Quest 7(3) by Academy of Science of South Africa

Science Science for for South South Africa Africa

ISSN 1729-830X ISSN 1729-830X

Volume 7 • Number 3 • 2011 Volume 3 • Number 2 • 2007 R29.95 R20

Australopithecus sediba: the 'missing link'?

Out of Africa: origins of humankind

Early migrations: humans populate the world

African fractals: old designs for new ideas

Unravelling our origins: genetics at work Early engineers: fire as a tool

Sc A c Aacdaedmeym yo fo fS c i ei ennccee ooff SS o u u tt hh AAffrri c i ca a

Make a positive contribution by qualifying yourself with a undergraduate or postgraduate degree in Natural Sciences, Agricultural Sciences, Mathematical Sciences, Building Sciences or Computer Sciences.

T: 051 401 2531 natagri@ufs.ac.za www.ufs.ac.za/natagri

A Better World Is

Possible

Cover stories

Out of Africa Quest looks at how geneticists have traced humans back to Africa 5

The human journey 60 000 years ago humans left Africa. Quest explains

The dawn of humankind Quest finds out how science is unravelling human origins

Using fire for more than light and warmth

Contents Volume 7 • Number 3 • 2011

Kyle Brown and Curtis Marean Early modern humans used fire to make tools, evidence of complex behaviour 16

Humankind rising

Regulars

Shirona Patel Australopithecus sediba provides us with more evidence about modern human origins

African fractals: new futures for old traditions

Neaderthals: closer than we think – p.10 • Peking man – p.10 The Middle Stone Age – p.15 • Fractals – p.26 11

Science news Settling Asia: two waves – p.11

Ron Eglash Mathematics in African culture

Fact files

Local science South Africa’s top science learners awarded – p.27 • Honours for local researcher – p.31 • SAIAB news – p. 46 • ASSAf news – p.47

Books

Diary of Events

Mike Lucas

Subscription form

Sea levels are seldom stable and they are on the move again

Backpage science • Mathematics puzzle

Features 28

Should we worry about sea level rise?

Air quality in the Dasspoort Tunnel: a multidisciplinary, multi-institution collaboration Caradee Wright, Rebecca Garland and Patricia Forbes A team approach to looking at air quality

Coral reefs: a world beyond our imagination Hanlie Malherbe These wonderful ocean communities are under threat

Smoking, tomato juice and infants' lungs Gert Maritz Can tomato juice prevent the lung damage caused by smoking?

Quest 7(3) 2011 1

Science Science for for South South AfricA AfricA

ISSN 1729-830X ISSN 1729-830X

Volume 7 • Number 3 • 2011 Volume 3 • Number 2 • 2007 r29.95 r20

Australopithecus sediba: the 'missing link'?

Out of Africa: origins of humankind

Early migrations: humans populate the world

African fractals: old designs for new ideas

Unravelling our origins: genetics at work Early engineers: fire as a tool

Sc A c AAcdAedmeym yo fo fS c I eI eNNccee ooff SS o u u tt hh AAffrrI c I cA A

Images: Wits University, Kyle Brown and Curtis Marean and Wikimedia commons

SCIENCE FOR SOUTH AFRICA

ISSN 1729-830X

Editor Dr Bridget Farham Editorial Board Roseanne Diab (University of KwaZulu-Natal) (Chair) Michael Cherry (South African Journal of Science) Phil Charles (SAAO) Anusuya Chinsamy-Turan (University of Cape Town) George Ellis (University of Cape Town) Peter Vale (University of Johannesburg) Correspondence and The Editor enquiries PO Box 663, Noordhoek 7979 Tel.: (021) 789 2331 Fax: (021) 789 2233 e-mail: ugqirha@iafrica.com (For more information visit www.questinteractive.co.za) Advertising enquiries Barbara Spence Avenue Advertising PO Box 71308 Bryanston 2021 Tel.: (011) 463 7940 Fax: (011) 463 7939 Cell: 082 881 3454 e-mail: barbara@avenue.co.za Subscription enquiries Patrick Nemushungwa and back issues Tel.: (012) 349 6624 e-mail: Patrick@assaf.org.za Copyright © 2011 Academy of Science of South Africa

Published by the Academy of Science of South Africa (ASSAf) PO Box 72135, Lynnwood Ridge 0040, South Africa Permissions Fax: (021) 789 2233 e-mail: ugqirha@iafrica.com 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 Graphic Design Illustrations James Whitelaw Printing Paradigm

2 Quest 7(3) 2011

Living together

ome 60 000 years ago humankind started the great move out of Africa and modern humans populated the world in great waves of migration. 2011 is the International Year of People of African Origin. I have seen some pretty rigid interpretations of this while reading around the subject recently, but I prefer to interpret this as meaning all of us – the entire world population. We all come from Africa and this fact should not be forgotten in the rush to establish national boundaries and personal identities. As I write, the world is yet again in economic turmoil and to me the goal posts have shifted irrevocably – no bail out schemes are going to take us back to where we were. This could be a good thing if it reduces the materialism that has wrecked our planet, but one worrying effect of the financial crisis in Europe and the USA is increasing animosity towards immigrants, increasing tightening of national borders and reluctance to provide aid to those parts of the world where it is desperately needed, such as Somalia. This is ironic, given that the science of the past few years has clearly shown us that we are all one people and that these boundaries are modern constructs that have no basis in science. As Western nations fight to retain their unsustainable life styles, they will become less and less inclined to accept immigrants into their societies, failing to recognise another fundamental feature of humankind – the urge to migrate. It could be argued that modern migration is more about escaping poverty and hardship in a home country than simply an urge to explore. But the early migration of our ancestors was almost certainly prompted by inhospitable climates, poor food supplies and, in later waves of movement, hostile incomers. So nothing has really changed – migration is a common human urge whatever the reason and migrants bring new blood, new ideas and economic activity to the countries they move to. How do we get away from this prejudice and fear of the unknown – the migrant? This is where science comes into its own. Science deals with facts and observations and hypothesises around those observations. A scientific world view allows clear and rational thought and provides a way of understanding the world around us without myth and superstition. By understanding the origins of humans and the fact that race is a fallacy, we can break down stereotypes and end bigotry and prejudice and welcome new people into our communities. For more good science see www.questinteractive.co.za

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

Out of Africa We are all descended from a common African ancestor. Quest shows how geneticists have traced the human population back to Africa.

he year 2011 was designated as the International Year for People of African Descent. That means all of us. About 60 000 years ago humans first started to venture out of Africa. It was these migrations that peopled the Earth – the descendants of a small group of Africans now make up the global population, so every one of us can regard ourselves as of ‘African descent’. How do we know this? There are genetic markers in modern people that can be used to trace where people came from and to map when and where ancient humans moved around the world. Genetic markers The cells that make up our bodies contain a nucleus that contains genetic material called chromatin. When the cells divide, the chromatin is organised into chromosomes, which carry our genetic material, deoxyribonucleic acid (DNA). Humans have 23 pairs of chromosomes. Of these, 22 are autosomes – that is chromosomes that contain the genetic material for normal body cells – and one pair are the sex chromosomes, the chromosomes that determine a person’s sex. Men carry one Y chromosome and one X chromosome. Women carry two X chromosomes. For most of our genome we get half of our DNA from our father and half from our mother. That is, 23 chromosomes from our father and 23 chromosomes from our mother. Your genome is the sum of all your genetic information, which is encoded in the DNA.

Mutations are random changes in the sequence of DNA – essentially random spelling mistakes in the long sequence of letters that make up our DNA. The Y chromosome

The Y chromosome is what determines sex in humans. Men have Y and X and women have two X chromosomes. The Y chromosome does not have a matching counterpart, so most of it – called the nonrecombining region (NRY) – does not get shuffled during recombination every generation. The Y chromosome is passed down only through the male line – and is changed only by random mutation. The Y chromosome can therefore be used to trace the male line back through history.

The normal complement of chromosomes in a human – called a karyotype. Image: US National Library of Medicine

Mitochondrial DNA

But we cannot only trace our ancestry through the male line. The DNA that is found only in the mitochondria – the power generators of our cells – is called mitochondrial DNA (mtDNA). There are no mitochondria in the head of a mature sperm, so your mitochondria come only from your mother. Men do not pass their mtDNA to their offspring. Mitochondrial DNA carries a region in which the rate of mutation is up to 100 times greater than the rate of mutation in the DNA in the cell’s nucleus – this is called the hypervariable region (HVR 1 and 2). This region is very short and so can easily be scanned (sequenced) to show the mutations that have been passed down through the female line. Genetic markers through the generations Genetic markers are inherited and passed down through the generations – and their complex story can be traced backwards in time. The way in which these markers are passed down is also affected by other evolutionary

▲ ▲

Each half is a shuffled combination of the DNA that was passed down to us through all our distant ancestors as well as our parents. This shuffling process is called recombination. It is essentially a genetic mixture of everyone who has come before us. This mix is difficult to interpret. But, fortunately there are parts of the genome that are not shuffled when they are passed from parent to child.

In these parts of the genetic code the only variation is through mutations. When these mutations are passed down through the generations, they become the genetic markers tracing specific lines of descent.

A diagram of a human cell, showing the nucleus containing chromatin.

DNA – the way in which genes are passed from organism to organism.

Quest 7(3) 2011 3

Mitochondrial Eve You have probably heard of ‘Mitochondrial Eve’. Mitochondrial Eve – traced through mtDNA – is the woman from whom all living humans are descended on their maternal side – the most recent common ancestor. She is the female counterpart of Y chromosome Adam – the male most recent common ancestor – although they lived thousands of years apart. Mitochondrial Eve is estimated to have lived in Africa around 200 000 years ago. This date for Eve suggests that modern humans originated relatively recently in Africa and spread from here. Once in Europe and Asia, there was probably some mixing with the less modern human species already present in these areas. But eventually all these other species died out, leaving only the anatomically modern humans from Africa. Branches on the line of female inheritance are identified by one or more unique markers that give a mtDNA signature – this is called a haplotype. A haplotype is a combination of DNA

Random drift or selection in the female line will trace back to a single female, such as Mitochondrial Eve. Image: Wikimedia commons

forces – natural selection, genetic drift and migration. Natural selection ensures that favourable characteristics survive in a population and unfavourable ones tend to die out. The cumulative effect is to produce populations that are adapted to survive in their particular environments. The Y chromosome DNA, passed from father to son, and mtDNA passed

4 Quest 7(3) 2011

sequences (or mutations) at different places on the chromosome that are passed on together. These mtDNA haplotypes are sorted into more or less related groups, with more or less recent common ancestors. From this, scientists put together a DNA family tree where the branches are clades, which is a group that consists of a species and all its descendants. A clade is a single branch on the tree of life and the species can be extinct or still in existence today. Common ancestors such as Eve sit at branching points in this tree. The mitochondrial clade which Mitochondrial Eve defines is the species Homo sapiens sapiens – anatomically modern humans. Mitochondrial Eve’s haplogroup is L – which is the haplogroup that contains all surviving mitochondrial lineages today. Beware of fallacies. Mitochondrial Eve was not the only woman alive at the time. Studies of the DNA that originates in the nucleus of cells show that the size of the human population never dropped below tens of thousands. There may have been many other women who were alive at Eve’s time who could have passed down their mtDNA. But, sometime in the past, those lines of descent included at least one male who did not pass on his mother’s mtDNA, so breaking the line of descent. Every person alive today can, probably, trace their maternal line of ancestry back to Mitochondrial Eve. Mitochondrial Eve was not alive at the same time as Y chromosome Adam. Adam probably lived in Africa, but Eve lived about 50 000 – 80 000 years earlier. Mitochondrial Eve is the most recent common matrilineal ancestor to all modern humans, not the most recent common ancestor. The most recent common matrilineal ancestor is only valid when we are looking at mtDNA. Important points in the ancestry of modern human populations n All humans alive today have a most recent common ancestor that was probably alive only 5 000 years ago – this is true even for people born on different continents. n The identical ancestors point – this is the point at which all humans alive today had exactly the same set of genealogical ancestors alive – probably just a few thousand years before the most recent common ancestor and far more recently than Mitochondrial Eve. n Y chromosome Adam was also likely to have been alive long before the identical ancestors point.

from mother to son and daughter, only vary if there are occasional mutations. These mutations are called markers and it is these markers that are the genetic signposts for tracing human evolution. Geneticists can follow these markers back through time to where and when they first occurred and are able to identify the most recent common

ancestor of everyone alive who carries a particular marker. The many branches of the human family tree, represented by groups carrying a given marker, can be followed back to points on the tree where a mutation split a branch in two directions. Eventually, these branches can be followed back all the way to a common African root – the common ancestor. ❑

The human journey Early modern humans probably left Africa around 60 000 years ago. Quest looks at how this happened. Origins Let’s start 200 000 years ago. Of course no one is sure exactly when modern humans first appeared. But between 1967 and 1974 Richard Leakey, a palaeoanthropologist working in Ethiopia, and his team found two skulls in the Omo River Valley. They were named Omo I and Omo II. They were dated to about 195 000 years ago. Parts of the fossils are the earliest classified by Leakey as Homo sapiens. Much further south in Africa, on the South African coast, the Klasies River Cave system contains many artifacts from the Middle Stone Age – about 60 000 – 130 000 years ago. Large collections of shellfish and seal and penguin bones – called middens – show that the early humans who occupied these caves caught and ate fish and foraged for shellfish. They also had tools that were made of nonlocal materials, which suggest very modern behaviour (see Using fire: A breakthrough in human evolution in this edition of Quest). The Apollo 11 Cave in the Huns Mountains in Namibia was used for over 70 000 years by anatomically modern humans. The cave contains paintings that were, until recently, the oldest known African art, dated to about 27 000 – 23 000 years ago.

Image: John Atherton

A map of early human migrations. Key: 1: Homo sapiens; 2: Neanderthals; 3: Early hominids. Image: Wikimedia commons

that made the Sahara more hospitable. This probably led to the migration of groups of the African populations of early modern humans to what is now the Middle East. As this region became drier, people would have been forced to move again. The route that these migrants took to the Middle East is not known for sure. But however they got there, they will have found their route back to Africa blocked by the expansion of the Sahara Desert. The desert was at its driest between 20 000 and 40 000 years ago, when the Saharan Gateway closed and isolated migrants outside Africa. ▲ ▲

First steps: The Saharan Gateway From our understanding of genetic markers, we know that all humans lived in Africa until at least 60 000 years ago – because that is when Y chromosome Adam was living in Africa. So when did the journey begin? As the last Ice Age set in, Africa would have suffered from severe droughts rather than extreme cold. But, around 50 000 years ago the climate was changing. This drier climate was interrupted by a period of warmer weather and wetter climates

A 1979 photograph of the excavations at the Klasies River Mouth Cave.

Rock art from the Apollo 11 Caves in Namibia. Image: Wikimedia commons

Quest 7(3) 2011 5

The map shows the probable extent of land and water at the time of the last glacial maximum, 20 000 years ago and when the sea level was probably more than 110 m lower than today. Image: Wikimedia commons Lake Toba is the crater lake that resulted from the eruption of the volcano. Image: Wikimedia commons Colonising Australia

From the Middle East these early humans spread out into Europe and elsewhere in Asia. Remarkably, they also arrived in Australia, very soon after they had left Africa. The archaeological record in Australia shows that the continent was colonised 40 000 – 60 000 years ago – probably 10 000 years before Europe was peopled. The climate of the time may have forced the migrants to remain south, favouring the warmer climates to which they were adapted. This incredible journey was possible because the continents were not in the configuration that they are now. There were shifting landmasses and lower sea levels during the glacial Pleistocene period. Massive ice caps trapped much of the Earth’s water and modern-day Sumatra and Borneo were joined in a landmass called Sunda, which was separated by only 100 kilometres of open water from Sahul – which was a landmass made up of Australia, New Guinea and Tasmania. The Last Glacial Maximum is the period in the Earth’s climate when ice sheets were at their maximum extension – between 26 500 and 19 000-20 000 years ago. This marked the peak of the last glacial period. During this time, huge ice sheets covered much of North America, northern Europe and Asia. They had a profound effect on the Earth’s climate, causing drought, desertification and a dramatic drop in sea levels.

Sea levels in some places were 100 metres lower than they are now. These short stretches of relatively calm water might have led the African migrants to follow the shores of the Arabian

6 Quest 7(3) 2011

An artist’s impression of what the eruption of the volcano, Toba, may have looked like from about 80 km above it. Image: Wikimedia commons

Peninsula, India and Southeast Asia, hopping from island to island and eventually settling in Australia. We don’t know when this happened or whether there was more than one migration. When the glaciers retreated and sea levels rose, Australia was isolated. The Sahul Strait that separates Australia from Southeast Asia is one of the deepest bodies in the world. It was open water for nearly 50 million years and so there was never a continuous land bridge between the two continents. This is shown by the major differences in plants and animals found on the Australian and the Asian side of the strait. Surviving catastrophy These migrant populations of Homo sapiens did not move around the world

without encountering potential disaster. Around 71 000 years ago, the volcano Toba, on the island of Sumatra, exploded, violently and catastrophically. The eruption lasted for about six weeks, during which time almost 3 000 km3 of ash and rock were spewed into the air. The ash drifted west across Asia, blocking the Sun completely. Plants and animals died within days and most of India was covered with a blanket of searing-hot ash 6 m deep. The world was plunged into six years of volcanic winter, followed by at least 1 000 years of global cooling. Humans suffered greatly – and it is possible that the entire human population was reduced to less than 10 000 individuals. ❑

The Khoisan people.

Image: Marczawel.com

From local research into our ancestry to working out the genetic lineages of the earliest modern humans in southern Africa, Quest looks at how science is unravelling the origins of humankind.

The dawn of humankind

Interpreting mitochondrial DNA results Scientists from the MRC, NHLS and Wits University have been taking samples of blood from volunteers across South Africa to determine our genetic ancestry.

How are the results interpreted?

After they obtain samples of a volunteer’s mtDNA control region (this region does not code for any proteins and is highly prone to mutations) sequence in the laboratory, they compare the person’s sequence profile for this region (e.g. #HS as shown below) to a published sequence called the Cambridge Reference Sequence (CRS). They use about 800 base pairs of sequence from two specific regions within the control region where mutations are more concentrated and

therefore referred to as ‘hypervariable regions (HVRI and HVRII)’. They start reading the HVRI between positions 15961 to 16561 (starting at the position of the ▼ to the end of the sequence below) and HVRII (positions 31 to 407; data not shown). If a person’s sequence differs from the CRS at any position, they note the position and mark the change(s) or mutation(s) as shown in red in the diagram. Using the information, they then list the mutations and the positions at

HVRI

▲ ▲

e can reconstruct human history using a number of different methods. In the absence of written records, scholars have made use of information from disciplines as diverse as linguistics, archaeology, physical anthropology, cultural anthropology, history and paleo-anthropology to reconstruct their prehistory. The most direct account of our past is inferred from the fossil record. Skeletal remains have been instrumental in establishing the evolution of human ancestors in Africa, and they have also provided important information about the evolution of modern Homo sapiens. We all identify with the family unit: our siblings, parents, grandparents, great-grandparents and so forth. We are quick to recognise certain physical traits (characteristics) like hair colour, nose shape, etc., as well as behavioural traits, like temperament, voice, etc., that we attribute to having been inherited from one and/or the other parent. The concept of ancestry is deeply rooted in the different cultures. Paying respect to our ancestors is part of our cultural evolution. The thread that connects us biologically with our ancestry is stored in the human genome that carries biochemical instructions that determine inherited traits, and contains an indelible record of our evolutionary past.

