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Science for South Africa

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

ISSN 1729-830X

Volume 9 | Number 3 | 2013

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

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


Research that can change the world

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

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C

ontents Volume 9 | Number 3 | 2013

Cover Stories 3 The universal genetic code

Quest examines the revolution

6 First human genome sequenced on the African continent

Wiida Fourie-Basson reveals Stellenbosch University’s cutting edge

10 DNA analysis reveals the true origin of the chameleon

Quest talks to Krystal Tolley about the role of DNA in elucidating the origins of the chameleon

14 DNA sequencing, velvet worms and conservation

Wiida Fourie-Basson explains how understanding the DNA of these little-known animals is vital to their conservation

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30 The oldest scorpion

Quest investigates one of the oldest land animals found in southern Africa

32 Short tails, hind limbs and evolution in birds

Quest looks at research that tells us that short tails are vital to modern bird morphology and ecology

34 Tiny technology reaching for the stars

Helen Henninger shows how nanotechnology is moving into space

Features 16 Golden Wattle’s promiscuous relationships ensure invasion success

Wiida Fourie-Basson looks at the way that alien invasives are potentially changing the bacterial make up of local soils

20 DNA and the complexity of life – infinitely more questions than answers

Wiida Fourie-Basson interviews Stellenbosch University palaeontologist Juries van den Heever

22 The Public Understanding of Biotechnology (PUB) Programme

SAASTA engages the public

26 The odd couple

250 million years ago two different species shared a burrow. Quest explains the significance of this

38 Emerging leaders: seven South African women take on Silicon Valley and STEM

TechWomen and the future

42 iSimangaliso’s coelacanths

News of these wonderful living ‘fossils’

Regulars 13 Fact file

Geological time

44 Careers

Bioinformatics

46 ASSAf news 47 News

Science as art • Power of populations

48 Books 50 Subscription 51 Astronomy news 53 Back page science • Mathematics puzzle 9| 3 2013

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Science for South AfricA

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

iSSn 1729-830X

Volume 9 | Number 3 | 2013

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

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

Images: www.thehistoryblog.com, Stellenbosch University, Krystal Tolley, Dai Herbert, NASA/JPL-Caltech

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

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

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

Permissions Fax: 0866 718022 e-mail: ugqirha@iafrica.com Subscription rates (4 issues and postage) (For other countries, see subscription form) Individuals/Institutions – R100.00 Students/schoolgoers – R50.00

The universal code T

here are two major facts that underpin the science of biology. One is evolution and the other – which adds to the body of evidence for evolution – is the universal genetic code, embodied in DNA. When Crick and Watson published their series of papers on the double helical structure of DNA in 1953, they took biology firmly into the realm of hard science. And at the same time, this further understanding of the molecule rooted evolution firmly as the basis for all life as we know it. DNA is universal – it is found in every living organism, from humans to microorganisms. Without our understanding of this molecule – and its relative RNA – we would have no biotechology – no genetic engineering (although controversial), no DNA profiling in forensic investigations, no applications of bioinformatics, and less understanding of evolutionary biology and anthropology. Understanding DNA is even allowing a form of digital storage using the genetic code – potentially providing a ‘memory’ that can last for ever. However, it is important to realise that the discovery of the structure of DNA was not made entirely by the two people whose names are most often associated with it. The history of DNA research is a long one. The molecule itself was first isolated in 1869. Even the mode of replication of genetic material was proposed as long ago as 1927 by Nikolai Koltsov, who proposed that genetic traits would be inherited by a ‘giant hereditary molecule’ made up of ‘two mirror strands that would replicate in a semi-conservative fashion using each strand as a template’. The following year, Frederick Griffith actually saw this at work when he found that the ‘smooth’ form of the bacterium Pneumococcus could be transferred to the ‘rough form’ of the same bacteria by mixing smooth and rough – providing the first clear suggestion that DNA carries genetic information. It was another technology – X-ray diffraction – that was needed to elucidate the structure of DNA and in 1937 William Astbury produced the first images showing that DNA had a regular structure. The vital final piece of evidence was provided by Rosalind Franklin and Raymond Gosling, using X-ray diffraction, backed up by the work of Maurice Wilkins and his colleagues, who provided evidence of the structure of DNA in X-ray patterns in living cells. Rosalind Franklin, in particular, played a pivotal and often overlooked role in understanding the structure of DNA. It is likely that her X-ray diffraction images were shown to Watson without her knowledge or approval. There are unpublished drafts of papers that show that she had independently worked out significant aspects of the structure of the DNA helix and it was one of her reports that convinced Crick and Watson of the correct final structure of the double helix. But her work was published third in the series of three Nature articles on DNA – led by the paper by Crick and Watson, which only hinted at her contribution to their hypothesis. Franklin died aged 37 of ovarian cancer. Crick and Watson went on to share the Nobel Prize for Physiology or Medicine in 1962. Science is about team work. It is important never to let ambition get in the way of integrity.

