and skin penetration. In humans, poisoning symptoms include: excessive sweating, salivation and lacrimation, nausea, vomiting, diarrhoea, abdominal cramp, general weakness, headache, poor concentration and tremors. In serious cases, respiratory failure and death can occur. Organophosphate-insecticide active ingredients include among others: Acephate, Azinphos-methyl, Chlorpyrifos, Chlorpyrifos methyl, Diazinon, Dichlorvos, Dicrotophos, Dimethoate, Disulfoton, Ethion, Ethoprop, Fenamiphos, Fonofos, Malathion, Methidathion, Naled, Oxydemeton methyl, Parathion (ethyl), Parathion (methyl), Phorate, Phosmet, Profenofos, and Terbufos. Organophosphate poisoning and safe handling Organophosphates poison insects or mammals by inhibiting the actions of an enzyme called acetylcholinesterase (AChE) found in the synapse (space between neurons) between nerve and muscle cells. In the body, AChE plays an important role of maintaining normal nerve impulse transmission from nerve fibres to smooth and skeletal muscle cell, glandular cells and automatic ganglia, as well as in the central nervous system. This it achieves by ensuring

that free acetylcholine (AChol), an impulse-transmitting substance, is immediately cleared (by facilitating its breakdown) from the synapse soon after the transmission of the nerve impulse. AChol is synthesized in neurons through the action of the enzyme choline acetyltransferase, stored at the ending of the neurons in membraneenclosed vesicles (synaptic vesicles) and released in response to a nerve impulse travelling down the neuron. Inhibition of the action of AChE results in the accumulation of AChol in the synaptic cleft which then produces a maintained depolarization of the cell membrane, with pain due to overcontraction as one of the first symptoms. In the presence of inhibitors AChol keeps stimulating the postsynaptic membranes and the nervous system soon goes wild, causing contraction of the muscles in uncontrollable spasms and eventually death. As the saying goes, prevention is always better than cure. The challenge then is to educate communities on the safe use of insecticides as well as their differences in toxicities. Toxicity of an insecticide is generally measured by the amount, in grams or milligrams, required to produce some specific toxic effect. A toxic dose, on the other hand is the defined as milligram of chemical per kg of subject (species) weight. A chemical’s toxicity is often described by its ‘LD50’ value, which is the single dose estimated to be lethal to half the group of test animals. The World Health Organisation (WHO) has developed a classification based on the degree of likely hazard for organophosphate compounds and other pesticides. The four categories differentiating the different levels of toxicity are (1) extremely hazardous (class Ia), (2) highly hazardous (class Ib), (3) moderately hazardous (class II) and (4) slightly hazardous (class III). A number of precautionary measures are therefore to be taken when using insecticides. These include (1) reading of the instructions for use and safety warnings on the label of the container and adhering strictly to warnings given, (2) ensuring that there is adequate ventilation when applying insecticides, (3) ensuring that insecticides do not come into contact with foodstuffs and water supplies, (4) wearing protective clothing such as gloves and gas masks, (5) washing hands with soap and water after administering insecticides, (6) ensuring safe disposal of insecticides and empty containers. Insecticide poisoning in South Africa Insecticide poisoning poses a serious health problem especially in developing countries with the key risks including cancer, birth defects and disorders of the nervous and the endocrine systems. According to statistical notes from the department of health (RSA, 2005) a total of 1462 cases and 72 deaths resulting from insecticide poisoning have been reported in South Africa since 2001. However, since many cases go unreported, it goes without saying that these figures are not a true reflection of the real situation. Ranked according to the number of cases reported, the province with the highest cases of poisoning was the Free State, followed by Gauteng, then Northen Cape and Western Cape. North West and Limpopo provinces reported the least number of cases and no reports were received from Mpumalanga, Eastern Cape and KwaZulu-Natal. The figures indicated that the most affected are young people in the