▼start of sequence data

CRS 15961 GAAAAAGTCT TTAACTCCAC CATTAGCACC CAAAGCTAAG ATTCTAATTT AAACTATTCT #HS 15961 GAAAAAGTCT TTAACTCCAC CATTAGCACC CAAAGCTAAG ATTCTAATTT AAACTATTCT CRS 16021 CTGTTCTTTC ATGGGGAAGC AGATTTGGGT ACCACCCAAG TATTGACTCA CCCATCAACA #HS 16021 CTGTTCTTTC ATGGGGAAGC AGATTTGGGT GCCACCCAAG TATTGACTCA CCCATCAACA CRS 16081 ACCGCTATGT ATTTCGTACA TTACTGCCAG CCACCATGAA TATTGTACGG TACCATAAAT #HS 16081 ACCGCTATGT ATTTCGTACA TTACTGCCAG CCACCATGAA TATTGTACGG TACCATAAAT CRS 16141 ACTTGACCAC CTGTAGTACA TAAAAACCCA ATCCACATCA AAACCCCCTC CCCATGCTTA #HS 16141 ACTTGACCAC CTGTAGTACA wTAAAAACCCA ATCCACATCA AAACCCCCTC CCCATGCTTA CRS 16201 CAAGCAAGTA CAGCAATCAA CCCTCAACTA TCACACATCA ACTGCAACTC CAAAGCCACC #HS 16201 CAAGCAAGTA CAGCAATCAA CCCTCAACTA TCATACATCA ACTGCAACTC CAAGGCCACC CRS 16261 CCTCACCCAC TAGGATACCA ACAAACCTAC CCACCCTTAA CAGTACATAG TACATAAAGC #HS 16261 CCTCACCCAC TAGGATACCA ACAAACCTAC CCACCCTTAA CAGTACATAG TACATAAAGC CRS 16321 CATTTACCGT ACATAGCACA TTACAGTCAA ATCCCTTCTC GTCCCCATGG ATGACCCCCC #HS 16321 CATTTACCGT ACATAGCACA TTACAGTCAA ATCCCTTCTC GTCCCCATGG ATGACCCCCC CRS 16381 TCAGATAGGG GTCCCTTGAC CACCATCCTC CGTGAAATCA ATATCCCGCA CAAGAGTGCT #HS 16381 TCAGATAGGG GTCCCTTGAC CACCATCCTC CGTGAAATCA ATATCCCGCA CAAGAGTGCT CRS 16441 ACTCTCCTCG CTCCGGGCCC ATAACACTTG GGGGTAGCTA AAGTGAACTG TATCCGACAT #HS 16441 ACTCTCCTCG CTCCGGGCCC ATAACACTTG GGGGTAGCTA AAGTGAACTG TATCCGACAT CRS 16501 CTGGTTCCTA CTTCAGGGTC ATAAAGCCTA AATAGCCCAC ACGTTCCCCT TAAATAAGAC #HS 16501 CTGGTTCCTA CTTCAGGGTC ATAAAGCCTA AATAGCCCAC ACGTTCCCCT TAAATAAGAC CRS 16561 ATCACGATG #HS 16561 ATCACGATG end of sequence data

Quest 7(3) 2011 7

African haplogroups. The colours in the tree show different haplogroups. The oldest groups of mtDNA sequences have been found in haplogroups L0, and all subsequent groups are also known by a letter. The nomenclature of haplogroups commonly found in Africa has been recently revised and now also includes L4, L5 and L6 (not shown in the figure).

The movement of haplogroups across the world. About 60 000 years ago a founder group moved out of Africa and their descendants, through the natural process of mutation, formed the haplogroups M and N. These groups in turn gained a foothold during the last Ice Age in Asia, Australia and parts of Europe and evolved their own specific types. So, for example, Europe is populated by the haplogroups H, I, J, K, T, U, V, W and X; Asia by A, B, C, D, E, F, G, M, and Y; the Americas by an Asian branch with A, B, C, D and X ; Papua New Guinea by P and Q; and Australia by further M and N types.

#HS’s sequence places this sequence in a sub-branch of haplogroup U called U2. What is a mtDNA haplogroup?

A young San hunter from Namibia.

Image: Wikimedia commons

which they occur as follows: MtDNA HVRI variation: 16051A-G, 16234C-T, 16254A-G In other words, at position 16021, #HS’s sequence has changed to a G whereas the reference sequence has an A at this site. Similarly, at position 16201, #HS’s sequence has a T whereas the CRS has a C, and so on. Note, #HS’s sequence is the same as the CRS at all the other positions except the three nucleotide positions indicated in red above. The same procedure is followed for noting mutations in hypervariable region II (HVRII). Some of the changes/mutations characterise the branching pattern of the mtDNA tree. We call these informative sites. For example, the presence of the G at position 16021 in

8 Quest 7(3) 2011

Haplogroups are groups of branches that share a common nucleotide change. For example, the mutation at position 16390 is found in all subbranches of haplogroup L2. The subbranches of L2 can be resolved further due to the presence of additional informative sites and other changes. The substitution at position 3594 is found in haplogroups L3, M, N and R. However, M and its derivatives all have the substitution at position 10400, N the substitution at position 10873 and R the substitution at 12704. Many of the informative sites that give the mtDNA its branching pattern occur outside the control region in the coding regions of the mtDNA molecule. There is reasonable agreement between the informative sites that distinguish haplogroups outside the control region and substitutions in the control region when deriving haplogroups. When the haplogroup cannot be derived from sequence data only the scientists use the informative markers to help them to derive the mtDNA haplogroup. The Khoi and San: Their role in genetic research The most recent genetic research supports the idea of a single origin for anatomically modern humans. As you

have seen in this article and in the previous articles, maternally inherited mtDNA has been vitally important in this model and this research suggests that our most recent maternal common ancestor was in sub-Saharan Africa and that there was a single wave of dispersal that populated the rest of the world much later. But, although we can now say that modern humans originated in Africa, we still do not know that much about early modern human population structure and their dispersal routes. At our present level of knowledge, human mtDNA evolutionary development and history (phylogeny) can be divided into two daughter branches, L0 and L195. A clade is a group consisting of a species and all its descendants – a single ‘branch’on the evolutionary tree.

The L195 branch is far more widespread and has given rise to almost every mtDNA lineage found today, with the two clades on this branch, (L3)M and (L3)N forming most of the non-African genetic diversity and marking the out-of-Africa dispersal 50 000 – 60 000 years ago. The current sub-Saharan African gene pool is a rich mix of L0 and L195 clades. The illustration shows the proposed gradual maternal movements, (A) and (B). (A) suggests an initial prolonged

Maternal gene flow within Africa.

Image: The American Journal of Human Genetics 2008; 82: 1130-1140

Right: Simplified human mtDNA groupings. The L0 and L195 branches are shown in green and brown. The branches are made up of haplogroups L0–L6 which, in their turn, are divided into clades. Khoisan and non-Khoisan clades are shown in blue and purple, respectively. Clades involved in the African exodus are shown in pink. A time scale is given on the left. Approximate time periods for the beginning of African LSA modernisation, appearance of African LSA sites, and solidisation of LSA throughout Africa are shown by increasing colours densities. Image: The American Journal of Human Genetics 2008; 82: 1130–1140

A royal lineage Nelson Mandela took part in a DNA study, headed by Professor Himla Soodyall from Wits University, that traced his ancestral geographic origins. Professor Soodyall looked at Mandela’s mtDNA and his Y chromosome. In the classification system that we have just discussed, Mandela is a descendant of the L1 group – the branch of descent closest to the oldest root of humanity. He also has genetic material that shows that he has roots in the Niger-Congo region.

colonisation (brown) by anatomically modern humans (1) is followed by a dispersal wave (green) of a split of the population (2) and the localisation of L0d and L0k to southern Africa (3). (B) suggests an early Homo sapiens division in a hypothetical migration zone (1) resulted in two separately evolving populations (2) and the localisation of L0 (green) in southern Africa and L105 (red) in eastern Africa. A subsequent dispersal event of the L0abf subset from the southern population and its mergence with the eastern population (brown) is suggested (3), resulting in the former population composed only of L0d and L0k and the latter composed of L105 and L0abf. Later dispersal waves from the eastern African population parallel the beginning of African Late Stone Age (LSA) approximately 70 000 ybp (4). Rapid migrations during the LSA (5) brought descendants of the eastern

Nelson Rolihlahla Mandela. Image: Wikimedia commons

African population into repeated contact with the southern population, peaking during the Bantu expansion (6). The Khoi and San (Khoisan) peoples of South Africa are regarded as a unique relic of hunter-gatherer lifestyles and are thought to carry paternal and maternal genetic lineages belonging to the deepest clades known among modern humans. Current research suggests that the Khoisan matrilineal ancestry split off from the rest of the human mtDNA pool between 90 000 and 150 000 years ago. As well as the Khoisan, scientists estimate that there were around 40 other evolutionarily successful lines flourishing in subSaharan Africa during the period of modern human dispersal out of Africa around 60 000 – 70 000 years ago. It was only much later, at the beginning of the Late Stone Age (LSA), about 40 000 years ago, that there was incorporation of genes from additional

Does mtDNA explain the different races? While there is reasonable agreement between someone’s geographic region of ancestry and mtDNA haplogroup distribution (see the map in the main text), people who identify with different races can have mtDNA lineages from the same haplogroup. For example, while L-lineages are more common in Africa, some people who are white from Europe can also have mtDNA L-lineages if their maternal ancestry stemmed from Africa at some point in their history. The mixing and reshuffling of the chromosomal genes that contribute in shaping a person’s physical appearance produce the traits that are commonly associated with particular races. However, the mtDNA inherited in an offspring from a mixed ancestral background would have inherited his/ her maternal mtDNA lineage unchanged over many generations. In fact, in South Africa, about 8 – 10% of people who self-identify as white have inherited mtDNA lineages from indigenous African ancestors.

lines into the Khoisan mtDNA pool. This process was accelerated even further during far more recent Bantu expansions from central Africa. By the time that the Bantu peoples expanded into southern Africa the local population had already formed small, separately evolving isolated populations. ❑ Futher reading Have a look at: www.ibm.com/solutions/ genographic/us/en/. This is the web site of the Genographic Project – a Landmark Study of the Human Journey. Also: https://genographic.nationalgeographic.com/ genographic/index.html. This National Geographic web site also provides loads of interesting information about our origins and the movement of people across the world.

Quest 7(3) 2011 9

FactFile Q

Neanderthals: closer than we think modern humans by adulthood. Neanderthals were larger and stronger than modern humans, with robust bone structure and particularly strong arms and legs. At one time they were thought to be completely carnivorous, but in 2010 scientists reported finding cooked plant matter in the teeth of a Neanderthal skull.

Did Neanderthals interbreed with early modern humans?

Neanderthal anatomy

This has been a controversial subject. There are caves in a limestone ridge on Mount Carmel, which overlooks the coast of Israel, that were occupied by early modern humans from about 100 000 years ago. There is evidence that, perhaps as early as 80 000 years ago, member of another species also occupied the caves – Neanderthals who were escaping from a cold spell in Europe by moving south into the modernday Middle East. The question that scientists have fiercely debated for many years is whether or not early modern humans mated with Neanderthals in areas where they occured together. The archaeological evidence from these caves sheds no light on the question and early work on Neanderthal DNA from bones suggested that there was no gene swapping. Some scientists thought that Neanderthals did mate with early modern humans, either in the Middle East or Europe. Others thought that the modern humans leaving Africa completely replaced Neanderthals with little or no interbreeding. But last year an international team of scientists published a report of their analysis of the DNA of three female Neanderthals who lived in Croatia more than 38 000 years ago. By comparing the partial Neanderthal genome that they worked out from these bones with the complete genomes of five living humans from different parts of the world, they found that both Europeans and Asians share 1% and 4% of their nuclear DNA with Neanderthals. This shows that early modern humans interbred with Neanderthals after the modern humans left Africa, but before they spread into Asia and Europe.

Evidence from fossil finds suggests that Neanderthals had brains the same size as modern humans at birth, which became larger than

Have a look at Science 7 May 2010, Vol 328, Newsfocus, ‘Close Encounters of the Prehistoric Kind’. www.sciencemag.org.

A Neanderthal skull from La Chapelle-aux Saints, France. Image: Wikimedia commons

N A mounted Neanderthal skeleton, American Museum of Natural History. Image: Wikimedia commons

A comparison of the skulls of Homo sapiens and a Neanderthal. Image: Wikimedia commons

eanderthals are an extinct member of the genus Homo who lived in the Pleistocene Era in Europe and parts of western and central Asia. The first early modern humans with Neanderthal-like characteristics appeared in Europe as early as 600 000 – 350 000 years ago. By 130 000 years ago true Neanderthal characteristics had appeared. The species is called after the Neander Valley in Germany because a Neanderthal fossil skull and parts of the skeleton was found in this valley in 1856. The first Neanderthal skulls were discovered in Belgium in 1829. The original Neanderthal discovery is regarded as the beginning of palaeoanthropology as a discipline. The bones of over 400 Neanderthals have been found to date. By 50 000 years ago Neanderthal characteristics had disappeared in Asia and by 30 000 years ago in Europe – Neanderthals had been replaced by anatomically modern humans, Homo sapiens.

Peking man

eking man is the name given to a fossil of Homo erectus that was discovered in 1929 during excavations at Zhoukoudian near Bejing in China. The cave contains the remains of more than 40 individual specimens of Homo erectus that were dragged there by predators. Dates from stone tools and the sedimentary layers that contained the oldest fossils show that Peking man was present in this part of China about 750 000 years ago during a relatively mild glacial period – similar to the modern day climate in southern Siberia.

10 Quest 7(3) 2011

The museum at Zhoukoudian with a reconstruction of Peking man’s head in the entrance. Image: Wikimedia commons

A replica of the skull of Peking man. Image: Wikimedia commons

Replicas of some of the skulls found at Zhoukoudian. Image: Wikimedia commons

Q Science news

Settling Asia: two waves not one

The very latest research on human settlement shows that there was a two-wave settlement of Asia. Quest reports.

esearch published online in the journal Science in September overthrows the idea that all Asians arose from a single migration of modern humans. The findings come from a human hair that was obtained almost a century ago by the British anthropologist Alfred Court Haddon. He travelled the world collecting, among other things, samples of human hair. A young Australian Aboriginal man gave Haddon a lock of his long, reddish-brown hair. The hair was eventually taken back to England where it lay in a museum drawer for 90 years. Modern geneticists have now extracted enough DNA from the hair to sequence the first complete genome of an Aboriginal who was born before there was mixing with immigrant European populations. The lead author of the study, Eske Willerslev, an evolutionary biologist from the University of Copenhagen, says that this genome shows that Australian Aboriginals are one of the oldest continuous populations outside Africa. The genome shows that the young man’s ancestors were part of an early wave of modern humans who swept out of Africa at least 60 000 years ago and travelled rapidly by land and sea along the coast of Asia, landing in Australia about 50 000 years ago. A second wave later populated much of Asia, including China. Another study, published in The American Journal of Human Genetics, in the same week in September, also shows an initial southern migration to Southeast Asia, followed by multiple separate migrations into Asia. DNA extracted from an archaic human in Siberia and from living Asians and Australians suggests that ‘[Aboriginal] Australians and Melanesians seem to be descended from a separate, earlier migration than the ancestors of [other] Asians,’ says senior author Mark Stoneking of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. The first wave branched off into Asia about 60 000 – 75 000 years ago, with a second migration, when European and mainland Asians diverged, was much later – probably 25 000 – 40 000 years ago.

Modern Australian Aboriginal men.

Image: Wikimedia commons

Aborignal ancestors left Africa and quickly travelled south (orange line) to Melanesia and Australia, interbreeding with Denisovans on the way. Other modern humans (brown line) headed to Asia in a later, second wave. In 2010, researchers sequenced the genome of an archaic girl who lived at least 30 000 years ago in Denisova Cave, Siberia. She was not a modern human, but a descendent of Homo erectus, an ancestral species that left Africa almost 2 million years ago. Her people had interbred with the ancestors of living Melanesians, who inherited about 5% of their nuclear DNA from Denisovans. But no Denisovan DNA has been found in the Han Chinese, suggesting that they arrived in Asia in a migration that did not mix with the Denisovans. Have a look at Science vol 333, 23 September 2011, News&Analysis, www.sciencemag.org.

The upper section of site PP5-6.

The Pinnacle Point site PP5-6..

Image: Kyle Brown/Curtis Marean

Using fire for Early modern humans improved the manufacture of stone tools using fire, showing evidence of complex behaviour. By Kyle Brown and Curtis Marean. Pinnacle Point site PP5-6 from the edge of the sea. Image: Kyle Brown/Curtis Marean

Curtis Marean, the project director. Image: Kyle Brown

he controlled use of fire was a breakthrough in human evolution. It allowed cooking and meant that early communities were able to generate warmth and light, which also provided protection from predators. There is evidence of cooking as far back as 790 000 years ago, but eventually fire was used for more complex technologies such as firing clay for ceramics and heating ores to make metals. But how did early modern humans get from using fire for simple tasks such as heating and producing light and using it as an engineering tool to alter raw materials? This is not well understood, but it signals an important technological advance that leads to the industrial technologies of today. During the African Middle Stone Age (280 000 â&#x20AC;&#x201C; 235 000 years ago),

12 Quest 7(3) 2011

many stone tool features appear that are only found to occur much later in Europe and Asia. One example is the production of tools with many parts including handles, glue, and replaceable

cutting edges, called blades. Blades are defined by archaeologists as stone chips that have a length more than twice their width. Many tools were probably also made from bone.

The entrance to PP5-6.

Q Archaeology

Image: Kyle Brown/Curtis Marean

more than light and warmth Kyle Brown flintknapping.

Image: Curtis Marean

Blade tools from Pinnacle Point Site 5-6. Image: Kyle Brown/Curtis Marean

A reconstruction of how blade tools might have been hafted or set into a handle. Image: Kyle Brown/Curtis Marean

Collecting silcrete to make tools.

grained stone for some of their more carefully made tools. In Still Bay, archaeologists have found thin, symmetrical leaf-shaped tools that are skillfully flaked on both sides, made from a stone called silcrete. At Pinnacle Point, there is the early occurrence of small silcrete blade tools that are carefully retouched (or reshaped) to make crescent-shaped tools that could be glued into handles. ▲ ▲

Most of the stone that early modern humans used for making their tools during the Middle Stone Age (MSA) came from sites close to where people lived, but early modern humans probably also gathered rock from distant places as they needed it. Coastal MSA cave sites such as Pinnacle Point, Blombos Cave, and Klasies River show that the early modern humans between 75 000 – 60 000 years ago preferred fine-

Image: Kyle Brown/Curtis Marean

Quest 7(3) 2011 13

Heat treatment fires require a large supply of firewood as the fire needs to stay hot for 12 – 20 hours. Image: Kyle Brown/Curtis Marean

Silcrete samples placed in the sand in preparation for heating. The wire is a temperature probe that records the temperature of the fire during the experiment. These samples are covered up by sand prior to building the fire. Image: Kyle Brown/Curtis Marean

The archaeological layers at site PP5-6.

14 Quest 7(3) 2011

Image: Kyle Brown/Curtis Marean

Silcrete is a type of stone that is found mainly in Africa and Australia. Silcrete, as the name suggests, contains a high percentage of the element silica, and forms by precipitating or cementing of other rocks that have weathered or broken down. Silcrete stone tools are common in coastal MSA archaeological sites in southern Africa after about 70 000 years ago.

One of the ways that archaeologists learn about how stone tools were manufactured is to try themselves to make and flake or ‘flintknap’ tools. Flintknapping is the process of striking a stone with another hard object – usually wood, bone, or another stone – to drive off a sharp chip or flake. Kyle Brown and his colleagues found it particularly difficult to make replicas of the stone tools because the silcrete that they had collected was so difficult to flake until – by experimentation – they discovered how to use the properties of fire to improve their tools! The African Middle Stone Age occurred between about 280 000 to 35 000 years ago.