Design and layout Creating Ripples Graphic Design Illustrations James Whitelaw Printing Seriti Printing Pty Ltd

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Bridget Farham Editor – QUEST: Science for South Africa 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.


The universal

genetic code

Understanding the structure of DNA revolutionised the science of biology. Quest looks at the history and science behind this fundamental molecule.

O

n 25 April 1953, Francis Crick and James Watson published a series of papers in the journal Nature that described the double helix structure of deoxyribonucleic acid (DNA). Their clarification of the structure of the molecule that underlies the genetic code marked the beginning of modern biology. Combine the understanding of DNA – and so the genetic code – with our modern understanding of evolution and we have the means to understand how life works and how it began around four billion years ago. The genetic code DNA is a long molecule that holds the genetic information for all organisms – plants, animals or mico-organisms – literally the universal genetic code of life. DNA is a nucleic acid. The other important nucleic acid in the genetic code is ribonucleic acid (RNA). DNA, RNA and proteins make up the three major large molecules that are essential for all known forms of life on Earth. DNA is a double helix, made up of two intertwined sugar and phosphate chains, linked by four chemical bases – adenine (A) and guanine (G) which are purines and thymine (T) and cytosine (C) which are pyrimidines. Cytosine always pairs with guanine and adenine always pairs with thymine – C-G and A-T. The backbone of the double helix is made up of alternating sugars (deoxyribose) and phosphate groups – the bases are attached to the sugars. The two strands of DNA run in opposite directions to each other. It is the sequence of the four bases along the backbone that encodes genetic information. The information is read using the genetic code, which specifies the sequence of amino acids within proteins. Amino acids are the building blocks of proteins. The code is read by copying stretches of DNA into the related RNA in a process called transcription. The DNA in cells is organised into chromosomes. A chromosome is a single piece of coiled DNA that contains many genes and other elements that regulate cell behaviour. Chromosomal DNA encodes most or all of an organism’s genetic information. In complex organisms – eukaryotes – the DNA is in the form of chromosomes in the nucleus of the cell. In less complex organisms – prokaryotes – the DNA is found free in the cytoplasm of the cell. The history of DNA research DNA was first isolated in 1869 by a Swiss doctor – Friedrich Miescher – who found a microscopic substance in the pus in old bandages. Because he found it in the nuclei of cells he called it ‘nuclein’. In 1878 Albrecht Kossel isolated the nucleic acid component of the molecule and later isolated the bases. In 1919, Phoebus Levene identified the base, sugar and phosphate