44 Quest 4(4) 2008

Further reading A guide to promote best practice with organophosphates (2000), published by the Occupational Safety and Health Service, Department of Labour, Wellington New Zealand. organophosphates.pdf, accessed 17 September 2008. Carlson K. (2000). Louis Kuo finds new way to degrade pesticides. The Lewis & Clark Chronicle. Dippenaar R., Diedericks R. (2005). Paediatric organophosphate poisoning – a rural hospital experience. South African Medical Journal, Vol. 95 (9), pp 678–681 Health Living Today, insecticides.htm, accessed 17 September 2008 Munnecke D.M. (1976). Enzymatic hydrolysis of organophosphate insecticides, a possible pesticide disposal method. Applied and Enviromental Microbiology, pp 7–13 Organophosphate poisoning, eDocuments/General_-_organophosphate_Poisoning_-_Health_ Education_952005234949_245.pdf, accessed 17 September 2008 Organophosphates, BiologyPages/I/Insecticides.html, accessed 17 September 2008 Organophophate Insecticides,, accessed 17 September 2008 Statistical Notes (2005), Department of Health (RSA), facts/stats-notes/2005/pesticides.pdf, accessed 17 September 2008 Synapses, htm#synapses, accessed 17 September 2008 Wang A.A., Chen W., Mulchandani A. (2005). Detoxification of organophosphate nerve agents by immobilized dual functional biocatalysts in a cellulose hollow fiber bioreactor. Biotechnology and Bioengineering, Vol. 91, pp 379–386 World Health Organisation (1990). Public health impacts of pesticides used in agriculture. WHO (Geneva) World Health Organisation (1990). Childhood pesticide poisoning. Information for advocacy and action. WHO (Geneva)

age group 15–19 years with the least affected being the older age groups (45 years and older). The cases reported by race revealed that Africans were the most vulnerable, accounting for 79% of all the cases reported, followed by the coloured (13%), white (6%) and the Asian (1%) communities. In terms of gender, the figures revealed that males were more affected than females. Disposing of organophosphates – in search of a safer solution The careless disposal practices of unused insecticides or their containers are a common cause of insecticide misuse and environmental contamination. Since there is so much at stake in the use of these chemical poisons, extreme care is needed for all who use or plan to use any of these toxic substances. Currently, the commonly used methods for disposing of organophosphates include rinsing and incineration (burning to ash with the emission of gases). How safe these methods are, however, is still an issue for debate and most scientists agree that both methods of disposal pose a serious environmental hazard. For the past few decades scientists have been searching for efficient ways of disposing these toxic chemicals in a more environmentally safer manner. In the process of looking for ways to degrade pesticides, Louis Kuo, a professor of chemistry at Lewis and Clark College, Oregon, found a new chemical method to break down the complex molecular structure of two pesticides, parathion and paraoxon. He uses an organometallic catalyst (metallocene) to degrade these pesticides with water at very mild reaction conditions. His approach renders the pesticides much less harmful to the environment. Biotechnological methods with promising results, such as enzymatic hydrolysis of organophosphates, have also been reported by a number of scientists, among them Douglas Munnecke and Aijung Wang and coworkers. Clearly it is through concerted efforts like these that hopefully a lasting solution would be found that can best address the use and disposal of organophosphates in a pursuit for a toxin-free environment. ■ Bassie Marvey is a lecturer in the Department of Chemistry, North-West University.

Quest 4(4) 2008 45

Diary of events Q Shows and exhibitions

Lectures & Conferences

Iziko Planetarium, Cape Town. For the School holidays!

n 5–7 December “Safring 60th Anniversary Ringing Conference” This conference is intended for ringers but trainees and people with an interest in ringing are welcome to attend. More details are on our web at http://safring. (scroll to the bottom and use the sub-menu on the side). Registration is open. Venue: Emzemvelo Nature Reserve, Gauteng.

A basic guide to Stargazing

Davy Dragon goes to the Moon Davy Dragon finds a strange bug that seems to be lost. He thinks it is a moon-bug and decides to take the bug back to the Moon. But is the Moon the bug’s home? Join us and find out! 6 December–20 January Monday to Friday: 12:00 & 13:00 (excluding 25 December, there is no 13:00 show on 24 & 31 December) Saturday – 12:00 • Sunday – 12:00 Plus 24, 25, 31 January & 1 February – 12:00 Especially for children aged 5–12

Drawings by the acclaimed cartoonist, Tony Grogan. In this 45-minute presentation we give you a basic understanding of the night sky and how it changes throughout the year. We introduce some easily recognisable constellations, explain the nature of stars and the galaxy in which we live and give basic information on using binoculars and small telescopes. From 6 December Monday to Friday – 14:00 (excluding 24, 25 & 31 December) Tuesday evening – 20:00 (& sky talk) Saturday – 14:30 Sunday – 14:30 Suitable for teenagers & adults Please note that the last show on 24 & 31 Dec is at 12:00 and that we are closed on 25 December.