Silcrete and fire Silcrete is usually thought to be easy to flake. But, when Kyle Brown and his colleagues tried to reproduce the tools that they found in their dig sites, they found that the silcretes in their raw quarried form were difficult to flake consistently into the types of tools they were finding in their excavations. The researchers knew that in Australia, indigenous stone tool makers (called knappers) heated silcrete with fire – heat treatment – to make the material easier to flake. Silcrete responds particularly well to heat treatment provided the temperatures are carefully controlled and the stone is not heated or cooled too quickly. So Brown and his co-workers heated the South African silcrete samples in sand beneath a fire pit over a period of many hours and then allowed the silcrete to cool slowly. When they tried making stone tools using their heattreated silcrete, they found a remarkable change in the ease with which the material could be shaped into tools. They could now flake the stone to consistently produce tools that looked like the tools found at their sites. This led them to make a systematic study of silcrete heat treatment to further

understand how the technique was used in the South African MSA. One of the questions that needed to be answered was whether or not the silcrete was intentionally or accidentally heated. In order to test this, they selected stone from archaeological layers where there was no evidence that the artefacts were burned after they were discarded on the ground. The science team used a number of independent laboratory techniques for recognising changes in the stone due to heating. Then they measured the shininess (gloss or surface lustre) of the stone artefacts. The gloss measurements were compared with those of the team’s modern experimental samples. This is important because artefacts that have been heated before they are flaked will have smooth shiny surfaces once they are fractured (broken). Artefacts that are accidentally burned in a fire do not show this characteristic gloss. The gloss analysis showed that the MSA tools were intentionally heated prior to flaking to improve their flaking qualities. The significance of fire The evidence that early modern humans used fire as an engineering tool is enormously significant. It allowed groups to use local materials, even if this stone is of poorer quality than rock from more distant sources, although this does mean that they needed a good supply of firewood to use as fuel. It also suggests that early modern humans had a very good understanding of fire and how it could be skillfully used to change the physical properties of the materials they found on the landscape in which they lived. In other words, if they did not have exactly what they needed, they could engineer something from other materials around them using fire. Fire and behaviour There is recurring evidence of early symbolic behaviour and complex technologies in South Africa from around 71 000 years ago, before these same technologies and behaviour were found outside Africa. Archaeologists still debate when modern human behaviour first appeared. However, there is increasing evidence that symbolic behaviour – behaviour that involves communicating with others using pictures or language that is characteristic of modern human cultures – had appeared by at least 80 000 – 70 000 years ago and perhaps

Right: A silcrete flake showing rough surface of the material prior to flaking and the smooth glossy surface that occurs once the heated stone has been flaked. Image: Kyle Brown/Curtis Marean Right below: Refitted block of silcrete showing the appearance of heated (red) versus unheated silcrete from the same nodule. Image: Kyle Brown/Curtis Marean

earlier during the African MSA. Archaeologists working at Pinnacle Point believe that the process of heat treatment, which involves many careful steps to be successful, would have required language to pass this skill from one generation to the next. The results collected by Brown and his colleagues show that at this same time, early modern humans regularly used fire to increase the efficiency and quality of their stone tool manufacturing process. This means that these early communities had to make the jump to a totally new association between fire, its heat and a structural change in stone that meant that it was easier to flake. This shows creative thought and the ability to take a new observation and make it useful. Their results also show that heat treatment technology may have originated at least 164 000 years ago. This heat treatment technology in Africa may help to explain the presence of advanced tools in the African MSA – the same tools that were rare in the Middle Palaeolithic of Europe and Asia where Neanderthals

were the most common humans. As these early modern humans moved from Africa into Europe and Asia, their ability to use fire as an engineering technology may have given them a behavioural advantage over the Neanderthal populations that lived there. ❑ Kyle Brown has been involved in research into African archaeology and human origins since 1995 and has conducted work in the United States, Kenya, Israel and southern Africa. He is finishing his PhD in Archaeology at the University of Cape Town, where he specialises in the analysis of stone tools and the experimental reproduction of technology from southern Africa. Kyle has assisted in directing excavations at Pinnacle Point since 2006. Curtis Marean is an archaeologist at the Arizona State University in Tempe who studies early modern humans in South Africa. He is the Associate Director of the Institute of Human Origins at ASU, and specialises in human adaptation, evolution and diversity and societies and their natural environments. He also has a keen interest in conservation and biodiversity.

Q FactFile

The Middle Stone Age The Middle Stone Age (MSA) is a period in the development of human technology between the Palaeolithic (Old Stone Age) and the Neolithic (New Stone Age). It is a period of African prehistory that began around 280 000 years ago and which ended around 50 – 25 000 years ago, although certain MSA stone tools originated as far back as 550 – 500 000 years ago. Anatomically modern humans – Homo sapiens – were present during the MSA. Early physical evidence comes from the Gademotta Formation in Ethiopia, The Kapthurin Formation in Kenya and Kathu Pan in South Africa. The period is marked by the appearance of artifacts – stone tools – which were usually manufactured from local materials and bone. This period is also the first time that there is evidence of people using locally available materials such as shells for decoration or jewellery. On the south coast of South Africa, for example, Nassarius shell bead have been found. There are even earlier examples of jewellery from Taforalt Caves in Morocco.

Scratched ochre and bone tools.

Image: Wikipedia

Complex behaviour and language One of the most important aspects of the MSA is that this was the period when evidence of complex thought and behaviour was first found. Quite how modern humans developed complex thought and behaviour is controversial. It is likely that a vast patchwork of complex events led to modern human behaviour. The Pinnacle Point site in South Africa has particularly rich evidence for the presence of

complex thought (see also Quest volume 6(4)). This evidence includes the oldest confirmed use of ochre for decoration and shellfish for food. Evidence from elsewhere (Klasies River Cave, South Africa and Howiesons Poort shelter, South Africa) suggests that MSA people were hunters with behaviour patterns that were similar to those of modern humans. It is likely that MSA people managed food resources by deliberately burning the veld to encourage the growth of plants with corms or tubers. Foraging groups seemed to be based on families, the people used colour for symbolism, artefacts were exchanged and living space formalised – all of which suggests very modern behaviour patterns. Ochre is found at some early MSA sites and is common after about 100 thousand years ago. Many archaeologists think that the fact that ochre was used in a symbolic, colour-related way suggests that the people using it for these abstract concepts could not have done this without a language. Formal bone tools are often associated with modern behaviour and could also be examples of a material culture that is associated with modern language.

Migration

Blades from the caves at Blombos.

Image: Wikipedia

By about 80 – 50 thousand years ago, MSA humans had spread out of Africa to Asia, Australia and Europe and by about 30 thousand years ago they had replaced Neanderthals and Homo erectus. Genetic and anatomical data support the hypothesis that it was in central/ southern Africa that Homo sapiens originated.

Quest 7(3) 2011 15

New evidence suggests that Au. sediba is the best candidate for the genus Homo. By Shirona Patel.

Humankind rising ‘I

Above: Prof. Lee Berger with the cranium of Au. Sediba. Image: Wits University

Top: The Cradle of Humankind World Heritage Site. Image: Wits University

16 Quest 7(3) 2011

t’s a complete surprise, not at all what we expected, and we should accept it for what it is,’ says Professor Lee Berger, a Reader in Human Evolution and the Public Understanding of Science at the University of the Witwatersrand, Johannesburg, commenting on the unique combination of features demonstrated by Australopithecus sediba, never before seen in an early human ancestor. A series of five papers based on new evidence pertaining to various aspects of the anatomy of the species Au. sediba (announced in April 2010 by Berger et al), was published in the prestigious journal Science on 9 September 2011. This is one of the largest collection of scientific papers ever produced by an African-based team or university, on a single subject to be published in a journal of this impact level. The evidence published in Science is based on two individuals from the site – MH1 (the juvenile male) and MH2 (the adult female). The papers reveal several world firsts, including the most complete hand ever described in an early hominin, the most complete undistorted early hominin pelvis ever discovered, the most accurate reconstruction of an early hominin brain, new pieces of the foot

and ankle, and one of the most accurate dates ever achieved for an early hominin site in Africa. ‘The fossils demonstrate a surprisingly advanced but small brain, a very evolved hand with a long thumb like a human, a very modern pelvis, but a foot and ankle shape never seen in any hominin species that combines features of both apes and humans in one anatomical package,’ explains Berger. ‘The many very advanced features found in the brain and body, and the earlier date make it possibly the best candidate ancestor for the genus Homo, more so than previous discoveries such as Homo habilis.’ The brain Some of the best technology in the world has been used to analyse the Au. sediba fossils. The cranium was scanned by the European Synchrotron Radiation Facility located in Grenoble, France. The scan, at a resolution of around 90 microns (half the width of a human hair), is the most accurate ever produced for an early human ancestor and presents fine details of the anatomy of Au. sediba’s brain. Dr Kristian Carlson from the Institute for Human Evolution at the University of the Witwatersrand, and lead author on the paper reporting the brain analysis,

Q Palaeontology

Another reconstruction of Au. sediba’s skull, by Dr Kristian Carlson. Image: Wits University

Au. sediba MH1 and MH2 skeletons. Image: Courtesy of National Geographic, published in August 2011

explains that the brain demonstrates a surprising mix of characters. ‘The overall shape of the MH-1 endocast groups closely with that of humans. Given the small brain of Au. sediba (around 420 cc), these results are consistent with a model of gradual neural (brain) reorganisation in the front part of the brain. However, the size of Au. sediba’s brain is strikingly inconsistent with a model of gradual brain enlargement, which is what has been hypothesised previously for the transition from Australopithecus to Homo.’

The pelvis As with the brain and the hand, the pelvis (hip bone) of Au. sediba demonstrates a combination of earlier hominin shape and form with later human shape and form. This is according to the lead author on the pelvis, Dr Job Kibii, also from the Institute for Human Evolution at the University of the Witwatersrand. ‘The pelvis of Au. sediba is short and broad like a human pelvis, creating more of a bowl shape than in other australopiths like Lucy,’ reveals Kibii. ▲ ▲

The hand Dr Tracy Kivell, a researcher in the Department of Human Evolution at the Max Planck Institute for Evolutionary Anthropology in Germany, is the lead author on the paper describing the earliest, most complete fossil hominin hand post-dating the appearance of stone tools in the archaeological record. ‘In our paper, we investigate the presence of several features that have been associated with human-like precision grip and the ability to make stone tools,’ elaborates Kivell. ‘Au. sediba has many of these features, including a relatively long thumb compared to the fingers, even longer than that of modern humans, that would facilitate thumb-tofinger precision grips. More importantly,

Au. sediba has more features related to tool-making than the OH 7 hand that was used to originally define the “handy man” species, Homo habilis.’ However, Au. sediba also has anatomical features that suggest that the hand was still capable of the powerful flexion needed for climbing in trees. ‘Taken together, we conclude from the mosaic morphology of the Au. sediba that it had a hand still used for arboreal locomotion [moving in trees] but also capable of human-like precision grips. In comparison with the hand of Homo habilis, Au. sediba makes a better candidate for an early tool-making hominin hand and the condition from which the later Homo hand evolved,’ concludes Kivell.

The Au. sediba skull reconstruction formed from the scan of the cranium. Image: Courtesy of the ESRF and Wits University

Au. sediba hand.

Image: Peter Schmid, Wits University

Quest 7(3) 2011 17

is wrong, and it is therefore probably a hypothesis that has been refuted in the entire human lineage. The shape and form of the Au. sediba pelvis suggests that there is a need to look at other explanations for the origins of modern pelvic shape,’ suggests Kibii.

Pelvis of Au. sediba MH1.

Image: Peter Schmid, courtesy of Wits University

‘At the same time it retains some of the features of earlier hominins, particularly in the size of the joint that links the sacrum with the vertebral column and the length of the front part of the pelvis. Parts of the pelvis are indistinguishable from that of humans, and it has a sigmoid shape (s-shape) along the top of the blades. It is surprising to discover such an advanced pelvis in such a smallbrained creature because of previous ideas as to the origin of the shape of the human pelvis.’

Pelvis of Au. sediba MH2. Image: Peter Schmid, courtesy of Wits University

Kibii’s paper further refutes the Obstetric Hypothesis – a scientific theory developed more than three decades ago that suggests that the evolution of the larger brains of early Homo was the reason for the human pelvis to be shaped differently to that of early hominins like Lucy, which are broader, flatter and more flaring. ‘Au. sediba, with its small brain, proves that at least in this lineage, the Obstetric Hypothesis for the origins of the human shaped pelvis

The foot and ankle The female MH-2 ankle is one of the most complete ankles ever found. Only Little Foot’s ankle is nearly as complete. ‘If we had not found the bones in articulation, we would certainly not have considered them to be part of the same individual, let alone the same species,’ comments Dr Bernhard Zipfel, the Curator of Senior Collections at the University of the Witwatersrand, who is the lead author on the foot and ankle paper. ‘Of all the evolutionary specialisations that define the human species, the foot is thought to be one of the most important, and is pivotal in allowing the evolution of arguably the most critical defining character of hominins – habitual upright walking or bipedalism.’ The ankle joint is mostly human-like

Frequently asked questions How were the individuals preserved? The site where the fossils were discovered is technically the infill of a de-roofed cave that was about 30 – 50 metres underground just under 2 million years ago. The individuals appear to have fallen, along with other animals, into a deep cave, landing up on the floor for a few days or weeks. The bodies were then washed into an underground lake or pool probably pushed there by a large rainstorm. They did not travel far, maybe a few metres, where they were solidified into the rock, as if thrown into quick-setting concrete. The rock they are preserved in is called calcified clastic sediment. Over the past 2 million years the land has eroded to expose the fossil bearing sediments. Did they die at the same time, or was it a catastrophe? The hominin skeletons were found with the bones either in partial articulation or in close anatomical association, which suggests that the bodies were only partially decomposed at the time of deposition in the lower chamber. This further suggests that they died very close in time to each other, either at the same time, or hours, days or weeks apart. Other animals have been found with them – equally complete – including sabretoothed cats, hyenas, antelopes, mice, birds and even snails. There is also plant material that has been found. How old are the children you have found? The juvenile MH-1 is around 10 – 13 years old in human developmental terms. He was probably a bit younger in actual age (perhaps as young as eight or nine) as he is likely to have matured faster than humans. The age estimate is based on modern human standards by which the eruption stages of the teeth are evaluated and the degree of development of the growth centres of the bones. Studies are presently underway to attempt to precisely determine the age of this child at death. The other young hominins found at the site are still under study and no exact, or even good, estimates of their age have yet been made. How old is the female skeleton? Based on the extreme wear of her teeth, MH-2 is probably at least in her late twenties or early thirties but it is very difficult to determine the age of an adult at death because her bones would have completed growing.

18 Quest 7(3) 2011

Did she have children? It is sometimes the case that females develop small pits on the back side of the pubic bone when they deliver a baby (caused by stress on the ligaments crossing the front of the pelvis). These pits are known as ‘scars of parturition’ and MH-2 may have one such scar. However, these pits can also be produced by other factors, and thus they are not always indicative that a female has given birth. It is likely that a female Australopith of her age would have had children. If she did have children, would the child be large-brained or small-brained? The estimated adult brain size based on the MH-1 juvenile is approximately 440 cm3, which is slightly below the average for Au. afarensis (Lucy’s species) and Au. africanus (Mrs. Ples’ species). This suggests that, like australopiths, sediba gave birth to small-brained babies (based on the relationship of adult to neonatal brain size in chimpanzees, australopiths are thought to have given birth to babies with brains of about 153 – 201 cm3). How do you know the child is a male? There are features of the face that help us determine that the child is a male. The muscles of the child are larger than those of the MH-2 skeleton, even though it is a child. We can now directly compare the male and female pelvises. Are they related to each other? We are not sure at this stage, but given the very short time of accumulation and the varying age of the individuals, it is likely that they are related. Detailed studies are being designed to address this important question. How does a brain endocast form? With every heartbeat, the brain pounds out its shape on the developing skull of a child, eventually leaving a beautiful impression of the external shape and form of the brain on the inside of the skull. By mapping the contours of this surface, a clear image of the original brain located in the skull can be produced. This resolution changes through time and the endocasts of children thus tend to be clearer than those of adults.

Au. sediba foot and ankle.

in form and inferred function, and there is some evidence for a humanlike arch and Achilles tendon. ‘However, a startling feature is that Au. sediba is ape-like in possessing a more gracile calcaneal (heel) body and a more robust medial malleolus (shin bone) than expected. This suggests that Au. sediba may have practiced a unique form of bipedalism, and would have almost certainly climbed trees,’ adds Zipfel. ‘It is also surprising that with parts of the heel being more primitive than earlier hominins like Lucy, it may mean that Au. sediba did not descend from this lineage.’ The word gracile means slender or graceful and in this context suggests that the heel bone was more like that in modern humans.

Dating When the fossils were announced in 2010, their age was announced as being between 1.78 and 1.95 million years old. At the time, the team had not discovered the top of the deposit, which was only discovered in late 2010. The deposit is capped by a flowstone (a limestone layer), that was dated using the Uranium-Lead dating method and found to be the same age as the flowstone at the base of the deposit. This allowed the team, using palaeomagnetic dating,

Why is the hand unique? The hand is one of the very special features of human lineage, as it is very different from the hand of the apes. Apes have long fingers for grasping branches or for use in locomotion, and thus relatively short thumbs, making it very difficult for them to grasp like a human. Au. sediba has, in contrast, a more human-like hand that has shortened fingers and a very long thumb, although at the same time it appears to have possessed very powerful muscles for grasping. The team has interpreted this as being a hand capable of tool manufacture and use, but still in use for climbing and certainly capable of a human-like precision grip. However, the Au. sediba hand is still primitive in many ways compared with modern humans, and the team does not suggest that Au. sediba was the only hominin around 2 million years ago capable of making tools. For example, the Au. sediba hand morphology is very different from the hand bones that were used to define the first tool-maker, Homo habilis or the ‘handy man’. This may suggest that there were many different hominins making tools with different types of hand morphology around the same time period. Compared with the hand of Au. afarensis – Lucy’s species – Au. sediba has fingers that are shorter (thus, a proportionately longer thumb) and less curved, suggesting that Au. sediba was not moving around in the trees as much as Lucy. Au. sediba has broader finger tips, stronger muscles of the thumb and a more human-like wrist that also suggest it had better manipulative abilities than Lucy and her kin. What is a precision grip? A precision grip is a grip that involves the thumb and one or more fingers, but the palm is not actively involved. There are several different types of precision grips, but the most common one people think of is the ability to touch the end of your thumb to the tip of your index finger. Other precision grips include a pad-to-side grip between the thumb and the side of the index finger, such as when turning a key in a lock, or a pad-to-pad ‘baseball’ grip, like when gripping a ball with just your fingertips. Other primates are capable of some precision grips but humans are unique in their ability to use these grips forcefully and for fine manoeuvring of objects within the hand. Au. sediba would have, without a doubt, had an excellent precision grip.

to identify a very specific, well-dated reversal of the Earth’s magnetic poles that occurred between 1.977 and 1.98 million years ago. ‘The new date of the fossils is one of the most accurate dates ever achieved in the early hominin record,’ says Dr Robyn Pickering from the University of Melbourne, lead author on the paper on dating. ‘This is a remarkable 3 000 years in 2 million years, or an incredible 0.15% error in the date.’ Cosmogenic dating was also used to

▲ ▲

The ankle bones were taken apart virtually using CT scans and images to segment the separate bones. These digital bones were then printed out and cast so that they could be studied by scientists.

Image: Peter Schmid, Wits University

Does Au. sediba imply that Homo habilis was not a tool-maker? No, but the answer is a bit more complicated than that. The OH 7 hand bones were found in the early 1960s in direct association with stone tools. Thus the OH 7 hand was assumed to be capable of making stone tools, which was key to including these fossils within the genus Homo and naming of the species Homo habilis or the ‘handy man’. Since this time, few have questioned the tool-making ability of Homo habilis. When a direct comparison between the bones preserved in Au. sediba and the OH 7 ‘handy man’ hand bones is made, their anatomy is very different. The OH 7 hand appears to have a derived large, robust thumb and very broad finger tips, while the Au. sediba thumb is gracile and the fingers tips are not quite as broad. In contrast, OH 7 still has fingers that are strongly curved and the wrist bones are more like those of African apes, while Au. sediba is more derived or human-like in these features. This difference in morphology implies two (though not necessarily mutually exclusive) scenarios: (1) that both species are capable of making tools but that they do this with different anatomy or (2) that the OH 7 hand does not in fact belong to Homo habilis, but is instead the hand of another early hominin species. Either way, it is likely that many hominin species were capable of making stone tools given that stone tools appear in the archaeological record long before either Au. sediba or Homo habilis are known to have lived. However, the lack of complete hand bones in the fossil record and our poor understanding of how the human hand functions and what morphology is necessary to make tools has limited our ability to determine exactly which species made tools and when and how tool-making first evolved. Au. sediba has shed new light on these questions. Have you found tools on sites? Excavations have not yet been conducted, so it is premature to speculate whether any tools in direct association with Au. sediba will be found. The hand and brain morphology suggest that Au. sediba may have had the capacity to manufacture and use complex tools. With these ape-like features, how do you know that Au. sediba was a habitual biped? The distal tibia or leg bone contacts the ankle bone perpendicular to

Quest 7(3) 2011 19

The cranium of the juvenile skeleton of Au. Sediba. Image: Brett Eloff, Wits University

interpret the landscape formation and to determine the depth of the cave at the time of deposition. Into the future Palaeontology is clearly an area in which South Africa punches above its weight and it provides a platform for collaboration with some of the best minds and resources in the world.

Since its discovery in August 2008, the site of Malapa has yielded well over 220 bones of early hominins, representing more than five individuals, including the remains of babies, juveniles and adults. Given the open access policy of the team, Au. sediba is already one of the best-studied hominin species yet discovered. ‘The preservation at Malapa is

the shaft of the leg bone, like that of modern humans. This is indirectly related to the position of the knee required for upright walking. In addition, there is evidence of a longitudinal arch and strong Achilles tendon insertion at the back of the heel, both being requirements of bipedalism. Au. sediba, however, practised a unique form of upright walking, not exactly like that of humans, with some degree of tree climbing. Why can’t you date the fossils themselves? The fossils themselves are too old to be dated directly with something like radio-carbon dating. Radio-carbon dating methods can only be used to date fossils around 50 000 years. The fossils themselves do not contain materials suitable for dating and the team therefore has to rely on dating the rocks that contain them to achieve accurate dates. What is a flowstone/speleothem? A specific type of rock forms within caves – the most common variations of this are stalagmites and stalactites. A flowstone is the same type of material as a stalagmite (calcium carbonate or lime) but instead of growing upwards and forming pillar-like structures, the flowstone flows out across the floor of the cave to form a layer of calcium carbonate. These layers are usually a few centimetres thick but can be up to several metres thick. A speleothem is a technical term used to describe any type of rock forming in a cave, so stalagmites, stalactites and flowstones are all types of speleothems. What is uranium-lead dating? When the flowstone rocks are formed, uranium gets trapped in them and decays by natural processes to form lead. Members of the team know the rate at which uranium decays and by measuring the amount of uranium and lead present in the rocks today, you can calculate the age of the rocks. In this way the uranium acts as a clock, which starts ticking once the rocks are formed. The amounts of uranium and lead are extremely small – in the parts per million and even the parts per billion range. In order to measure such small abundances of these elements, powerful machines called mass-spectrometers are used. The samples are prepared in a laboratory in Australia, the uranium and lead isotopes are isolated and concentrated from the rocks and collected for measurements.

20 Quest 7(3) 2011

excellent and there are certainly organic remains preserved like plant remains,’ says Berger. ‘There are some indications that even the soft tissues of animals are preserved, including possibly skin. This material is presently under study by a worldwide based team of experts, who are attempting to prove or disprove the existence of such important material, and to develop methods to study specimens that have never been found before in the early hominin record.’ These amazing discoveries have been made without any excavation, which is only scheduled to begin in early 2012, through the generous funding of local and international donors from the public and private sectors. ‘The team studying these fossils is one of the largest ever assembled in the history of archaeology or palaeontology. With more than 80 scientists, students and technicians from across the globe involved in the study, the team’s expertise includes specialists in geology, information technology and graphics, functional morphology, anatomy and physics,’ explains Berger.

What is palaeo-magnetic dating? The Earth’s magnetic field currently runs from north to south, which is known as a NORMAL field state. However, at various times throughout the Earth’s history, the field has reversed by 180 degrees in what is known as a REVERSED field state. The timing of such major field changes is recognised for the last 7 million years (Ma) based on studies of sea floor spreading zones, where these changes are recorded like a bar code, as well as the radiometric dating of volcanic rocks. This bar code of field change is known as the Geomagnetic Polarity Time-Scale (GPTS). The direction of the Earth’s field is preserved in cave sediments when water flushes these sediments into pools of water. When the sediment settles out of suspension in water the magnetic minerals orient themselves to the contemporary magnetic field. The sediments then become compacted and cemented, preserving the magnetic field direction. By measuring sediments in caves and comparing the polarity with the GPTS, the age of the sediments, and therefore the fossils within them, can be determined. What happens during a palaeo-magnetic reversal event like the one seen in the rocks of Malapa? We are not sure, but there may be severe changes in weather patterns as well as exposure to increased solar radiation as the Earth’s magnetic field fluctuates. How was the site and the fossils discovered? In the mid-1990s, Prof. Lee Berger had conducted an expedition across southern Africa, funded by the National Geographic Society and designed to map fossil sites using the then relatively new technology of GPS and to discover new sites. While the expedition discovered many new caves and fossil-bearing localities (over 100 caves and four new fossil sites in the Cradle of Humankind World Heritage Site), it did not yield any major discoveries. In early 2008, using Google Earth to spot caves in the Cradle of Humankind World Heritage Site, Berger renewed the exploration programme in the area. With the assistance of new technology available, Berger discovered, over a few months, more than 600 caves and more than three dozen new fossil sites in one of the most explored areas on the planet. On the 1 August 2008, while mapping with his dog Tau, Berger

‘Glocal’ Impact The global unveiling of the latest evidence pertaining to Au. sediba, has without a doubt shifted the international interest in palaeosciences, including the study of distant human relatives, to South Africa. News of the discovery of the two skeletons featured in 99 countries on six continents across the world in April 2010, and indeed there is significant interest from almost every continent about the evidence revealed in 2011. The discovery topped the Time Online readership polls and was described by Time and Google as one of the best scientific discoveries in 2010. It has attracted the attention of the likes of Sir Richard Branson, President Jacob Zuma, former vicepresident of the United States Al Gore and Google co-founder Paul Allen. Palaeoscience has been lauded as a niche area in South Africa and government, through the Department of Science and Technology, is due to release a national palaeosciences strategy in the near future. ‘The response has truly been

Prof. Lee Berger and his dog Tau enter a cave at the site in the Cradle of Humankind.

overwhelming – the world has embraced these fossils for what they are, and there is still much more to come,’ says an enthusiastic Berger. ‘We are already working on some amazing new research, which is likely to see the light of day in the near future. We will soon be able to recreate the habitat in which these individuals

discovered the fossil site of Malapa. On the 15 August he returned to the site with Dr Job Kibii, Tau and his then 9 year-old son, Matthew. Within minutes, Matthew had discovered the first piece of hominid, belonging to the MH-1 skeleton. Two weeks later, Berger discovered the remains of the adult female skeleton MH-2 and since then the site has yielded one of the most remarkable records of early human origins of any site on the planet. What does Australopithecus sediba mean? Australopithecus means ‘southern ape’, after the genus of the Taung child, named by Prof. Raymond Dart, also from the University of the Witwatersrand, Johannesburg. Sediba means natural spring, fountain or wellspring in Sotho, an appropriate name for a species that might be the point from which the genus Homo arises. As the hominids were also found preserved in an ancient underground lake or spring, the name also relates to their place of discovery. What is a hominid/hominin? A hominid is a member of the taxonomic family that includes humans, chimpanzees, gorillas and their extinct ancestors. Hominins are members of the human branch after the human lineage split from that of chimpanzees, and thus include living humans and extinct human ancestors, such as the Australopiths. Hominins are characterised by bipedal locomotion, although this may not have been the case for the very earliest members of the group, and relatively small canine teeth. Later members of this group (those in the genus, Homo) are characterised by larger brains than those of living apes like chimpanzees, bonobos, gorillas, orangutans and gibbons. How does this find relate to Lucy? Australopithecus sediba is approximately a million years younger than Lucy. Some scientists feel that Lucy’s species, Au. afarensis, gave rise to Au. africanus, and in these papers the team is suggesting that Au. africanus or something earlier than Au. africanus gave rise to Au. sediba. There is some evidence, based upon the combination of primitive and advanced foot and ankle features seen in sediba, that it does not descend from Lucy’s species or africanus, but comes from some as yet unidentified lineage of early hominin. Additionally, the very advanced nature of sediba’s hand suggests it may not give rise to Homo habilis, which

Image: Wits University

lived, tell you exactly what they ate and whether they reproduced. Watch this space!’ ❑ Shirona Patel is the Communications Manager at Wits University. She writes on behalf of Prof. Lee Berger, Dr Kristian Carlson, Dr Tracy Kivell, Dr Job Kibii, and Dr Bernhard Zipfel.

although later in time, has a more primitive hand, even though Homo habilis is some 200 000 – 300 000 years younger than sediba. Has the new species named last year been accepted by the scientific community? There is broad acceptance of the species Au. sediba among scientists as something previously unknown to science. Very little debate has occurred around whether these bones represent a new species. The debate has centred, largely, around whether the species should be placed in the genus Homo. So why is this not the genus Homo? The fossils have an overall body plan that is like that of other Australopiths – they have small brains, relatively small bodies and long and seemingly powerful arms. They do, however, have some features in the skull, hand and pelvis that are found in later definitive members of the genus Homo but not in other Australopiths. However, given the small brains and Australopithlike upper limbs, and features of the foot and ankle, the team has felt that keeping this species in the genus Australopithecus was the conservative thing to do. Nevertheless, sediba is turning out to be one of the most intriguing hominins yet discovered, and it certainly shows a mosaic of features shared by both earlier and later hominins. What about Homo habilis? Our study indicates that Australopithecus sediba may be a better ancestor of Homo erectus and it may certainly help to clear up some of this ‘muddle in the middle’. Even after a year, why is there still rock attached to the child’s skull? Due to the fragility of the base of the cranium of the specimen and to preserve part of the adhering matrix for future research as technologies improve, the team has decided to leave the specimen partially in rock. The team has been able to visualise this hidden part using some of the most sophisticated scanning technology available. Will there be more discoveries from Malapa? Malapa is already one of the richest early hominin sites ever discovered but excavations have not started yet. When they do, later this year, we expect to make even more remarkable finds at the site.

Quest 7(3) 2011 21

African fractals: new futures for old traditions

Figure 1: The Palace of Logone-Birni.

Image: Musée de l’Homme, Paris

Figure 2: Top, the first three iterations. Bottom, the third iteration, a fractal model for the palace of Logon-Birni.

Mathematics is all around us – in some of the places you would least expect it. Ron Eglash explains. What are fractals? Fractals are patterns that repeat themselves at many different scales. Fractal geometry was first applied in studies of natural systems: trees are branches of branches, mountains are peaks of peaks, and clouds are puffs of puffs. That is because nature makes use of self-organising processes in its constructions, so you get ‘self-similar’ patterns in nature’s designs. In 1986 I noticed a strange thing about African villages: if you look at them from an airplane, you see fractals. My initial hypothesis was that these structures, like those in nature, were simply the result of unconscious, ‘bottom-up’ forces. But after a year of fieldwork in West and Central Africa – interviewing indigenous architects, craft artisans, divination priests, hairstylists, and others – it became obvious that this was not the result of unintentional

22 Quest 7(3) 2011

social dynamics. Rather, fractal structures in Africa reflect an emphasis on similar underlying principles – recursion (repeated application of a rule), scaling and self organisation – in indigenous knowledge systems. They are, for the most part, intentional, conscious designs that not only provide a strong contradiction to the past stereotypes of African culture as ‘primitive’, but also offer exciting new repertoires for high tech development in the future. Figure 1 shows an aerial photo of the palace of the chief of Logone-Birni in Cameroon. Each complex is created by a process often called ‘architecture by accretion’ – in this case adding rectangular enclosures to pre-existing rectangles. Figure 2 shows a fractal simulation for the palace complex. The first iteration (top left of Figure 2) is a rectangle, but each side is

made up of both active lines (yellow) and passive lines (green). In the second iteration, the active lines are replaced by a scaled-down version of the first iteration. One more iteration gives a range of scales that is about the same as that of the palace. This is enlarged at the bottom of Figure 2. During my visit to LogoneBirni in the summer of 1993, they explained the structure in terms of a combination of patrilocal household expansion, and the historic need for defense. ‘A man would like his sons to live next to him,’ they said, ‘and so we build by adding walls to the father’s house’. In the past, invasions by northern marauders were common, and so a large defensive wall was needed. Sometimes the assembly of families would outgrow this defensive enclosure, and so they would turn that wall into housing, and build an

Q Mathematics

Figure 3: An aerial view of a Ba-ila settlement in southern Zambia. Image: Ron Eglash

Figure 4: Fractal pattern in Ba-ila settlement.

entrance is associated with low status (unclean, animals), and the back end with high status (clean, people). This scaling of social status is reflected by the scaling in the architecture of each family ring: the front of the ring is only fencing, as we go towards the back smaller buildings (for storage) appear, and towards the very back end are the larger houses. The two geometric elements of this structure – ring shape overall, and a status gradient increasing with size from front to back – echoes throughout every scale of the Ba-ila settlement. At the smallest scale, if we were to view a single house in the family

▲ ▲

even larger enclosure around it. These scaling additions created the tradition of self-similar shapes we still see today. Such architectural fractals abound in African village structures, some circular rather than rectangular, some much more diffuse, but still exhibiting a scaling characteristic. Figure 3, a Ba-ila settlement in southern Zambia, shows ring-shaped livestock pens, one for each extended family. Towards the back of each family ring we find the family living quarters, and towards the front is the gated entrance for letting livestock in and out. For this reason the front

ring from above, we would see that it is a ring with a special place at the back of the interior: the household altar. The settlement as a whole has the same shape: it is a ring of rings. The settlement, like the family ring, has a front/back social distinction: the entrance is low status, and the back end is high status. At the settlement entrance there are no family enclosures at all for the first 18 m or so, but the farther back we go, the larger the family enclosures become. At the back end of the interior of the settlement, we see a smaller detached ring of houses, like a settlement within the settlement. This is the chief’s extended family ring. At the back of the interior of the chief’s extended family ring, the chief has his own house. Enclosed by that ring is an alter of miniature houses representing the spiritual presence of ancestors. The scaling sequence allows a kind of infinite regress into the spiritual realm, just as fractals offer infinite regress. Since we have a similar structure at all scales, this architecture is easy to model with fractals. Figure 4 shows the first three iterations. We begin with a seed shape that could be the overhead view of a single house. In the next iteration, we have a shape that could be the

Quest 7(3) 2011 23

Figure 5: Rupert Auerbach’s ‘seed pod’. Figure 6: Envisioned evolution of squatter settlement using seed pod.

overhead view of a family enclosure. Finally, the third iteration provides a structure that could be the overhead view of the whole settlement. Fractal characteristics can also be seen in African textiles, paintings, sculpture, masks, religious icons, cosmologies, and social structures. Religious symbols include recursively nested calabashes, snakes of ‘infinite length’ coiled into a finite space, crosses-within-crosses-withincrosses, and other icons that express cosmologically nested infinities with their geometric recursion. I have detailed all of this in my book, African Fractals, and readers can try out the simulations (or design their own fractals) on our website (www. csdt.rpi.edu). Much of our use for these materials has been in precollege education, where we find statistically significant improvement in disadvantaged students using these materials (see Eglash et al 2006; Eglash and Bennett 2009, Eglash et al in press). But there have also been some exciting new applications in development, especially that related to architecture. From shanty-towns to selforganised cities in South Africa One of the most exciting developments related to African fractals has been the work of Rupert Auerbach, a postgraduate student

24 Quest 7(3) 2011

in architecture at University of Cape Town. Auerbach observed that the post-apartheid conversion of squatter settlements has proceeded with haste, in part because the urgent need to address health dangers. But these ‘instant communities’ of monotonous block houses do very little to help the formation of stable family units with regular income and access to good education. The poorest of the poor then face maintenance and utility bills; two families often have to share the single room they can afford. The stress on quick and cheap housing reduces concerns for environmental sustainability. The cost associated with employing commercial contractors to demolish informal settlements and build these instant communities has also meant a constantly growing housing backlog. As an alternative, Auerbach noted that many squatter settlements, contrary to stereotypes, show a great deal of creativity and ingenuity in their use of recycled materials and appropriated technologies. Architects such as John Turner have noted the potential for allowing squatters to develop their own housing since the late 1960s, and more recently writers such as Stewart Brand have described their positive ecological characteristics. Putting these insights together with the idea of the traditional African settlement plan of organic fractal growth, Auerbach proposed a ‘seed pod’ (Figure 5). This cluster of essential amenities includes the Ecosan composting toilet (created and

produced in South Africa), grey water processing for a food garden, laundry, kitchen, solar cell, etc. Structural elements would be created from bamboo, which can be grown locally with little input. Rather than demolish squatter settlements, the seed pod would provide the essential functionality, and allow dwellers to incorporate it into their existing buildings, or create new buildings around it. Auerbach suggests that organic growth patterns, such as fractals, would be the probable result (Figure 6), providing a less monotonous layout than the current system produces. The plan would provide sustainable and affordable housing, draw on the creativity of the local inhabitants, and instill pride in neighbourhoods that were the result of local design. A new university in Angola A non-profit organisation, SHAREcircle, has awarded the commission of a master plan for a new university to US-based Hanbury, Evans, Wright, Vlattas and Company, architects and planners. The plan, which will include the design of a first academic building for Angola Central Highlands University, was the result of an international design competition. One of SHAREcircle’s requirements was that the design include a fractal layout. The winning plan used the Angolan tradition of lusona drawings to create its recursive form. The Tchokwe people of Angola had a tradition of creating patterns

Figure 7: Lusona sand drawings.

than think of science and technology as a ‘culture free’ practice inhabited only by equations and physics, we can approach it as a practice informed by the entire spectrum of human experience, and combine the rigour of science with an emphasis on local meaning, social justice, and environmental sustainability. ❑

Figure 8: Layout for Angola Central Highlands University. Image: Courtesy of Hanbury, Evans, Wright, Vlattas, and Company.

by drawing lines in the sand, called lusona. Mathematician Paulus Gerdes was the first to note that the lusona sand drawings show the constraints necessary to define what mathematicians call an Eulerian path: the stylus never leaves the surface and no line is re-traced. But lusona have another geometric property: they tend to use the same pattern at different scales; that is, successive iterations of a single geometric algorithm. Figure 7 shows the first three iterations of one of the dozens of lusona that were recorded by missionaries during the nineteenth century, when the lusona tradition was still intact. The reports indicate that the lusona may have been used in an age-grade initiation system; rituals that allowed each member to achieve the status of reaching the next, more senior level of identity. By using more complex lusona, the iterations of social knowledge passed on in the initiation become visualised by the geometric iterations. A perfect design tradition

for the layout of a new university (Figure 8). Conclusion The indigenous tradition of fractals in African design offers a wealth of new ideas for future development, from education to architecture. Fractals can be applied to nearly every area of science and technology. For example, Coppens (2009) provides an extensive list of fractal nanostructures, some with implications for improving environmental sustainability, such as distribution of oxygen over a hydrogen fuel cell (which would only produce water vapour as a by-product) or filtering impurities from water. Fractals can be used in medical diagnosis to detect irregularities in cells or organs, in cell phones to improve the reception of antenna, and in geology to model earthquake activity. Fractals characterise the ‘bottom-up’ structure of Internet web links, social entrepreneurship, and other ‘wikinomics’ phenomena. Rather

Dr Ron Eglash received his BS in Cybernetics, his MS in Systems Engineering, and his PhD in History of Consciousness, all from the University of California. A Fulbright postdoctoral fellowship enabled his field research on African ethnomathematics, which was published by Rutgers University Press as African Fractals: modern computing and indigenous design, and recently appeared as his TED talk (http://www. ted.com/index.php/talks/ron_eglash_on_ african_fractals.html). He is a Professor of Science and Technology Studies at Rensselaer Polytechnic Institute, where he teaches design of educational technologies and graduate seminars in social studies of science. His ‘Culturally Situated Design Tools’ software, offering math and computing education from indigenous and vernacular arts, is available for free at www.csdt.rpi.edu. Recently funded work includes his NSF Triple Helix (http://www.rpi.edu/about/inside/issue/ v4n11/eglash.html) project, which brings together graduate fellows in science and engineering with local community activists and K-12 educators to seek new approaches to putting science and innovation in the service of under-served populations. References Brand, Stewart. ‘Stewart Brand on New Urbanism and squatter communities’. http://newurbannetwork.com/article/stewart-brandnew-urbanism-and-squatter-communities-13243. Eglash, R. African Fractals: modern computing and indigenous design. New Brunswick: Rutgers University Press. 1999. Eglash, R, Bennett, A, O’Donnell, C, Jennings, S, and Cintorino, M. ‘Culturally Situated Design Tools: Ethnocomputing from Field Site to Classroom.’ American Anthropologist, 2006. 108: 347-362. Eglash, R. and Bennett, A. ‘Teaching with Hidden Capital: Agency in Children’s Mathematical Explorations of Cornrow Hairstyle Simulations.’ Children, Youth, and Environments 2009. 19. Eglash, R, Krishnamoorthy M, Sanchez J, Woodbridge, A. ‘Fractal Simulations of African Design in Pre-college Computing Education’. ACM Transactions on Computing Education, In press. Turner, John F C and Fichter, Robert, Eds Freedom to Build, dweller control of the housing process. New York: Macmillan. 1972.