The Sky Tonight An interesting live lecture on the current night sky is presented every Saturday and Sunday. You will receive a star map and be shown where to find the constellations and planets that are visible this month. Saturday – 13:00 • Sunday – 13:00 Suitable for teenagers & adults

n Botanical Society of South Africa (Bankenveld Branch), Gauteng: Bird Identification Walk with Ella Jansen van Vuuren (6 Dec, meet at the main entrance to the Walter Sisulu National Botanical Garden at 06:00); Frog Walk with Ella Jansen van Vuuren (14 February 2009, meet at the main entrance to the Walter Sisulu National Botanical Garden at 18:00); Mushroom Walk with Marieka Gryzenhout, Microbiology Dept, Pretoria University (21 Feb 2009, meet at the Nestlé Environmental Education Centre, Walter Sisulu National Botanical Garden at 09:00); Geology and Ecology Walk with Nick Grobler and Ella Jansen van Vuuren (28 Feb 2009, meet at Main Entrance to the Walter Sisulu National Botanical Garden). Booking essential. Contact Karen by phoning (011) 958 0529 (mornings only) or e-mail

n 14 March, 2009 “Indiginous Trees” A full day course with Andrew Hankey, Specialist Horticulturist, Walter Sisulu National Botanical Garden. If you have always wanted to know how to identify your trees, this is the course for you. Venue: Nestlé Environmental Education Centre Walter Sisulu National Botanical Garden. Booking essential. Contact Karen by phoning (011) 958 0529 (mornings only) or e-mail

Diarize n 1 December – World AIDS Day n SciFest Africa, the national science festival, takes place from 25–31 March 2009 in Grahamstown in the Eastern Cape. Explore the space around you in workshops, talkshops, exhibitions and lectures and realise the fun side of science in the science Olympics, soap box derby, science shows, quizzes and theatre. Learn about black holes, the origin of species, amusing research, skin bleaching, hypertension, naked science, sports drinks, vultures, lasers, pond slime and so much more. Join SciFest Africa and thousands of other visitors to celebrate science through world class edu-tainment. Visit for more information. n The International Year of Astronomy (2009). For developments in astronomy in South Africa and for details about how to join the AstroNet e-mail list, visit n Partial solar eclipse, Monday, 26 January 2009. Will be seen all over South Africa between about 07:00 and 09:30.

Serving Africa's needs in understanding fishes and aquatic environments Situated in Grahamstown in the Eastern Cape, SAIAB is an internationally recognized centre for the study of aquatic biodiversity, serving the nation through the generation, dissemination and application of knowledge to understanding and solving problems on the conservation and wise use of African fishes and aquatic biodiversity. Research in the institute is directed at marine and freshwater fish taxonomy, systematics, genetics, biology, ecology, ethology, conservation, management and environmental issues. SAIAB houses world-famous collections of marine fishes from the Atlantic, Indo-Pacific and Antarctic Oceans, as well as freshwater fishes from Africa and adjacent islands. Its collections are national assets that are held in perpetuity for the benefit of science and future generations. The collections include biological specimens, genetic samples, photographic images, original scientific illustration artwork, spatial data and publications. It is an information hub for African fish, fisheries and aquaculture. Contact us: Private Bag 1015, Grahamstown, 6140, Tel +27 (0)46 6035800, Fax +27 (0)46 6222403, email, web

46 Quest 4(4) 2008 © SAIAB 2007. Illustrations by Elaine Heemstra and Dave Voorveldt. Layout by Magriet Cruywagen

Diary of events Q Shows and exhibitions

Lectures & Conferences

Iziko Planetarium, Cape Town. For the School holidays!

n 5–7 December “Safring 60th Anniversary Ringing Conference” This conference is intended for ringers but trainees and people with an interest in ringing are welcome to attend. More details are on our web at http://safring. (scroll to the bottom and use the sub-menu on the side). Registration is open. Venue: Emzemvelo Nature Reserve, Gauteng.

A basic guide to Stargazing

Davy Dragon goes to the Moon Davy Dragon finds a strange bug that seems to be lost. He thinks it is a moon-bug and decides to take the bug back to the Moon. But is the Moon the bug’s home? Join us and find out! 6 December–20 January Monday to Friday: 12:00 & 13:00 (excluding 25 December, there is no 13:00 show on 24 & 31 December) Saturday – 12:00 • Sunday – 12:00 Plus 24, 25, 31 January & 1 February – 12:00 Especially for children aged 5–12

Drawings by the acclaimed cartoonist, Tony Grogan. In this 45-minute presentation we give you a basic understanding of the night sky and how it changes throughout the year. We introduce some easily recognisable constellations, explain the nature of stars and the galaxy in which we live and give basic information on using binoculars and small telescopes. From 6 December Monday to Friday – 14:00 (excluding 24, 25 & 31 December) Tuesday evening – 20:00 (& sky talk) Saturday – 14:30 Sunday – 14:30 Suitable for teenagers & adults Please note that the last show on 24 & 31 Dec is at 12:00 and that we are closed on 25 December.


The Sky Tonight An interesting live lecture on the current night sky is presented every Saturday and Sunday. You will receive a star map and be shown where to find the constellations and planets that are visible this month. Saturday – 13:00 • Sunday – 13:00 Suitable for teenagers & adults

n Botanical Society of South Africa (Bankenveld Branch), Gauteng: Bird Identification Walk with Ella Jansen van Vuuren (6 Dec, meet at the main entrance to the Walter Sisulu National Botanical Garden at 06:00); Frog Walk with Ella Jansen van Vuuren (14 February 2009, meet at the main entrance to the Walter Sisulu National Botanical Garden at 18:00); Mushroom Walk with Marieka Gryzenhout, Microbiology Dept, Pretoria University (21 Feb 2009, meet at the Nestlé Environmental Education Centre, Walter Sisulu National Botanical Garden at 09:00); Geology and Ecology Walk with Nick Grobler and Ella Jansen van Vuuren (28 Feb 2009, meet at Main Entrance to the Walter Sisulu National Botanical Garden). Booking essential. Contact Karen by phoning (011) 958 0529 (mornings only) or e-mail

n 14 March, 2009 “Indiginous Trees” A full day course with Andrew Hankey, Specialist Horticulturist, Walter Sisulu National Botanical Garden. If you have always wanted to know how to identify your trees, this is the course for you. Venue: Nestlé Environmental Education Centre Walter Sisulu National Botanical Garden. Booking essential. Contact Karen by phoning (011) 958 0529 (mornings only) or e-mail

Diarize n 1 December – World AIDS Day n SciFest Africa, the national science festival, takes place from 25–31 March 2009 in Grahamstown in the Eastern Cape. Explore the space around you in workshops, talkshops, exhibitions and lectures and realise the fun side of science in the science Olympics, soap box derby, science shows, quizzes and theatre. Learn about black holes, the origin of species, amusing research, skin bleaching, hypertension, naked science, sports drinks, vultures, lasers, pond slime and so much more. Join SciFest Africa and thousands of other visitors to celebrate science through world class edu-tainment. Visit for more information. n The International Year of Astronomy (2009). For developments in astronomy in South Africa and for details about how to join the AstroNet e-mail list, visit n Partial solar eclipse, Monday, 26 January 2009. Will be seen all over South Africa between about 07:00 and 09:30.

Serving Africa's needs in understanding fishes and aquatic environments Situated in Grahamstown in the Eastern Cape, SAIAB is an internationally recognized centre for the study of aquatic biodiversity, serving the nation through the generation, dissemination and application of knowledge to understanding and solving problems on the conservation and wise use of African fishes and aquatic biodiversity. Research in the institute is directed at marine and freshwater fish taxonomy, systematics, genetics, biology, ecology, ethology, conservation, management and environmental issues. SAIAB houses world-famous collections of marine fishes from the Atlantic, Indo-Pacific and Antarctic Oceans, as well as freshwater fishes from Africa and adjacent islands. Its collections are national assets that are held in perpetuity for the benefit of science and future generations. The collections include biological specimens, genetic samples, photographic images, original scientific illustration artwork, spatial data and publications. It is an information hub for African fish, fisheries and aquaculture. Contact us: Private Bag 1015, Grahamstown, 6140, Tel +27 (0)46 6035800, Fax +27 (0)46 6222403, email, web