Quest 7(3) 2011 25

FactFile Q A Julia set, closely related to the Mandelbrot set. Image: Wikimedia commons

A Mandelbrot set is a famous example of a fractal. Image: Wikimedia commons

A fractal flame.

Image: Wikimedia commons

A snowflake seen through an optical microscope. Image: Wikimedia commons

Fractals

T High voltage breakdown within a block of acrylic creates a fractal Lichtenberg figure. Image: Wikimedia commons

A fractal is formed when pulling apart two glue-covered acrylic sheets. Image: Wikimedia commons

26 Quest 7(3) 2011

he definition of a fractal is ‘a rough or fragmented geometric shape that can be split into parts, each of which is (at least approximately) a reduced-size copy of the whole’. The idea of fractals goes back to the 17th century, but serious mathematical study of fractals did not occur until a century later. The word fractal was invented by Benoît Mandelbrot in 1975. The word comes from the Latin fractus, which means broken or fractured. A mathematical fractal is based on an equation that undergoes iteration, a form of feedback based on recursion. Recursion in mathematics is the process of repeating items in a self-similar way. A Mandelbrot set is a particular set of mathematical points whose boundary generates a distinctive and easily recognisable two-dimensional fractal shape. The set is closely related to the Julia set, which generates similarly complex shapes.

Fractals are a mathematical construct, but they are also found in nature. A fractal often has the following features: n It has a fine structure at arbitrarily small scales. n It is too irregular to be easily described by traditional Euclidean geometry (the kind you learn at school). n It is self-similar. n It has a simple and recursive definition. Fractals look the same at all levels of magnification so are thought to be infinitely complex. A good example of a natural object that can be approximated by a fractal is a snowflake.

Other fractal patterns Lichtenberg figures are branching electric discharges that sometimes appear on the surface or the interior of insulating materials. They are called after the German physicist Georg Christoph Lichtenberg who originally discovered and studied them.

The two top performers in this year’s National Science Olympiad were Martinette Rossouw of Hoërskool Delmas in Mpumalanga (Life Sciences) and Shavan Sookdeo of Star College in KwaZulu-Natal (Physical Science). In the photo are, from the left, Ms Beverley Damonse, Executive Director of the South African Agency for Science and Technology Advancement, Rossouw, Deputy Minister of Science and Technology Derek Hanekom, and Sookdeo. Image: NSF/SAASTA

South Africa’s top science learners awarded In March, over 24 000 learners from around South Africa and SADC countries – the largest number ever in the 47 years of the competition – wrote the National Science Olympiad test.

n March, over 24 000 learners from around South Africa and SADC countries – the largest number ever in the 47 years of the competition – wrote the National Science Olympiad test. On 30 June 2011 the winners of this competition were presented with awards at a ceremony at the Gallagher Convention Centre in Midrand. Mr Derek Hanekom, Deputy Minister of Science and Technology, keynote speaker at the awards event, applauded the winners for their excellent achievement. The National Science Olympiad is a flagship programme of the South African Agency for Science and Technology Advancement (SAASTA). SAASTA is a business unit of the National Research Foundation (NRF) and is committed to steering young minds towards careers in science, technology and innovation. ‘As an organisation, our role is to change lives and make a contribution towards providing South Africa with skilled human capacity, especially in the critical areas of science and technology (SET,)’ says Ms Beverley Damonse, Executive Director of SAASTA. ‘Our success in this field is evident from a number of professionals who are actively involved in the economy of this country and who have indicated that they, to a certain extent, occupy their positions in society because they were identified and nurtured through our interventions, in particular the National Science Olympiad.’ ‘It is encouraging to note that participation and performance have been steadily improving over the past few years,’ says Dr Jabu Nukeri, Manager of SAASTA’s

Science Education unit. ‘Participation in this year’s Olympiad has been the highest ever since the National Science Olympiad’s first round in 1964.’ The Olympiad test consists of a number of curriculum-based and general science and technology questions for Grades 10-12 learners. There are two Olympiad papers that candidates can select from: Physical and Life Sciences. Several prizes are awarded to the learners who perform best in various categories of the Olympiad and to the top performing schools. The project is sponsored by Harmony Gold Mining Company, the fifth largest gold producer in the world. Prizes include laptop and desktop computers, iPods, laboratory equipment and book vouchers, invitations to attend a Science Focus Week in Pretoria, a trip to the UK to attend the London International Youth Science Forum for the top five learners, and participation in the Australian Science Focus Week for three top performers in the lower grades. The 130 best achievers arrived in Pretoria on Sunday, 26 June for a week of edutainment and exposure to careers in SET. Learners were treated to lectures, excursions and industry visits to a Harmony Gold mine, the National Zoological Gardens, Necsa, Agricultural Research Council, Sci-enza Science Centre, the Johannesburg Observatory and Forensic Laboratories. The five learners who will be attending the London International Youth Science Forum are: Best overall marks in Physical Science: Mr

Shavan Sookdeo, a Grade 12 learner from Star College, KwaZulu-Natal Best overall marks in Life Science: Ms Martinette Rossouw, a Grade 11 learner from Hoërskool Delmas, Mpumalanga Best marks in Physical Science in Grade 12: Ms Danielle Prinsloo, Hoërskool Delmas, Mpumalanga Best marks in Life Science in Grade 11: Mr Jason Saroni, African Leadership Academy, Gauteng Best marks from a disadvantaged school in Physical Science: Mr Phuti Chokoe, Shakoleng Secondary School, Limpopo. Three learners have been selected to attend a Science Focus Week in Australia in January 2012. They are: Best marks in Physical Science in Grade 10: Mr John Keto, African Leadership Academy, Gauteng Best girl learner in Life Science in Grade 10: Ms Tion chon Dong, African Leadership Academy, Gauteng Best girl learner in Physical Science in Grade 11: Ms Esmané Steyn, Queenstown Girls High School, Queenstown, Eastern Cape. The London International Youth Science Forum took place from 27 July to 10 August this year. The Forum brings together over 300 students of the sciences from almost 60 countries on the five continents. The learners participated in a programme of lectures and demonstrations from leading scientists, visits to industrial sites and research facilities. Registration for the 2012 National Science Olympiad will open in October this year. Please visit www.saasta.ac.za for more information.

Quest 7(3) 2011 27

Should we worry about sea-level rise? Sea level gradually changes over millions of years as a result of natural geological processes. But since the 1800s sea levels have been on the move again. Mike Lucas explains why. The Antarctic Circumpolar Current The Antarctic Circumpolar Current (ACC) is an ocean current that flows from west to east around Antarctica. This current is the dominant feature of the Southern Ocean and is the largest ocean current – approximately 125 Sverdrups (a Sverdrup is a unit measure of volume transport [a million cubic metres per second] which is used almost exclusively in oceanography to measure the transport of ocean currents). The ACC connects the Atlantic, Pacific and Indian Ocean basins and is the main exchange pathway between these basins. The ACC is driven by strong circumpolar westerly winds that are found in the latitudes of the Southern Ocean.

hen the first oceans appeared on Earth about 4 000 million years ago, sea levels rose and fell due to crustal plate movements, which changed the position, shape and volumes of the ocean basins. These continuing geological processes still result in extremely gradual changes in sea level over millions of years. But when the Drake Passage between Antarctica and South America opened up about 35 million years ago, the Antarctic Circumpolar Current formed, separating warm tropical waters from Antarctica. This made the Antarctic continent cool and freeze, which contributed to global cooling, and the Greenland ice cap also formed in the northern hemisphere. The formation of the Antarctic and Greenland ice caps, which contain 90% of Earth’s freshwater, have since played a pivotal role in more rapid sea-level changes, and could do so again within the next 100 to 200 years, if not sooner. Past and present sea level Sea-level changes during the glacialinterglacial periods of the last 800 000 years have been recovered from icecore records. During periods of ice

formation when global cooling occurs, sea level falls as ice mass accumulates. During warming periods, sea level rises as the ice caps melt. This has resulted in cyclical changes in sea level of about 130 m over thousands of years. During the current interglacial period of general ice retreat and melt since the last glacial maximum 23 000 years ago, sea level has been rising steadily. The current mean sea-level reference point is 125 m higher than it was at the last glacial maximum. Sea level has in fact varied very little over the last 6 000 years or so as we have enjoyed a relatively warm and stable climate (Figure 1). But with the onset of global warming, could that all change abruptly – and should we worry? Since the 1800s sea level has been on the move again due to climaterelated impacts of ocean warming and land-based ice melt. The amount of sea-level rise varies around the globe from about 1.5 – 3.5 mm per year only. Early observations of sea-level rise from about the 1870s to the present have been collected from tide guages placed at coastal observation stations around the world. Such measurements need to be corrected for tidal cycles and slow vertical movements of the Earth’s crust,

The Antarctic Circumpolar Current (ACC) is the strongest current system in the world oceans, linking the Atlantic, Indian and Pacific basins. Image: Wikimedia commons

Figure 1: Past and present changes in sea-level rise relative to a 1993 reference point of zero metres. Estimates of past change come from ice-core records.

28 Quest 7(3) 2011

Figure 2: Total measured sea-level rise for 1993 – 2003 was 2.8±0.7mm per year, while the total was 3.3±0.4mm per year for 1993 – 2007. The discrepancy between the totals and the sum of their parts is sea-level rise that is not yet explained. Estimated sea-level rise values contain considerable uncertainty, as shown by the variance (±) around the globally averaged rates.

Q Climate change

The Rhone Glacier is easily accessible so its size has been observed since the 19th century. The glacier has lost around 1 300 m during the last 120 years, leaving a track of scarred and naked stone. Image: Wikimedia commons

This image shows the formation of numerous glacial lakes at the ends of receding glaciers in Bhutan in the Himalaya. Image: NASA

making the observations difficult to interpret. However, since 1990 we have been able to measure sea-level rise using satellite altimetry, so estimates of global open-ocean sealevel rise have been transformed and are now extremely accurate. Satellite altimetry use satellites that measure the distance from the satellite to a target surface by measuring the satellite-to-surface round-trip time of a radar pulse. When this is combined with the precise location of the satellite, these measurements can be used to measure the height of the surface of the sea.

3 m respectively if their respective ice caps were to catastrophically collapse. This is currently in the realm of Hollywood disaster movies, but is not impossible in the distant future. The problem is we don’t know how distant – or how soon? Sea-level changes around South Africa Sea-level rise around southern Africa follows global trends. Analyses of about 50 years of tide gauge data show that sea-level rise along the west coast of South Africa is about 1.87 mm per year. Trends for the south coast are 1.47 mm per year and 2.74 mm per year for the east coast. Some of these regional differences are attributable to warming of the Agulhas Current since the 1980s, which causes local thermal expansion of the ocean. Other causes of variability are due to regionally different rates of crustal movement and long-term changes in atmospheric pressure. Declining barometric pressure (west coast) adds to sea-level rise, while increasing ▲ ▲

Satellites show that the globally and annually averaged sea-level rise from 2003 – 2008 was about 3.4 mm a year, as shown in Figure 1. On the face of it this seems a trivial amount. But if we examine the causes of current sea-level rise, it is clear why there is growing concern from scientists, politicians and local municipalities charged with protecting low-lying coastal regions, cities and towns from the sea.

Causes of sea-level rise Current climate-related rise in sea level is attributable to thermal expansion of the oceans, melt-water run-off from land-based glaciers, and from Greenland and Antarctic ice-cap melt. The relative contributions of these components to sea-level rise is illustrated in the pie charts in Figure 2. What is notable from these pie charts is a distinct upward trend in the overall contribution of land-based icemelt from approximately 1.2 mm per year (42%) for the 1993-2003 period to approximately 1.8mm per year (54%) for the 1993 – 2007 period. This trend has now accelerated to 80% for the 2003 – 2008 period. It is quite clear that landbased mountain glaciers are fast disappearing in most parts of the world, but what really sets alarm bells ringing around the world is the overall increased contribution by the Greenland and West Antarctic ice-cap melts. Although their contribution to sea-level rise so far is small, they could add a cataclysmic 6 – 7 m and

The Furtwängler Glacier at the summit of Kilimanjaro. Between 1976 and 200 the area of this glacier was almost halved (from 113 000 m2 to 60 000 m2). Image: Wikimedia commons

Quest 7(3) 2011 29

An island in the Maldives, which would almost certainly be swamped by any significant rise in sea level. Image: Wikimedia commons

Figure 3: Evolution of global mean sea level between 1800 and 2100 based on observations for the nineteenth and twentieth centuries and model projections for the twentyfirst century.

barometric pressure (east coast) reduces sea-level rise. As elsewhere, these changes are certainly modest, where the threat appears snail-like in the speed of its advance. Sea level can, however, be rapidly and dramatically amplified by storm surges resulting from concurrent high tides (adding 1– 2 m), bad weather or tropical cyclones (adding 0.5 – 1 m) and resultant freak waves (adding 1 – 5 m or more). This has already happened. In March 2007, an extreme storm coinciding with high spring tides produced waves of about 8.5 m that crashed into the KwaZuluNatal coastline, causing significant damage to coastal property and infrastructure. Past records show that waves of 7 m occur every year along the South African coast, while waves exceeding 10 m occur every 20 years. What sea-level rise does, therefore, is to slowly but relentlessly increase the frequency of these events, which will be compounded as the oceans warm. This is because heat lost from the oceans fuels both the frequency and intensity of tropical storms, further adding to the impact of sea-level rise.

30 Quest 7(3) 2011

This satellite image of Bangladesh clearly shows the country’s vulnerability to rising sea levels. Image: NASA

Future projections If you want to build your dream beach-front house, or a luxury pad on an idyllic Pacific atoll, or a simple beach house by the water’s edge on a quiet lagoon or estuary – think again. According to IPCC AR4 (2007), projected sea-level rise into the 21st century will ‘likely accelerate’, resulting in a mean global sea-level rise of 0.22 – 0.50 m by the year 2100 (see Figure 3). The problem is that the IPCC AR4 is almost certainly too conservative. When that report was written, polar ice-cap melt was so poorly understood that its significance was underestimated. Now, new studies that link ice-cap melt directly to warmer atmospheric and oceanic temperatures forecast a sea-level rise of 0.55 – 1.2 m by the year 2100. The projected range given clearly underscores the uncertainty of ice-sheet dynamics, but there are worrying signs of accelerating icesheet melt at the margins, particularly in Greenland and in West Antarctica. So should we worry? A 1 m rise in sea-level would overwhelm small island states such as the Maldives (averaging

2.1 m above MSL), as well as low-lying islands in the Pacific, while 17 000 km2 of Bangladesh would be flooded, making 15 million people homeless. A sea-level rise of 1.5 m would flood 22 000 km2 and affect 18 million people in a country poorly equipped to defend itself. But because of South Africa’s generally elevated geography, a 1 m rise in sea-level would have far less impact, affecting only regionally vulnerable areas such as the Cape Flats region of the Western Cape, specifically Muizenberg for example. If Polar ice sheets melt, then what? The first question to ask is if there is indeed any evidence of ice-sheet melt? In 2006, British Antarctic scientists estimated that 90 km3 of the West Antarctic ice sheet were collapsing into the ocean each year, adding just 0.25 mm per year to global sea-level rise. But the West Antarctic is unstable, and is being eroded from below by warm water. Similarly, Greenland ice-sheet melt is also accelerating. If both ice sheets collapsed catastrophically,

This satellite image shows melt ponds on the Greenland ice sheet. Image: NASA

sea level would surge by about 3 m and 7 m respectively, bringing to life Hollywood disaster scenarios. But could this happen; and if so when? Although unlikely in the short term, the answer to this depends on how fast global warming proceeds and what the temperature rise will be. If the answer is just 2 °C, which is what we hope for, then polar ice sheets will probably not collapse completely. But if temperature rises by 4 – 6 °C and oceans warm substantially, then ice-cap melt and sea-level rise of 3 – 7 m magnitude within the next 100 years becomes a possibility. However the uncertainties are substantial. Our real problem is that we have very little understanding of ice dynamics. For example, if melt water seeps down to the bed rock on which the ice caps sit, as has been seen in Greenland, then scientists suppose that this would lubricate ice-sheet movement over the bed rocks and accelerate their collapse into the sea. But measurements of such processes are complex and we currently rely on computer simulation models to make predictions that have considerable uncertainties. Even so, both scientists and politicians alike

A map of west Antarctica. Image: Wikimedia commons

are looking nervously over their shoulders, watching, waiting and planning for high water. It’s not if – but when and by how much. ❑ Associate Professor Mike Lucas is employed within the University of Cape Town’s Zoology Department. He is also an Honorary Research

Associate at the National Oceanography Centre (NOC) in Southampton, UK. He conducts much of his research in the North and South Atlantic, as well as in the Southern Ocean and in the Benguela upwelling system. He is a member of the southern African SOLAS Network, which forms part of the International SOLAS Project.

Honours for local researcher N elson Mandela Metropolitan University’s senior Zoology lecturer, Dr Kwezi Mzilikazi, has been selected as an honorary ambassador scientist for the Alexander von Humboldt Foundation. Dr Mzilikazi is recognised as Africa’s first black evolutionary physiologist, thanks to her ground-breaking research on how small mammals cope with challenges posed by their environment. Her selection follows an earlier appointment in 2006/07 when she was a Humboldt Fellow and spent a year conducting postdoctoral research at Marburg University in Germany. As an honorary ambassador, Dr Mzilikazi is expected to raise awareness about the programmes and activities of the prestigious Foundation which promotes academic cooperation among scientists internationally. As a result of her earlier work in Germany, Dr Mzilikazi set up a whole animal energetics laboratory for teaching and research in the Zoology Department. This laboratory boasts a fully computerised system which can measure oxygen consumption, carbon dioxide production, water loss and activity levels in at least five individual animals (mammals, birds and reptiles) at the same time. ‘By understanding the physiological responses of animals, we’ll be better able to predict how they will respond in the face of global climate change. We’ll also be able to predict which animals are most likely to be at risk and therefore identify which species require conservation priority,’ she says. In addition, she also set up a second research laboratory in

which mitochondria (sources of energy) from different tissues can be isolated and their metabolic rates measured under different conditions. This hard-working researcher has put together a surgery facility that will enable her to implant dataloggers and transmitters into animals for the purposes of body temperature monitoring, both in the laboratory and under field conditions. ❑

Quest 7(3) 2011 31

The team.

Figure 1. The location of the tunnel.

Image: Lesa van Rooyen

Image: Google Earth

Air quality in the Daspoort Tunnel: a multidisciplinary, multi-institution collaboration Road tunnels with pedestrian walkways may pose a risk to the health of drivers, pedestrians and cyclists. In this study, a unique team of scientists, university students and school geographers worked together to assess air quality and vehicle and pedestrian traffic in the Daspoort Tunnel, Pretoria. By Caradee Wright, Rebecca Garland and Patricia Forbes.

hen the Air Quality Officer from the City of Tshwane Department of Environmental Management, Juan Mostert, mentioned that he was concerned about the air quality in the Daspoort Tunnel, particularly because schoolchildren walk through the Tunnel regularly, a unique project team developed an innovative plan. A group of six

learners from St Maryâ&#x20AC;&#x2122;s Diocesan School for Girls and their geography teacher, Jacqui Brown, also took part in the study. The plan was to measure ambient air quality, particularly the concentration of particulate matter (dust) in the tunnel, while counting the number of vehicles and pedestrians/cyclists passing through the tunnel.

What makes the Daspoort Tunnel and its air quality so interesting? The Daspoort Tunnel is 573 metres long and travels from north to south through the Daspoort System in Pretoria (Figure 1). It was designed and built with two lanes for vehicles, one lane for each direction of traffic flow, and two pedestrian walkways, one on

The Daspoort Tunnel The Daspoort Tunnel was built during the late 1960s and completed in the early 1970s (Figure 1). The tunnel was designed to have two traffic lanes and two footpaths, with a ventilation shaft midway. It was estimated during the time of construction that approximately 6 000 vehicles would use the tunnel per day. A report written in 1970 in the Journal of the South African Institute of Mining and Metallurgy described a visit by 43 members of the Institute to see progress made during tunnel construction. An Engineer described the challenges they faced tunnelling into two different types of rock on either side of the mountain: hard quartzite on the northern side and soft shale on the southern side. In 1974, the CSIR conducted measurements of carbon monoxide in the Daspoort Tunnel using DrĂ¤ger tubes at a height of 1 m above ground level to represent the average breathing zone of motorists in the tunnel. A range of carbon monoxide levels was found, with the maximum concentration not corresponding to the peak traffic density, which was ascribed to increased air turbulence under higher traffic flow conditions. They concluded that carbon monoxide concentrations both inside and outside the tunnel did not present a hazard to either pedestrians or motorists at that time. The authors also commented that although the results were sometimes over the guidelines, they would not have a negative impact on people because the time they spent in the tunnel was short. They also commented that the

32 Quest 7(3) 2011

winter results may be slightly different as a result of atmospheric inversion layers. A follow-up study was done during winter months and the results again revealed that the carbon monoxide concentrations inside and outside the tunnel were not harmful to drivers and cyclists, although the maximum carbon monoxide concentration was higher than in the previous study. However, they noted that the situation was acceptable for pedestrians only if they spent less than 30 minutes in the tunnel. Although the tunnel complies by length for natural ventilation only, the authors noted that the increased traffic volume may pose a risk and therefore recommended a forced ventilation system. A third study was conducted where measurements were taken at three points in the tunnel (the entrance, the exit and the midpoint by the extraction fan), and measurements were taken with the fan working and not working. It was found that lead (from vehicles using leaded petrol) was reduced in the centre of the tunnel when the fans were operational. Besides concerns about air quality in the Daspoort Tunnel, there are reports of several vehicle and pedestrian accidents in the tunnel. Accident statistics quoted in a 1998 Pretoria Metro report stated that between 1992 and 1997, there were 280 vehicle-to-vehicle accidents, 61 vehicleto-object accidents and 25 pedestrian accidents, totalling 366 accidents in the tunnel or at the entrance to the tunnel in six years.

The team at work in the tunnel. Note the face masks.

each side of the road. The tunnel is a preferred thoroughfare for vehicles and people wanting to move between the north of Pretoria and the central business district. Schoolchildren, commuters and cyclists make regular use of the pedestrian walkways. Inside the tunnel there is soot on the walkway railings and inner walls. Vehicle headlights show soot suspended in the air over the road during peak hour traffic. The large fan at the top of the ventilation shaft is working, but the two ventilation fans in the tunnel have been damaged and do not work at the moment. These fans are supposed to direct air from both ends of the tunnel to its centre and the large extraction fan at the top should pull the dirty air up and out through the tunnel ventilation shaft on the surface. There is often a plume of smoke billowing from the tunnel ventilation shaft house exhaust on the surface during peak traffic periods, right next to a residential area.

Q Environmental Science

levels of exposure. The filters were weighed before and after sampling so that the quantity of PM in the air could be determined. On 28 July we used a portable instrument to measure the mass concentration of particulate matter that a pedestrian walking through the tunnel might be exposed to. This was measured by carrying the portable instrument on multiple ‘walkthroughs’ of the tunnel. In addition, a researcher returned on 11 August 2011 with the same portable instrument to perform more walk-throughs. Using this information, it was possible to begin to see the variability in the particle mass concentration at different points in the tunnel. What have we found so far? Air quality

From the time periods that we studied, it is clear that there are high levels of particulate pollution in the tunnel. We walked through the tunnel twice (28 July and 11 August) with the portable instrument that measures particulate matter mass concentrations. On both occasions, the average concentration for the particulate matter during the walk-through was >240 µg/m3 during morning rush hour traffic (07:00 – 8:30 am). We only used the portable instrument on one date during the offpeak measurements (10:00 –10:30 am on 28 July). On that day, the average particulate matter concentration for the walk-throughs was 162 µg/m3. While this is lower than the levels measured in rush hour traffic, they were also measured on a different day, so it is difficult to compare. The four graphs above (Figure 2 A, B, C, and D) show some results from the walk-throughs with the portable instrument. The first thing to notice is that all of the profiles and concentrations are highly variable.

Figure 2 A, B, C and D: These graphs show the fluctuations in particulate matter that occured during the periods measured.

This may be because the traffic going through the tunnel is also highly variable with regard to the volume of traffic, the types of vehicles, their speed, and the emissions of the vehicles. This dependence on the traffic that is in the tunnel can be seen clearly in Figure A, when a large truck (lots of emissions) passed at 7:46 and led to a spike in PM mass concentration to over 3 mg/m3. This value is almost 28 times greater than the 24-hour National Ambient Air Quality Standard for PM10 set by the Department of Environmental Affairs. The filter results also show high levels of PM inside the tunnel. PM levels were lower at the end of the tunnel compared with inside, which was also found from the walk-throughs. ▲ ▲

What did we do in the tunnel? The team visited the tunnel twice during winter 2011, on 21 June and 28 July during school term and on weekdays. For both visits, we counted vehicles, pedestrians and cyclists, and measured air quality in the tunnel during peak and off-peak hours. On 21 June we also measured the ambient air quality at the tunnel ventilation shaft house and walked through the tunnel to estimate how long a pedestrian would take to walk through the tunnel. Particulate matter (PM) was collected by drawing air through a filter using a portable sampling pump. Samples were taken at 1 m (people sitting in cars) and 1.5 m (people walking through the tunnel) above ground level to represent different

Image: Lesa van Rooyen

Quest 7(3) 2011 33

Health effects of PM (Air quality and health, Fact sheet N°313, Updated September 2011, World Health Organization) ‘The effects of PM on health occur at levels of exposure currently being experienced by most urban and rural populations in both developed and developing countries. Chronic exposure to particles contributes to the risk of developing cardiovascular and respiratory diseases, as well as of lung cancer. In developing countries, exposure to pollutants from indoor combustion of solid fuels on open fires or traditional stoves increases the risk of acute lower respiratory infections and associated mortality among young children; indoor air pollution from solid fuel use is also a major risk factor for chronic obstructive pulmonary disease and lung cancer among adults. The mortality in cities with high levels of pollution exceeds that observed in relatively cleaner cities by 15–20%. Even in the EU, average life expectancy is 8.6 months lower due to exposure to PM2.5 produced by human activities.’

Figure 3. The number of vehicles that passed through the tunnel every hour between 07:00 and 11:00.

Useful terms Particulate matter (PM): This is a general term used to describe a complex group of air pollutants that vary in size and composition. PM is a mixture of fine airborne solid particles and liquid droplets (aerosols).

Vehicle traffic, pedestrian and cyclist counts

More than 1 500 vehicles passed through the tunnel every hour between 07:00 and 11:00 (Figures 3 and 4). Total vehicle traffic counts were highest during peak hours and lowest during off-peak hours. Cars accounted for the largest proportion of vehicles passing through the tunnel in either direction. Traffic counts from 1998 showed that a total of 2 565 cars passed through the tunnel during the morning and 3 140 cars during the afternoon (no exact times were given, only AM/PM). Our results suggest that nowadays there is more vehicle traffic travelling through the tunnel than 10 years ago. There were 129 walkers and cyclists passing through the tunnel during the 07:00 – 08:00 peak hour on 28 July. Of these, 53 were children either walking or cycling to school. Children are particularly susceptible to the effects of air pollution because of their greater

34 Quest 7(3) 2011

Figure 4. The number of pedestrians and cyclists that passed through the tunnel every hour between 07:00 and 11:00.

breath-to-weight ratio. On average, about 27 people walked or cycled through the tunnel every hour between 08:00 and 11:00. While this number may seem small, it is likely that the same people are using the pedestrian walkways in the tunnel every day, and so potentially increasing their risk of exposure to air pollution. This pilot study has shown some interesting results which will be given to the City of Tshwane. A full study is needed to verify our findings. However, early results suggest that air quality in the Daspoort Tunnel may be above acceptable levels for a pedestrian walking regularly through the tunnel. The most exciting part of this project was working with a multidisciplinary, multi-institutional team. The university

students gained fieldwork and laboratory experience, and the learners were an active part of the research team, collecting and collating data which they will also use for a school project. ❑ Caradee Wright and Rebecca Garland are Senior Researchers in the CSIR Climate Studies, Modelling and Environmental Health Research Group. Patricia Forbes is a Senior Lecturer and Wynand Louw and Lebogang Phiri are students in the Chemistry Department at the University of Pretoria, whilst Ernst Bekker is a student in the Geography Department. Patricia Albers is a student at the School of Health Systems and Public Health at the University of Pretoria. Jacqui Brown is a Geography teacher at St Mary’s Diocesan School for Girls in Pretoria.

Research that can change the world

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

www.csir.co.za

Coral reefs: A world beyond our imagination Coral reefs are under threat from fishing and ocean warming and their loss will have major effects on ocean biodiversity. By Hanlie Malherbe.

A branching coral extending out into the waters of Sodwana Bay. Image: Adventure Mania, Sodwana Bay

Q Conservation

Above: A clown fish marking its territory in Sodwana Bay. Image: Adventure Mania, Sodwana Bay Top right: A school of reef fish in Sodwana Bay. Image: Adventure Mania, Sodwana Bay

Middel right: A moray eel.

Image: Adventure Mania, Sodwana Bay

Below right: A sea turtle, Sodwana Bay. Image: Adventure Mania, Sodwana Bay

▲ ▲

oral reefs are unique natural features that are found across the world. The Caribbean sea is home to about 9% of the world’s coral reefs, which cover about 52 000 m2. Most of these reefs are located close to the Caribbean Islands and the central American coast, with vertical walls dropping to great depths, prominent pinnacles rising from the ocean floor and limestone structures forming deep canyons that are paradise for divers. Closer to home, coral reefs are found in Mozambique and Sodwana Bay. Two-mile reef, Bazaruto archipelago in Mozambique, is known for its brilliant colours – an inspiration to every diver. Sodwana Bay is on the east coast of South Africa, in the Maputaland Marine Researve. It is the only scuba diving area along the Isimangaliso Wetlands Park. The reef complex is around 50 km and contains around 95 species of hard and soft corals, sponges, other invertebrates and around 1 200 fish species. The reefs contain vast 700 m-deep valleys and canyons. It was in one of these that the coelacanth was rediscovered on 27 November 2000. The marine life of the coral reefs of Sodwana Bay is spectacular. Amazing creatures, great and small, roam these waters. Two large filter-feeding manta rays approach closely, an eagle ray rummages for food, sea turtles rest under gullies in the reef, moray eels

Quest 7(3) 2011 37

A colourful sea slug.

Image: Adventure Mania, Sodwana Bay

A jelly fish in Sodwana Bay.

Image: Adventure Mania, Sodwana Bay

A silver fish in Sodwana Bay.

Image: Adventure Mania, Sodwana Bay

slowly swim by, and reef sharks disappear into the vast distance – spectacular sights. Brightly coloured fish marking their territory among unique corals capture the attention. Threats from human activity However, ever-increasing pressure is being experienced by coral reefs worldwide. Reef bombing for fishing and to create passages that can be navigated has major effects, not only for the destroyed region, but also on nearby ecosystems. The coral itself is negatively affected and fish species die off. Coral reefs have been harvested for limestone for building for centuries. Coral has also been collected for jewellery, ornaments and medicines. Climate change Along with these threats we know that the globe faces major coral reef destruction as a result of climate change. Rising water temperatures and ocean acidification are particularly worrying. Ocean water contains calcium carbonate, which allows it to neutralise changes in water acidity. Everincreasing carbon dioxide levels may exceed the ocean’s buffering capacity, which leads to a more acidic environment. Acidified water dissolves limestone, the basic structure of coral reefs. The current rate of carbon emission is likely to lead to further destruction of coral reefs, as they dissolve in the acidic ocean waters. Secretion of limestone may not occur fast enough to restore the dissolved limestone. Acidification, along with increasing water temperatures, will result in less diverse and more fragile coral reef systems. The potential loss of these highly integrated ecosystems, along with the creatures in their complex food webs, is a very real threat to marine biodiversity, which will in turn have negative impacts on us all. ❑ Hanlie Malherbe works in the Department of Conservation Ecology and Entomology, Stellenbosch University. She has a particular interest in marine ecology and volunteered on a marine conservation expedition, managed by Global Vision International in a remote village called Mahahual, Quintana Roo, Mexico, which opened her eyes to the threats to coral reefs. The expedition, in partnership with the Quintana Roo University and the non-governmental organisation Amigos de Sian Ka’an, is working to conserve fringing reefs of the Mesoamerican Barrier Reef. The main threats are development, intense tourism and environmental implications, such as increasing water temperatures, hurricanes and bleaching events.

38 Quest 7(3) 2011

Smoking, tomato juice and infants’ lungs Smoking during pregancy can cause permanent damage to an infant’s lungs, even before birth. While not suggesting that smoking is a good idea, Gert Maritz and his colleagues may have come up with a way to reduce that damage.

Nicotine Nicotine is the most active part of tobacco smoke and is rapidly absorbed across the respiratory tract of smokers. The lung seems to act as a reservoir for nicotine, which slows down the rate at which it enters the blood. It appears that the nicotine inhaled in each puff may take 30 – 60 seconds or longer to be absorbed. Once nicotine is in the pregnant woman’s circulation, it easily crosses the placenta and enters the fetal blood system. It can also enter the amniotic fluid surrounding the fetus and can be asbsorbed across the fetus’s skin. Nicotine also enters the breast milk and can reach concentrations that are two to three times those in the mother. In adults nicotine is cleared from the body through the liver – it is broken down by enzymes. But these liver enzymes are not well developed in the fetus and researchers have found higher concentrations of nicotine in the tissue of the fetus than in the maternal blood. This means that the cells of the developing lung and other organs are exposed to higher concentrations for longer periods of time, which will increase the negative

▲ ▲

cientists have known for many years that it is harmful to the unborn child for the mother to smoke during pregnancy. Unfortunately, many women still do so. The various components of tobacco smoke, nicotine in particular, can affect many organs in the fetus and the newborn child, potentially with life-long consequences. Recent studies show that nicotine can permanently affect the developing lungs in a way that means that the organ’s final structure and function are negatively affected. These changes can increase the risk of illnesses such as asthma and also speed up any reduction in lung function over the affected person’s life time. Research has shown that exposing the fetus and breastfeeding infant to tobacco smoke and nicotine changes the genetic programme that controls the development and ageing of the lungs in the child. There are changes in the conducting airways and the alveoli that reduce lung function, making the lungs more susceptible to obstructive lung disease and accelerating the ageing process in the lungs.

Muyunda Mutemwa, a PhD student doing her thesis on maternal nicotine exposure and the long-term impact on respiratory health in the offspring. Image: Gert Maritz

A: Normal lung with normal alveoli where gas exchange occur. B: Lung of an animal that was exposed to nicotine via the placenta and mother’s milk showing microscopic emphysema. The surface area for gas exchange of this lung is smaller than that of the control lung with normal alveoli. Image: Gert Maritz

The equipment that is used for cutting tissue samples, mounting them in wax and staining. Image: Gert Maritz

Quest 7(3) 2011 39

Biology & Medicine Q

A lung showing microscopic emphysema, with large open spaces with no alveoli. There is a smaller surface area available for gas exchange. This condition gets progressively worse, even if the individual stops smoking. The rats in this instance only received nicotine via the placenta and mother’s milk and, even though nicotine withdrawal took place six weeks earlier, they still developed emphysematous lesions. The structural changes that were present were microscopic emphysema – which is an increase in the airspaces in the lung tissue – an increase in lung volume from postnatal day 63 and thickening of the walls of the alveoli at postnatal day 84.

A normal lung showing senescent cells (brown/black cells). Image: Gert Maritz

The lung of an animal that was exposed to nicotine via the placenta and mother’s milk, showing more senescent cells than the control lung. This shows that the lung is ageing faster and is more susceptible to disease. Image: Gert Maritz

40 Quest 7(3) 2011

A normal lung, showing normal alveolar spaces.

effects on the developing cells. Nicotine is what is called genotoxic – it can damage the cell’s genetic material and it also causes the release of oxidants – substances that are also damaging to the cell. All these factors make it likely that long-term nicotine exposure causes changes in the genetic programme that controls lung development, the maintenance of lung structure and the ageing of lung tissue. This may make the lungs more susceptible to disease. Preventing the damage Professor Gert Maritz and colleagues working at the University of the Western Cape, Belville, decided to see if there was some way to prevent this damage to the lungs in the fetus and the newborn. They wanted to look at the long-term effect of maternal nicotine exposure on the stucture of the lungs and also to see if there was a way of supplementing the smoking mother’s diet that would lessen the damage. The team could obviously not use human subjects for this research and so used laboratory Wistar rats, who were mated and then randomly divided into three groups. One group received nicotine in doses of 1 mg/kg body weight/day. The second group received tomato juice and the third group received nicotine and tomato juice. There was a control group of rats who receive saline.