46 Quest 4(4) 2008 © SAIAB 2007. Illustrations by Elaine Heemstra and Dave Voorveldt. Layout by Magriet Cruywagen

Q Books

The longest journey The Story of Earth and Life. By Terence McCarthy and Bruce Rubidge (Cape Town: Struik Publishers. 2005)

Time’s arrow A Briefer History of Time. By Stephen Hawking with Leonard Mlodinow. (London. Bantam Press. 2005) The subheading of this book is ‘The science classic made more accessible’. If any of you have read the original “Brief History of Time’ by Stephen Hawking, unless you are already an outstanding physicist it is likely that, like me, you came away not much wiser! The original book was first published in 1998, was on the best seller list for 237 weeks and has sold about one copy for every 750 men, women and children on Earth. It addressed some of the most difficult issues in modern physics – which, although difficult – are also the most exciting. What do we really know about the universe? How do we know it? Where did the universe come from and where is it going? This new book still focuses on these questions. But, in response to feedback from readers of all ages, of all professions and from all over the world, this new version addressed these issues in a clearer and more leisurely manner. The original content has been retained and expanded, but without negatively affecting the length of the book or its readability. Although some of the more technical detail has been left out, the content more than makes up for this by a ‘more probing treatment of the material that is really the heart of the book’. The book has also been updated to include new theoretical and observational results. It now describes the recent process that has been made in finding a complete unified theory of all the forces of physics. This includes the exciting and controversial progress in string theory and the ‘dualities’ or correspondences between apparently different theories of physics that are an indication that there is, indeed, a unified theory of physics. Some forty years ago the mathematician and physicist Richard Feynman said, ‘We are lucky to live in an age in which we are still making discoveries. It is like the discovery of America – you only discover it once. The age in which we live today is the age in which we are discovering the fundamental laws of nature. The goal of this book is to share some of that excitement – a goal that it realises in an interesting and thought-provoking way.

The sub-title of this book is ‘A southern African perspective on a 4.6-billion year journey’ and what a journey that is! Terence McCarthy and Bruce Rubidge have put together a marvelous, colourful journey through the origins of the Earth and of life as we know it. The southern African region is rich in mineral resources – of global importance – but also has a record of life preserved in its fossils that is more extensive than any other region of the world. This record not only preserves the evolution of plants and animals, but that of the most self-important of animals – Homo sapiens. The content of the book ranges widely. As the authors themselves say, ‘… we wished to ensure that the content is accurate, or at least as accurate as such a work can be, given the divergent options that often exist in the earth sciences.’ True to their word, the text is accessible – so much so that it is difficult to put down once started. The story kicks off with a look at how the Earth works. But before this, the introduction takes us through the various stories of how the Earth began, with an intelligent and sensitive approach to the Judeo-Christian Creation story, as well as ideas about the Earth’s origins from cultures such as Ancient Greece. There follows a concise historical outline of the theories of origins and evolution that led to where we are today – in the earth sciences and life sciences. The chapter on how the Earth works is an excellent summary of earth sciences and provides a good introduction that makes the reader want to delve further. The subject matter ranges from the classification of minerals to what an earthquake is. Plate techtonics is covered in some detail – necessary for the theme of the book as the chapters continue through the formation of the Earth and the continents to the beginnings of life itself. By the time we get to early life the authors have provided excellent understanding of

not only how the Earth began, but how the southern African continent was formed and why it is that there is such a rich and varied fossil record present in this region. The rest of the book concentrates on the origins of life and the evidence for this through the fossil record – and – of course the evolution of humans. Each chapter starts with a ‘route map’ that outlines the geological time periods that are covered – making it an invaluable learning and teaching aid. The book is filled with colour photographs, excellent diagrams and fact boxes that supplement the main text. If you are looking for one book to cover earth sciences and evolutionary biology, this is it.

Natural history made (even more) fun Scatological verse. By Brian Warner (with illustrations by Tony Grogan). (Cape Town: the author in conjunction with Snailpress. 2007) It isn’t often that you will see a book of verse reviewed in a science publication, but in this case the review is justified. Brian Warner is the Emeritus Distinguished Professor of Natural Philosophy at the University of Cape Town. An astronomer by trade he has published more than one book of verse – all of them short, to the point and amusing. This collection follows on Dinosaur’s End and continues the ‘irreverent exploration of natural history topics’. For example, this little limerik: The boilers constructed by Watt Were so liable to rust and to rot The occurrence of thunder Always caused him to wonder On whether it was weather or not. And drawing on Gilbert and Sullivan, ‘From Florisbad to Sterkfontein I’m known for my sagacity At annual conference dinners I imbibe beyond capacity In short, in matters veg.e.table animal and mineral I am the total master in particular and general’ Illustraged by Tony Grogan, this little volume provides a fun approach to the sciences and scientists alike.

Quest 4(3) 2008 47

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48 Quest 4(4) 2008

Q Back page science Meet the world's first hand-held ultrasound imaging device

following right behind her – though no one could work out how.

Siemens Canada Limited’s new ACUSON P10 ultrasound system is claimed to be the world's first hand-held ultrasound imaging device. The new device weighs 725g and is roughly 50x100mm – that’s about the size of a PDA. But it’s said to be as capable as the imaging devices currently available, but which are so large that they are mounted on wheels. The new device allows doctors working in trauma units to get that essential ‘first view’, in what’s called the first ‘golden hour’ after a patient has arrived in ER. That means the doctor will have a better idea of the problem and be able to provide better treatment – and that means there’s a better chance that the patient will survive. The clinical tool easily fits into a lab coat pocket and can be worn around the neck, similar to a stethoscope. It enables the doctor to use imaging in the ER at the same time as the initial physical examination is performed.

Satellite navigation system for the disabled

White could be right We all know that white reflects the sun’s rays more than black does, so painting a garage roof or home’s roof white will tend to keep the interior cooler in summer. But there’s more to it than that… researchers in the US reckon that just 10m² of white-painted roof will offset a ton of carbon dioxide – quite apart from helping to keep your garage or home a lot cooler and saving on cooling costs. And there’s even more: the researchers have calculated that if the world’s 100 largest cities painted their roads white, as well as the darkcoloured roofs in each of them, it would offset 44 billion tonnes of carbon dioxide. That could help set back global warming by a decade or more.

GPS joins the fight against drugs A man in Colorado, in the United States, used a GPS tracking device to monitor his girlfriend's every move in order to combat her drug addiction. The GPS has been attributed to saving the woman's life. He secretly installed a tracking device in her car and was able to monitor exactly where she went, and when. He could even set boundaries, so that he’d know when she left a specific area. Then he would turn up at exactly the right time, as she was about to buy drugs, and stop the sale in its tracks. After a while, the people selling the drugs wouldn't even have anything to do with his girlfriend because they knew he would be

Navevo, one of the UK’s leading specialist GPS software developers, recently launched BBNav, claimed to be the first dedicated system specifically designed to support disabled drivers and those caring for the disabled, such as their families or carers. The system helps disabled drivers find parking bays for the disabled in 150 major towns and cities across the UK. It provides users with greater flexibility and choice when shopping, driving into town or just going out for the day, and includes all of the features found on a standard sat-nav but has been enhanced to provide detailed information to support disabled drivers. Clear colour-coded and numbered icons are displayed on the mapping while driving and allow the driver to easily search for a car park/parking bay of choice and navigate directly to it. The system holds information on more than 10 000 parking bays and over 40 000 places of interest, plus a database of over 20 000 places of interest tailored specifically for people with disabilities. And if you thought the disabled don’t enjoy a swim, you’re mistaken… more than 300 beaches with disabled accessibility are listed in the databank.

Arctic sea ice reaches lowest coverage for 2008 On September 12, 2008 the Arctic’s area of sea ice fell to 4.52 million square kilometres, NASA announced recently. That appeared to have been the lowest point of the year, as sea ice then began its annual cycle of growth in response to autumn cooling. The 2008 minimum is the second lowest recorded since 1979, and is 2.24 million square kilometres less than the 1979 to 2000 average minimum. While slightly above the record-low minimum set on September 16, 2007, this season further reinforces the strong negative trend in summer sea ice extent observed during the past 30 years. Before last year, the previous record low for September was set in 2005. In March, when the Arctic reached its annual maximum sea ice coverage during the winter, scientists from NASA and the data centre reported that thick, older sea ice was continuing to decline. According to NASA this perennial ice used to cover 50–60% of the Arctic, but over the 2007/2008

winter it covered less than 30%. Perennial sea ice is the long-lived layer of ice that remains even when the surrounding short-lived seasonal sea ice melts to its minimum extent during the summer.