Image: Gert Maritz

After the rats were born the team looked at changes in lung structure at 21, 42, 63 and 84 days after birth. It was clear that neither nicotine nor tomato juice had any effect on the growth of the offspring. The team also found that exposing the mother rats to nicotine during gestation and lactation had no effect on the lung structure of the offspring up to weaning. There was a deterioration in lung structure about three weeks after weaning – which is the time that the young rats would be expected to be experiencing nicotine withdrawal as the nicotine was cleared from their bodies. None of these structural changes were present in the offspring of the rats who had been given tomato juice. In conclusion Scientists are never certain that results obtained with laboratory animals will be the same in humans, but in this case the mechanisms underlying the process by which nicotine damages lung tissue in the fetus and infant are similar. Futher research will be needed before making the jump from the laboratory to daily life. However, it may be that pregnant women who smoke would be well advised to drink tomato juice daily to help to prevent any damage to the lungs of their unborn child. However, this in no way suggests that it is acceptable for pregnant women to smoke. This research simply suggests

Q FactFile The respiratory system

Lung diseases

The human respiratory system consists of the upper respiratory structures such as the nose, the trachea and the sinuses and the lower respiratory structures within the lungs. In humans the left lung has two lobes and the right lung has three lobes. Both lungs contain about 2 400 km of airways and 300 – 500 million alveoli, with a total surface area of about 70 m2. The respiratory system is functionally split between the conducting zone and the respiratory zone. The conducting zone contains the trachea, the bronchi, the bronchioles and terminal bronchioles. The respiratory zone contains the respiratory bronchioles, the alveolar ducts and the alveoli. The conducting zone has no gas exchange with the blood. This part of the respiratory system is reinforced with cartilage to hold the airways open. The conducting zone warms the inhaled air to 37 °C and also humidifies it. The inhaled air is cleaned of particles by the cilia that are found on the walls of the airways. The lungs are surrounded by the rib cage. Gas exchange with the blood takes place in the respiratory zone.

Asthma Asthma is a common, chronic inflammatory disease of the lungs. People with asthma suffer from coughing, wheezing and shortness of breath if they are not correctly treated. The disease is often associated with allergy. There are three components to asthma – inflammation of the small airways of the lungs, which causes the production of mucus and then bronchospasm. Bronchospasm is a sudden tightening of the muscles in the walls of the bronchioles, which causes difficulty breathing. Asthma can usually be completely controlled with the correct medication – a combination of an agent to prevent the inflammation and an agent to open up the airways. The disease is made worse by smoking or exposure to second-hand tobacco smoke.

Lung cancer Lung cancer used to be a rare disease. However, with increasing rates of smoking over the last 20 – 30 years, the disease has become more common. It is seldom seen in nonsmokers – and when lung cancer

occurs in non-smokers, it is usually a different type of cancer from that seen in smokers. Lung cancer is characterised by uncontrolled cell growth in lung tissues. The cancerous cells can spread (metastasise) to other parts of the body, particularly the brain and liver. Symptoms are shortness of breath, coughing (including coughing up blood) and weight loss. Lung cancer is difficult to treat and is often fatal.

Emphysema Emphysema – correctly called chronic obstructive pulmonary disease (COPD) – is a long-term, progressive disease of the lungs that causes shortness of breath. In people with the disease the tissues that support the shape and function of the lungs are destroyed, particularly the tissue around the alveoli. In emphysema, the alveoli cannot hold their shape when the person exhales. Emphysema is another disease that is almost exclusively caused by smoking or chronic exposure to air pollution. The disease is difficult to treat and people who suffer from it often find any kind of exertion difficult.

Left: A cross-section of a human lung. The white area in the upper lobe is cancer; the black areas are discolouration caused by smoking. Image: Wikimedia commons A diagram of the complete human respiratory system.

a way that women who find it impossible to stop smoking during pregnancy and breastfeeding could potentially prevent lung damage in their child. ❑ Professor Gert Maritz has been at UWC since 1975 and has a PhD in medical sciences and an MBA. He is a senior professor at the Department of Medical Biosciences, investigating the effect of factors such as

Image: Wikimedia commons

Right: This chest X-ray shows the characteristic barrel chest and flat diaphragm of a person with emphysema. Image: Wikimedia commons

placental insufficiency and preterm birth on lung development in the offspring and its long-term consequences on respiratory health. His main field of study is the effect of maternal nicotine exposure during pregnancy and lactation on lung development in the offspring. He is collaborating with researchers at the Monash University, Australia, the Medical Research Council and with Professor J Smith in the Department of Paediatrics at the University of Stellenbosch.

Muyunda Mutemwa is a PhD student in the Department of Medical Biosciences at UWC. Her MSc research was on maternal nicotine exposure during gestation and lactation During her PhD she will investigate the effect of maternal nicotine exposure on lung development in the offspring, its transgenerational effect and how to prevent it. She will complete her PhD by the end of 2012 and plans to obtain a postdoctoral position to expand her skills base as a researcher.

Quest 7(3) 2011 41

Books Q

The way we are Nature’s Gifts: Why we are the way we are. By Wilmot James. (Johannesburg. Wits University Press. 2010) Wilmot James is a member of the South African Parliament, an Honorary Professor in the Division of Human Genetics at the University of Cape Town and the Department of Sociology at the University of Pretoria and a Visiting Research Professor at the Open University in the United Kingdom. With so much to occupy him it is astonishing that he found the time to write this excellent book. James started life as a sociologist, but moved over to genetics through his association with the Africa Genome Education Institute, of which he was the founder and director. Nature’s Gifts is based on a series of lectures given at various institutions around the world and provides a readable and accessible look at genetics – and human genetics in particular. Starting with a look at the human genome, James takes the reader through the way in which genetics reduces humankind to the sum of its genes – and through this – shows the absurdity of concepts of race and skin colour as ways of ‘classifying’ and characterising people. Along the way he takes an usual approach to the way in which local archaeological sites such as Pinnacle Point have helped us to understand our origins and at science education generally. He also introduces two important South African scientists, Edward Roux and Eugene Marais – both pioneers in their fields. This book is fascinating. Not only does it contain a wealth of information, but it is an exponent of the importance of scientific world view – to my mind the only way that people can become enlightened, empowered and encouraged to think beyond the stereotypes that have allowed bigotry and prejudice through the ages.

On the brink The Protein Crunch: Civilisation on the brink. By Jason Drew and David Lorimer. (Cape Town. Print Matters Planet. 2011) We live in a turbulent world. As I write, European and American economic systems are in meltdown, threatening the stability of every country in the world. This economic turmoil comes at a time of increasing (and almost certainly linked) enviromental turmoil as we start to understand the way in which human activities have irrevocably changed the planet. Jason Drew’s introduction says that ‘the credit crunch has shaken our global economy, but it will recover. “The Protein Crunch” is far more serious and, if we open our eyes, it is unfolding right in front of us.’ I take issue with his statement about the global economy recovering, but that is another topic. However, his statement about the seriousness of what he calls ‘the protein crunch’ is hard to question. The theme of the book is food security – and he points out that our food comes from three sources – water, land and the seas and that all three of these natural resources are under increasing pressure from an increasing human population. Drew likens the

42 Quest 7(3) 2011

credit crunch to the way in which our environmental and food production systems are being stretched to ‘breaking point’ and ‘with food demand outstripping supply, food prices will inevitably increase’. With this increasing lack of food security comes civil unrest and political turmoil – all of which we are seeing around us during 2011. There are already reports of millions of environmental refugees, migrating to escape floods, drought and the failure of food supplies. Between them, Jason Drew and David Lorimer have explained human impact on Earth’s environmental systems and the resources on which we all depend. It makes for chilling reading, but the authors finish by challenging readers to be not simply passive recipients of disaster, but to act to find ways out of the impasse.

Upskilling scientists A Skills Standard for Budding Scientists: The essential guide to mastering skills in the FETphase science subjects. (Cape Town. Quickfox Publishing. 2008.) Since this book was written (and I apologise for taking so long to review it) the curriculum has changed yet again. However, the skills that this book outlines so well remain necessary. In fact, this book should become an essential requirement for all school science departments, for teachers and students alike, since these skills are not covered adequately in the new CAPS curriculum document. The book starts in what some may find a strange way for someone dealing with science skills – effective writing. But this may be one of the most important chapters in the book as communication is what ‘doing’ science is all about. There is little point in making world-shattering discoveries if you cannot effectively communicate your findings, both in the academic journals and in popular publications. The chapter that follows is on note taking – showing students how to organise information – another essential skill in science. The author carries on to working with data, starting with tables – their layout for different purposes and a very comprehensive look at graphs of various types and how they are used in the analysis and interpretation of data, as well as the use of scale. A very unusual section in any text book is ‘Thinking’ – an introduction to critical thinking, evaluating information, evaluating science, interpreting graphs, evaluating visual images and evaluating web information. In our crowded curriculum I would imagine there are few teachers who find the time to cover this essential skill (one that should be an examinable subject in the school curriculum!). Finally, the book gets down to ‘Doing’ – the scientific method and all that this entails. This is a superb and inexpensive book – make sure it is on the shelves of every school library.

The East African bush Field Guide to Common Trees and Shrubs of East Africa. By Najma Dharani. (Cape Town. Struik Nature. 2011) This is the fully revised and updated version of the book that was first published in 2002. East Africa, an area that includes Kenya, Uganda and Tanzania, is one of the richest areas on the African continent in terms of flora and fauna – largely as a result of the area’s diverse habitat and climate. The introduction contains a full colour map of the vegetation zones of East Africa, which will be useful not only to amateur naturalists using the book, but to teachers in the area when they cover the biodiversity of the region.

Q Books The book is divided into four parts – trees, shrubs, palms and mangroves. The subdivisions are arbitrary, but for the well-informed layperson (who is the target of the book) these are fairly distinct and easilyseen groupings. The species accounts within each part are arranged in alphabetical order (scientific names from A to Z) and each specifies the English and the more prominent African (local) common names, where these are known, the family to which the plant belongs and whether it is indigenous to the region or exotic. There is a short section on plants and traditional medicines and then an excellent section on the classification of plants – again useful in the classroom. The book is illustrated throughout with excellent colour photographs of the whole plant, its leaves and in many cases the bark and the seeds.

A singular man Challenging beliefs: memoirs of a career. By Tim Noakes, with Michael Vlismas. Cape Town. Zebra Press. 2011.) I first met Tim Noakes 27 years ago, when he was still in the Department of Physiology at the medical school at the University of Cape Town. Then he had his own office and one large room in the basement of the Physiology and Biochemistry Building. The large room was stuffed with all sorts of equipment – running treadmills, tanks in which people were totally immersed to work out their body fat percentage and nasty looking devices to hook onto people’s faces to work out VO2 max while running or cycling to your limits! The department was full of ernest young athletes – all of whom had an abiding passion for the science of sport – a passion encouraged and mentored by Tim’s own passion for the science. This book shows the full scope of the man who pours his enthusiasm, passion and integrity into every page. He starts with an eloquent account of Comrades marathon – an awe-inspiring event in anyone’s terms. And it is this that sets the scene for a career that made sports science into a recognised discipline around the world. The book covers Tim’s career in a series of chapters outlining major research findings in sports science – which also show how other excellent minds have become caught up in this fascinating branch of science and medicine. I am a keen recreational runner myself and have always devoured anything that Tim has written over the years. But I would venture to suggest that this book will fascinate anyone – even the couch potatoes among you!

Alien invaders Alien and Invasive Animals: a South African perspective. By Mike Picker and Charles Griffiths. (Cape Town. Struik Nature. 2011.) Alien plants and animals are very much a part of our lives,

everywhere in the world. But in a country such as South Africa, with its massive range of biodiversity and World Heritage sites such as the Cape Floral Kingdom, they are arguably more dangerous to the local species that they inevitably damage in some way. This book covers animals and it amazed me to find just how many alien and invasive animals we have in this country, right down to stick insects and spiders, mites and ticks. The book starts with a detailed account of what alien and invasive animals are and how they got here – followed by a historical perspective. There is an account of specific South African introductions across the terrestrial, fresh and sea water environments, with a discussion of the costs and consequences of these introductions. The authors also remind us that South Africa is an exporter of problem animals as well, such as the Miomantis preying mantid, a South Africa native first introduced into New Zealand in 1978. The section on prevention and control looks at the different management strategies that have been tried with varying degrees of success. Each of the species accounts is written by an expert in the field and the book is organised into sections by Order, e.g. Mammals, Birds and so on. It is illustrated with full colour photographs and there are distribution maps, showing the South African range and a world map, showing the native range of the species as well as other countries to which it has been introduced.

Gamebirds Gamebirds of southern Africa. By Rob Little and Tim Crowe, with illustrations by Simon Barlow. (Cape Town. Struik Nature. 2011.) This is the revised and updated second edition of the book, which was first published in 2000. Unusually these days, the book is illustrated by wonderful line drawings and paintings by Simon Barlow and the book starts with the artist’s notes and the story of each of the colour plates, which will be particularly interesting to anyone else who is involved in illustrating books dealing with plants and animals. The introduction to the biology of the birds starts with the distribution and classification of the various gamebirds found in the southern African region, as well as their evolution. The authors, world experts in their field, discuss how the study of gamebirds has contributed to virtually every biological discipline, from anatomy, behaviour and genetics through to parasitology and zoogeography. For example, research on the helmeted guineafowl has shown that its naked head acts like the car’s radiator to cool hot blood coming from the heart before it reaches the brain. It was the study of gamebird evolution that showed the significance of the breakup of the ancient continent of Gondwana. Gamebirds are also valuable species in the study of conservation, particularly because gamebirds are hunted. The species accounts are detailed, covering the scientific nomenclature, a description of the species, its distribution and habitat, its habits, food and feeding, breeding, classification and its status and conservation. The wonderful line drawings and colour plates make this a visually pleasing book. My husband, however, pointed out one major omission – there are no recipes!

Quest 7(3) 2011 43

Diary of events Q Shows and exhibitions Iziko Planetarium, Cape Town For children • For the October school holidays!

Michael Lion and the Star Pictures Once upon a time a little toy lion, called Michael, and his best friend, Bertie, went on a rather magical quest. Along their way the two friends met a few interesting characters and saw some amazing sights. But did they find what they were looking for? Join us and find out for yourself! 1 October – 9 October Monday to Friday – 11:00, 12:00 & 15:00 Saturday – 12:00 & 15:30 Sunday – 12:00 & 15:30 Especially for children aged 5 – 12 For the December-January school holidays!

Are you a creative thinker? Then join our academic profile on offer … • The vision of the NWU’s Potchefstroom Campus (NWU Pukke) is to become a researchdirected campus where excellence in both teaching-learning and research are mutually reinforcing.

Magic Milo and the Astronaut One day Magic Milo and his friend, Sammy Starfish, meet Major Tom who makes their dream come true by taking them on a magical trip into space. Join us and discover what it's like to be an astronaut! 10 December – 12 January Monday to Friday – 11:00, 12:00 & 15:00 Saturday – 12:00 & 15:30 Sunday – 12:00 & 15:30 (excluding 25 December)  Especially for children aged 5 – 12

• The North-West University (NWU) is an innovative institution, offering research in a structured and multidisciplinary environment organised into 22 research entities. This focused approach adopted by the NWU has resulted in increased research performance over a number of years.

Celestial Clouds: A celebration of astro-photography Images of our Milky Way and neighbouring galaxies reveal astonishing beauty. Aside from the multitude of stars, glowing clouds of gas are seen entangled with labyrinths of dark dust lanes. The clouds are the reservoir of material, from which new stars are formed, and to which old stars expel enriched material. They are fundamental to the existence of stars – and to our own well-being in the universe. 23 July – 4 December Monday to Friday – 14:00 (excluding 1 and 9 Aug, 5 Sep. 7, 28-30 Nov, 1 and 2 Dec) Tuesday evening – 20:00 (and sky talk) (excluding 29 Nov) Saturday – 14:30 Sunday – 14:30 9 August – 14:30 For teenagers and adults.

• An atmosphere of creative thinking is conducive to a strategy of expanding the NWU Pukke’s current fields of expertise or areas that are identified of being of critical importance to the country. • High profile intellectuals differentiate, identify and distinct the activities of the NWU Pukke in delivering Masters, Doctorate and post-doctoral fellows that is complementary to other research nationally, internationally and contributing towards the development of the next generation of academics.

NORTH-WEST UNIVERSITY YUNIBESITI YA BOKONE-BOPHIRIMA NOORDWES-UNIVERSITEIT

Innovation through diversity ™

POTCHEFSTROOM CAMPUS

44 Quest 7(3) 2011

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  16 June – 13:00 Suitable for teenagers and adults

A Basic Guide to Stargazing

BLACK KHAKI 082212

To view our fields of expertise, visit the website and/or mobisite Office of the Vice-Rector: Research and Planning 018 299 2606 enquiries@nwu.ac.za nwuresearch.mobi nwu.ac.za

The Sky Tonight

This presentation will give you a basic understanding of the night sky and how it changes through the year. We introduce some easily recognisable constellations, explain the nature of stars and the galaxy in which we live and give basic information in using binoculars and small telescopes. 3 October – 7 October Monday to Friday – 13:00 Suitable for teenagers and adults

2012: the end or the beginning? The famous Mayan Long Count would seem to indicate that, after three failed worlds, we are living in the fourth – and that will come to an end (perhaps) on December 22, 2012. Whether the Long Count defines the end of the world or not, the astronomical calculations that led to it are fascinating and indicate an astounding and accurate observation of those heavenly bodies that form part of the universe around us. Starts 10 December Monday to Friday – 14:00 (excluding the first Monday of the month, excluding school holidays) Tuesday evening – 20:00 (& sky talk) Saturday – 14:30 Sunday – 14:30 (excluding 25 December) Suitable for teenagers and adults

Table Mountain Table Mountain is more than a famous landmark – it is the only geographical feature on Earth to be represented as a constellation in the sky! Our planetarium presentation explores the remarkable geology and environment of Table Mountain – and the southern skies centred on its celestial counterpart. 12 December – 10 January Monday to Friday – 13:00 Suitable for teenagers & adults Planetarium entrance fees: Adults 19 years and older: R25,00 • Children, students and SA Pensioners: R10,00 • Booked school groups: R6,00 per learner. The Planetarium reserves the right to change or cancel advertised shows without prior notice. Closed for maintenance. The Iziko Planetarium is closed for maintenance on the first Monday of the month, excluding school holidays.

Birding Big Day 26 November 2011 Calling all backyard birders!  The annual BirdLife South Africa Birding Big Day is a fun, yet competitive day for South Africa’s birdwatchers – both beginners and competitive twitchers – while at the same time raising much-needed funds for the organisation’s important bird conservation work.   The entry form and bird checklists (English and Afrikaans) are available on the BirdLife South Africa website http://www. birdlife.org.za/events/birding-big-day. Diarise 26 November 2011 and help BirdLife South Africa Give Conservation Wings by participating in Birding Big Day!  For further information, please contact Nikki McCartney: 014 755-4390, 083 636 1060, events@birdlife.org.za

Talks, outings and courses Kirstenbosch Botanic Gardens Room to Grow Wednesday Talks Every second Wednesday (started 19 January 2011). 10:30-11:30. Free entry, but garden endtry fee applies. Booking not necessary. Venue: Sanlam Hall (Gate 2). Free talks by horticultural experts on gardening and horticultural topics. Contact: Cathy Abbot Tel: 021 464-6440, Email: cathya@wol.co.za

Diarise Forest Day – 7 December 2011 Forest Day – hosted annually on the sidelines of the UNFCCC Conference of Parties – aims to ensure that forests are high on the agenda of global and national climate strategies, and that those strategies are informed by the most up-to-date knowledge and experience. The event, now in its fifth year, has become one of the most influential events on forests worldwide. This year's Forest Day will have a particular African focus, looking at the humid forests of the Congo Basin and elsewhere, and the continent's wide expanses of dry forest areas. The need for greater awareness of the latest research on Africa's forests is underscored by predictions that the continent will be hit hard by climate change. World AIDS Day – 1 December 2011 This year marks the 23rd anniversary of World AIDS Day. First observed in 1988, World AIDS Day was initiated by health ministers from around the world who called for a spirit of social tolerance and a greater awareness of HIV/AIDS on an international scale. The theme for this year's observance is ‘Getting to Zero’ Zero New HIV Infections. Zero Discrimination and Zero AIDS Related Deaths.