Transformed cells produce insulin Researchers at the University of North Carolina at Chapel Hill School of Medicine in the US have transformed cells from human skin into cells that produce insulin, the hormone used to treat diabetes. The breakthrough may one day lead to new treatments or even a cure for the millions of people affected by the disease, researchers say. The approach involves reprogramming skin cells into pluripotent stem cells, or cells that can give rise to any other foetal or adult cell type, and then inducing them to differentiate, or transform, into cells that perform a particular function – in this case, secreting insulin. If it is successful, the research could potentially see insulin-producing cells being made from diabetic patients’ own reprogrammed cells.

Whales once walked If you’ve ever seen whales off Hermanus and the Cape coast, you’ll probably have seen the slapping their tails on the surface of the ocean – with a sound like a cannon going off. You also would have seen how the tail is divided into two large fins, called flukes. Scientists have long known that the earliest whales were four-footed, semi-aquatic animals. Scientists also know that some of the later species of early whales had tail flukes. However, there was always the question: when did the first flukes appear? Now that question appears to have been answered. According to recent research in the United States, a study of one of the earliest whale species, Georgiacetus vogtlensis, has found that it had bones in the tail that show that this whale didn’t have a tail fluke. What it did have were large hind feet, which it seems to have used as hydrofoils, using its hips to sweep them through the water to propel the beast forwards. Previous studies proposed that the earliest whales used to paddle through the water using all four legs. Then, as they evolved further, they eventually arrived at the motion they use today, of oscillating the tail up and down. And along the way, it now seems that one step towards the way whales swim today, was that of wiggling their hips when swimming.


Win a prize!

Here is a fun problem that looks a little easier than it really is. Using the numbers 1, 4, 5 and 6 you must make an answer of 24 according to the following rules: n Each number must be used exactly once. n The allowed operations are: addition, subtraction, multiplication and division. n Numbers may not be concatenated (e.g., it is not allowed to combine 1 and 4 to make 14). n Brackets are allowed. Give the two solutions to this problem.

Send us your answer (fax, e-mail, or snail-mail), together with your name and contact details, by 15:00 on Friday, 23 January 2009. The first correct entry that we open will be the lucky winner. We’ll send you a cool Truly Scientific calculator! Mark your answer “QUEST Maths Puzzle no. 8” and send it to: QUEST Maths Puzzle, Living Maths, P.O. Box 478, Green Point 8051. Fax: 0866 710 953. E-mail: livmath@ For more on Living Maths, phone (083) 308 3883 and visit

Solution to Q uest Maths Puzzle no. 7 The smallest positive integer that can’t be represented by such arithmetic expressions is 29. 1 = [(2 * 3) – (1 + 4)]; 2 = [(2 * 3) – (1 * 4)]; 3 = [(1 + 2) * (4 – 3)] ; 4 = [(3 + 4) – (1 + 2)]; 5 = [(1 + 4) * (3 – 2)]; 6 = [(4 – 2) + (1 + 3)]; 7 = [(3 + 4) * (2 – 1)]; 8 = [(2 + 4) + (3 – 1)]; 9 = [(1 * 4) + (2 + 3)]; 10 = [1 + 2 + 3 + 4]; 11 = [(2 * 3) + 1 + 4]; 12 = [(2 * 4) + 1 + 3]; 13 = [(3 * 4) + (2 – 1)]; 14 = [(3 + 4) * (1 * 2)]; 15 = [(3 * 4) + (1 + 2)]; 16 = [(1 + 3 + 4) * 2]; 17 = [(2 + 4) * 3 – 1]; 18 = [(2 + 4) * (1 * 3)]; 19 = [(2 + 4) * 3 + 1]; 20 = [(2 + 3) * (1 * 4)]; 21 = [(2 + 3) * 4 + 1]; 22 = [(4 * 3 – 1) * 2]; 23 = [(2 * 3 * 4) – 1]; 24 = [1 * 2 * 3 * 4]; 25 = [(2 * 3 * 4) + 1]; 26 = [(3 * 4 + 1) * 2]; 27 = [(2 * 4 + 1) * 3]; 28 = [(2 * 3 + 1) * 4]

Quest 4(4) 2008 49


South African PhD Project

Expanding the frontiers of knowledge

National Research Foundation

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