SAIAB News Q

Deploying the ROV – and OTN receiver. Image: SAIAB

The OTN project team. Image: SAIAB

Launch of the Ocean Tracking Network project The Ocean Tracking Network (OTN) project was launched in Pretoria on 2 August 2011. A global network of marine scientists is pooling research efforts to learn more about the mysterious lives of underwater creatures. The OTN will electronically tag thousands of marine animals with the aim of demystifying their migration patterns and providing answers to global problems such as disappearing fish stocks and climate change. The OTN project is a Canadian initiative based at Dalhousie University in Halifax and involves scientists working in all five of the world’s oceans. This $168-million conservation mega-project is funded by the Canada Foundation for Innovation-International Joint Ventures Fund, the Natural Sciences and Engineering Research Council of Canada and the Social Sciences and Humanities Research Council of Canada. In South Africa, the OTN has partnered with the South African Institute for Aquatic Biodiversity (SAIAB). A Memorandum of Agreement between the OTN and the SAIAB will task the SAIAB with facilitating this project in South African waters. It will be responsible for deploying and servicing the OTN receivers and providing administrative and data management services. A range of fish species and possibly other marine animals like turtles will be tagged with acoustic transmitters (coded pingers) and their whereabouts monitored by a network of receivers that will be strategically placed around the South African coastline, starting in Mossel Bay and Algoa Bay. The receivers will effectively create a ‘listening curtain’ that will log tagged animals as they swim by. Later deployments will also take place in False Bay and several other strategic sites along the south east coast into KwaZulu-Natal. It is hoped that the project might expand to other neighbouring coastal countries. The OTN receivers will compliment existing receiver arrays owned by independent researchers, which are currently working on the movement patterns of species such as white

46 Quest 7(3) 2011

sharks, raggedtooth sharks, dusky kob, leervis (garrick) and white steenbras. In addition to the movement data obtained from tagged animals, many of the study sites are also subject to oceanographic monitoring. For example a host of temperature probes and other logging instrumentation are moored in Algoa Bay, a sentinel long-term monitoring site of the South African Environmental Observation Network (SAEON). Consequently, the prospects of gaining a better understanding of the causes for observed movement patterns and potential climate change impacts will also become a reality. The deployment of OTN receivers will greatly

improve the listening capabilities in South Africa and shed light on the long-shore movements and migrations of studied animals. In particular, significant insights will be gained on the ‘greatest shoal on Earth’ – the sardine run. We know that the magnitude of the sardine run is influenced by environmental conditions. Hence, a warming sea may have catastrophic consequences for a host of predators that depend on this annual migration. Many important fishery species rely on this migrating food resource to reach their spawning grounds off KwaZulu-Natal and the livelihoods of many commercial fishers will also be affected if climate change affects these spawning events.

The real boss (Cowley) overseeing the deployment of an acoustic receiver in Algoa Bay. Image: SAIAB

Q SAIAB News

Q ASSAf News

Mysterious oarfish washed ashore The oarfish is an unsual find. By Siphokazi Nonyukela and Penny Haworth.

eldom seen, the rare, elongated oarfish, measuring between 3 – 8 m from nose to tail, is a likely source of myths about sea serpents. Recently, a 4 m long specimen was found washed up at Bokkomsbaai in the Western Cape by a commercial fisherman, Keith Boas. This ribbon-shaped, brilliant silver fish which has irregular blackish streaks and spots on its body and crimson dorsal and pelvic fins, is seldom seen far from the deep sea and is believed to be the longest bony fish in the ocean. After it was found the fish was taken to Fransmanshoek Conservancy at Vleesbaai for safe keeping where Ricco Menezies and colleagues from Cape Nature in Stilbaai maintained it in excellent condition. It was cleaned and blast frozen at Viking Fisheries and then transported to the South African Institute for Aquatic Biodiversity (SAIAB) in Grahamstown for preservation. SAIAB is a Research Facility of the National Research Foundation (NRF). ‘These fishes are seldom caught and they are mostly seen when washed ashore,’ said Dr Stephen Lamberth, Inshore Resources Researcher from the Department of Agriculture, Forestry and Fisheries. They are found in temperate and tropical oceans worldwide. They live in deep water and are rarely seen. Unlike other fish, the oarfish keeps its body straight and swims vertically in the water column. This movement makes it easier to spot prey silhouetted against the light from the surface. ‘They are a mystery to scientists and are commonly found to depths of 100 m and more where they feed on crustaceans and fish larvae,’ added Lamberth. On its arrival, the 4 m long deep water fish provided hours of fascination for curious SAIAB and Rhodes University Department of Ichthyology and Fishery Sciences (DIFS) staff and students. SAIAB and DIFS maintain strong relations as a large number of DIFS students are supervised by SAIAB. The fish is soaked in a bath of 10% formalin to be disinfected and ‘fixed’. This retards decomposition. With large specimens such as this, formalin is also injected into the flesh to ensure that the internal tissues and organs are also fixed and do not decay. Once fully fixed the specimen will be thoroughly rinsed and transferred into a storage bin containing ethyl alcohol. The SAIAB Collection has five other specimens of this species dating back to 1966. Tissue samples taken from the oarfish will be stored in SAIAB’s Biomaterials Bank for DNA sequencing. The oarfish specimen will be stored in SAIAB’s Collection Facility and will be used for research. This state-of-the-art storage facility is specially designed for the long-term preservation of aquatic specimens. For more information on SAIAB and its collections, visit http://www.saiab.ac.za/

The oarfish specimen, which was injected with formalin to preserve it. Image: SAIAB

Increasing participation of girls in science in sub-Saharan Africa Misconceptions about the intelligence of girls, gender disparity and inappropriate teaching methods are largely to blame for serious underrepresentation of girls in science subjects in sub-Saharan Africa. These observations are published in a policy-makers’ booklet, InquiryBased Science Education: Increasing Participation of Girls in Science in sub-Saharan Africa of the Academy of Science of South Africa (ASSAf). Primary education enrolment ratios in sub-Saharan Africa are the lowest in the world. In 2006, some 75 million children (55% of these being girls) were not in school worldwide and almost half of this number was from sub-Saharan Africa. Access to basic quality education for most of sub-Saharan Africa’s children remains problematic. Educating girls in sub-Saharan Africa is critical to achieving the Millennium Development Goals (MDGs) and especially those associated with improved maternal health, universal primary education, and reducing acute poverty in the region. Historically, in Africa the focus has been on educating boys rather than girls for political, social and economic reasons. Boys were groomed to fulfill societal roles outside the home as primary breadwinners, while girls were encouraged to focus on roles within the home as homemakers and caregivers. These gender-based socio-cultural practices have led to entrenched gender inequalities in education, the labour market, and the socio-political arenas. Studies have shown that men are still dominating in most science fields. Girls have been hindered in the pursuit of science based on a number of misconceptions. Some of these are that boys are smarter than girls, and that science is hard and therefore girls will not cope. Coupled with the lack of self-confidence, several other factors inhibit girls from studying science subjects. Among these are a lack of parental, guardian, teacher and role model support to encourage the pursuit of science. The study argues that inquiry-based science education (IBSE) can be used to make science appealing to girls and further build a love of science among girls, thereby addressing an urgent need in the region. IBSE is a pedagogical technique of teaching science, which enables students, especially girls, to build on their experiences and to develop understanding about the scientific aspects of the world around them through the development and use of inquiry skills. The booklet recognises the importance of IBSE in encouraging girls to participate in science and mathematics subjects at the primary school level. It provides recommendations to policy-makers on how to support IBSE implementation on the continent. A key recommendation relates to the integration of IBSE into the school curricula, and the need for policymakers to support pilot projects introducing IBSE into schools. Science academies in sub-Saharan Africa are well-placed to promote IBSE and should collaboratively provide evidence-based policy advice to governments on the importance and value of IBSE for girls. While the study takes cognisance of the challenges facing particularly teachers, the education system and girls in implementing IBSE, it makes specific recommendations on how to implement this technique for subSaharan Africa.

Quest 7(3) 2011 47

Subscription Q SUBSCRIBE NOW TO HAVE FOUR Quest ISSUES MAILED TO YOU! and place your order for back issues (subject to availability) SCIENCE SCIENCE FOR FOR SOUTH SOUTH AFRICA AFRICA

SCIENCE SCIENCE FOR FOR SOUTH SOUTH AFRICA AFRICA

ISSN 1729-830X ISSN 1729-830X

VOLUME 7 • NUMBER 2 • 2011 VOLUME 3 • NUMBER 2 • 2007 R29.95 R20

VOLUME 7 • NUMBER 1 • 2011 VOLUME 3 • NUMBER 2 • 2007 R29.95 R20

Chemistry: ‘queen of sciences’

& Marie Curie a star

The Periodic Table:

Physics at sub-zero space physics in Antarctica

fundamental to chemistry

SASOL’s Fischer Tropsch process:

Satellites with attitude Earth's magnetic field and space navigation

Space weather protecting today's technology for tomorrow

Stranger than fiction extra-solar planets and binary systems Acid mine drainage the cost of mining

South Africa at the forefront the CubeSats revolution Letting satellites work for us space operations in South Africa

SCIENCE SCIENCE FOR FOR SOUTH SOUTH AFRICA AFRICA

ISSN 1729-830X ISSN 1729-830X

iThemba LABS: accelerating protons Training to care: HIV counselling HIV prevention: male circumcision

VOLUME 6 • NUMBER 4 • 2010 VOLUME 3 • NUMBER 2 • 2007 R29.95 R20

Coastal living: early modern humans at the coast Targeted intervention: taking aim at men

a long history

Ecological networks: protecting biodiversity Scorched, frozen or flooded: climate change and weather

VOLUME 6 • NUMBER 3 • 2010 VOLUME 3 • NUMBER 2 • 2007 R29.95 R20

Laser processing: changing the face of materials science

fuel innovation

South Africa’s chemical industry:

ISSN 1729-830X ISSN 1729-830X

50 years of laser technology: from light shows to Petrie dishes

Shaping light: laser beams made to order

Lasers in the sky: understanding the atmosphere

Hoodia research: biotechnology to the fore

Optical tweezers: lasers and disease A C AACDAEDMEYM YO FO FS C I EI ENNCCEE OOFF SS O U TT HH AAFFRRI C I CA A SC OU

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

SC A C AACDAEDMEYM YO FO FS C I EI ENNCCEE OOFF SS O U U TT HH AAFFRRI C I CA A Cover 7(2).indd 1

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

19/07/2011 12:21

SCIENCE FOR SOUTH AFRICA

Subscription Survey form 2011

I would like to subscribe to 4 issues of Quest: Science for South Africa. My details are (please print): Please fill in and return this form if you are already a subscriber.

Title: _______________ Name/Initials: _______________________________ Surname: _______________________________________________________ Company/university/institution/school: ____________________________ Student number (to qualify for student rates): _______________________ Postal address: ____________________________________________________________________________________________________________________ ___________________________________________________________________________________________________________ Code: _________________ Work tel.: (

) ____________________________ Fax: (

Cell: ______________________________________

) ______________________________

Home tel.: (

) _________________________

e-mail: ______________________________________________________________________________

How did you hear about QUEST? ______________________________________________________________________________________________________ If you are already a subscriber, are you satisfied with the subscription service? When would you like your subscription to begin? (Please fill in below.) Volume Number: _______ Issue Number: _______

❑

Yes

❑ ❑ ❑ ❑

No Tick here if this is an institutional subscription Tick here if this is an individual/personal subscription Tick here if this is a gift subscription

Date: _____________________________________ Signature: ______________________________________________________________________________

Subscription rates* (4 issues incl. postage) Please tick appropriate rate. South Africa Neighbouring countries (Southern Africa) Foreign

❑ Individuals/institutions – R100.00 ❑ Individuals/institutions – R160.00 ❑ Individuals/institutions – R180.00

* No VAT is charged, as the publisher is not registered for VAT.

❑ ❑ ❑

Students/Schoolgoers – R 50.00 Students/Schoolgoers – R130.00 Students/Schoolgoers – R140.00

SUBSCRIPTION CONTACT DETAILS Payment options

Please select and tick your payment option below.

CHEQUE: Enclose your cheque in South African rands made payable to ACADEMY OF SCIENCE OF SOUTH AFRICA (together with this completed Subscription Form)

❑

DIRECT DEPOSIT: Use reference SUB and your name or institution's name on your deposit slip and deposit your subscription as follows:

❑

Bankers: Standard Bank Hatfield Account Number: 07 149 422 7 Branch code: 011545 Account name: Academy of Science of South Africa POST the completed Subscription Form together with your cheque or a legible copy of your cheque/deposit slip (include your name on the slip) to: Quest Magazine, PO Box 72135, Lynnwood Ridge, 0040, South Africa OR FAX the Subscription Form together with deposit slip to: QUEST SUBSCRIPTIONS 086 576 9519. Subscription enquiries: tel. 012 349 6624 OR e-mail: patrick@assaf.org.za OR quest_admin@assaf.org.za. For more information, visit www.questinteractive.co.za

48 Quest 7(3) 2011

Q Back page science Study identifies new way to treat common hospital-acquired infection Rachel Champeau Researchers at the David Geffen School of Medicine at UCLA and the University of Texas Medical Branch at Galveston have discovered a molecular process by which the body can defend itself against the effects of Clostridium difficile infection (CDI), pointing the way to a promising new approach for treating an intestinal disease that has become more common, more severe and harder to cure in recent years. Clostridium difficile causes diarrhoea and colitis by releasing two potent toxins into the gut lumen that bind to intestinal epithelial cells, initiating an inflammatory response. These toxins are released only when the Clostridium difficile bacteria are multiplying. When antibiotics are used to treat another infection, this changes the bacterial landscape in the gut and, in the process, may kill bacteria that under normal conditions would compete with Clostridium difficile for energy. Scientists believe that this may be what provides Clostridium difficile the opportunity to grow and release its toxins. The UCLA and University of Texas researchers found that on infection with Clostridium difficile, human cells in the gut are capable of releasing molecules that will neutralise these toxins, rendering them harmless. In animal studies, the researchers showed that using a drug to induce this process, known as protein s-nitrosylation, inhibited Clostridium difficile toxins from destroying intestinal cells. Source: UCLA

A new analysis of archaeocete skulls by University of Michigan palaeontologist Julia Fahlke and co-authors shows that asymmetry evolved as part of a suite of traits linked to directional hearing in water. ‘This means that the initial asymmetry in whales is not related to echolocation,’ said Fahlke, who is working with scientist Philip Gingerich at the University of Michigan Museum of Palaeontology. ‘Archaeocetes have characteristic wear patterns on their teeth that show that they've been chewing their food.’ By studying those wear patterns, she hoped to piece together how and what early whales ate and how their eating habits changed over time. Fahlke began examining archaeocete skulls, and found ‘they all showed a leftward bend when you look at them from the top down’. Interestingly, archaeocetes have structures similar to those that are known in toothed whales to function in directional hearing in water: fat bodies in their lower jaws that guide sound waves to the ears, and an area of bone on the outside of each lower jaw thin enough to vibrate and transmit sound waves into the fat body. This adaptation, along with the acoustic isolation of the ear region from the rest of the skull, appears to have evolved in concert with asymmetry. The link between asymmetry and directional hearing is not unique to whales, Fahlke said: ‘Owls have asymmetrical ear openings, which help them discriminate the rustling of leaves from the rustling of a mouse. Such ability would also be helpful when you're trying to detect prey in the water, so we interpret that the same kind of mechanism was operating for archaeocetes.’ Source: National Science Foundation

Living on the edge of poverty and national parks Abundant S-nitrosylation, green, in colon with colitis (right), compared with normal colon.

Ancient whale skulls and directional hearing: a twisted tale Skewed skulls may have helped early whales find the direction of sounds in water and are not solely a later adaptation related to echolocation, as previously thought. Asymmetric skulls are a well-known characteristic of the modern whale group known as ‘odontocetes’ or toothed whales. These whales also have highly modified nasal structures with which they produce high-frequency sounds for echolocation – a sort of biological sonar used to navigate and find food. The other modern whale group, ‘mysticetes’ or baleen whales, has symmetrical skulls and does not echolocate.

A decade-long study questions conventional wisdom about the relationship between national parks and poverty. If so many poor people live around national parks in developing countries, does that mean that these parks are contributing to their poverty? Yes, according to conventional wisdom, but no, according to a 10-year study of people living around Kibale National Park in Uganda that was published recently in the Proceedings of the National Academy of Sciences. ‘Often people have lamented that the poorest of the poor live on the edge of the parks, and the assumption is that it's the parks that are keeping people poor,’ said Lisa Naughton, a professor of geography at the University of Wisconsin-Madison. The issue matters, she said, because ‘people say we can't afford to protect biodiversity’ if that inflicts further economic

hardship on people who are already poor. To explore the relationship of parks, poverty and biodiversity conservation, Naughton and colleagues monitored 252 families living within three miles of Kibale National Park, starting in 1996. The general trend 10 years later was toward greater prosperity, as measured by access to clean drinking water, ownership of more livestock, and living under an improved roof rather than the traditional thatch. ‘Most of the households came out ahead, are a lot better off than when we started,’ said Naughton. ‘I go back every couple of years, and people are generally optimistic, some say they never imagined life would be this good.’ 10% of the families in the original study, however, sold or lost their land and moved away, which indicates severe poverty, said co-author Jennifer Alix-Garcia, an assistant professor of agricultural and applied economics at UW-Madison. Although one finds a disproportionate presence of the very poor at the park edge today, more of their very poor counterparts, who lived further away, were forced to sell or give up their land as well, said Alix-Garcia. ‘Apparently the park provides a source of insurance; they can hunt, or sell firewood or thatch from the park,’ she said. ‘It's misleading. If you look, you see more poor people living near the park. But when you look at the change in assets, you see that the poor people who live next to the park have lost less than poor people who live farther away.’ And that suggests that the park is unlikely to explain the increased poverty among its close neighbours. Parks, landscapes, societies and economies vary widely, and so it's hard to know how well the results will generalise, Naughton admitted. However, she said the study was one of the first to look at parks and poverty over the long term, and the results do undermine the conventional wisdom, namely that national parks are to blame for the poverty found at their borders. Source: National Science Foundation

A 10-year study shows people living around Kibale National Park in Uganda do not experience more poverty than people in other parts of the country. Here two kids are at edge of Kibale National Park. Image: Courtesy Lisa Naughton, University of Wisconsin-Madison

MIND-BOGGLING MATHS PUZZLE FOR Q uest READERS Answer to Maths Puzzle no. 17:

Q uest Maths Puzzle no. 18

3: there were 5 teams therefore a total of 10 games took place. Hence Fulton's points must take the total to 20.

Try to fill in the missing numbers. Use the numbers 1 through 9 to complete the equations. Each number is only used once. Each row is a math equation. Each column is a math equation. Remember that multiplication and division are performed before addition and subtraction.

Win a prize! Send us your answer (fax, e-mail or snail-mail) together with your name and contact details by 15:00 on Friday, 4 November 2011. 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. 18’ and send it to: Quest Maths Puzzle, Living Maths, P.O. Box 478, Green Point 8051. Fax: 0866 710 953. E-mail: livmath@iafrica.com. For more on Living Maths, phone (083) 308 3883 and visit www.livingmaths.com.

Quest 7(3) 2011 49

kids love chemistry Getting the next generations excited about chemistry is important for humankind’s future. That’s why we’ve created “Kids’ Lab” in 15 countries, where the young ones can learn about chemistry and science in a fun, hands-on way. Little students and test tubes finally getting along? At BASF, we create chemistry. www.basf.com/chemistry www.basf.co.za Tel: +27 11 203 2400

uppe marketing A05541