The structure of the DNA double helix. The atoms in the structure are colourcoded by element and the detailed structures of the two base pairs are shown in the bottom right. Image: Wikimedia Commons

nucleotide unit. Levene thought that DNA was made up of a string of nucleotide units linked by the phosphate groups in a short chain with the bases repeated in a fixed order. It was in 1937 that William Astbury produced the first X-ray diffraction patterns that showed that DNA had a regular structure. It was only in 1953 that James Watson and Francis Crick suggested what we now know to be the correct double-helix model of DNA structure. Their double-helix molecular model of DNA was then based on a single X-ray diffraction image – ‘Photo 51’ – taken by Rosalind Franklin and Raymond Gosling in May 1952 – as well as the information that the bases were paired, based on work that was done by Erwin Chargaff. DNA and biotechnology DNA is a code – a way of storing biological data – in the form of genes. During the 1960s scientsists ‘cracked’ this code and showed that – for all life – there are only 20 amino acids that are encoded by DNA in all life forms – from humans to mushrooms. The revolution of biotechnology arose as a result of the fact that all life shares this same universal genetic code. It took scientists until the 1970s to find ways to swap chunks of DNA between species – effectively designing specific characteristics. Humans have been doing something similar for the past 10 000 years through breeding and farming, but we now have tools to ‘edit’ DNA. Genetic modification has provided massive advances in our understanding of how life and diseases work. 9| 3 2013

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James Watson (R) and Francis Crick (L) at Cambridge University. Image: Cold Spring Harbour Laboratory Archives

James Watson and Francis Crick demonstrating their double-helix model of DNA. Image: www.thehistoryblog.com

The chromosomes in a man. Image: Wikimedia Commons

Genetic engineering

Genetic engineering is a process in which DNA from different organisms is purified and manipulated in the laboratory, allowing the modern technology of DNA recombination. Recombinant DNA is a man-made DNA sequence that has been put together from other DNA sequences. These sequences can then be introduced into other organisms – producing genetically modified organisms used in medical research and agriculture. Forensics – genetic profiling

Forensic scientists use DNA in body fluids, such as blood or semen, and from hair found at the scene of a crime to identify a matching DNA of an individual – who may be the perpertrator of that crime. This is called genetic profiling or genetic fingerprinting. DNA profiling was developed in 1984 by the British geneticist Alec Jeffreys and first used in forensic science to convict Colin Pitchfork in the 1988 Enderby murder case. Genetic profiling has also been used to identify victims in mass casualty events and victims in mass war graves. Bioinformatics

A single folded strand of RNA. Image: Wikimedia Commons

Ribonucleic acid (RNA) RNA is essential to the process of protein synthesis. Its structure is similar to that of DNA because it is also made up of nucleotides. But it differs from DNA because it is made up of a single strand of nucleotides and the sugar molecule is called ribose. RNA contains the bases adenine, guanine and cytosine, but contains uracil instead of thymine.

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Bioinformatics is the manipulation, searching and data mining of biological data – including DNA sequence data. There are now techniques to store and search DNA sequences which have led to advances in computer science such as string searching algorithms, machine learning and database theory. String searching algorithms find the occurence of a sequence of letters within a larger sequence of letters and were developed to search for specific sequences of nucleotides. The DNA sequence so found can be aligned with other DNA sequences to identify matching sequences and the specific mutations that make them distinct. These techniques are used to study phylogenetic relationships and protein function. Large DNA data sets – such


The major structures in DNA compaction; DNA, the nucleosome, the 10 nm ‘beads-on-a-string’ fibre, the 30 nm fibre and the metaphase chromosome. Image: Wikimedia Commons

as those in the Human Genome Project – can only really be interpreted if the locations of the genes and regulatory elements on each chromosome can be identified using bioinformatic techniques. Evolutionary biology and anthropology

DNA collects mutations over time, which are then inherited, so the molecule contains historical genetic information. Geneticists can work out the evolutionary history of organisms or groups of people – their phylogeny – by comparing DNA sequences. In evolutionary biology, population geneticists can learn the history of particular populations of species by comparing the DNA sequences within a species. This can be used in studies ranging from ecological genetics to anthropology. DNA digital data storage

This is a scheme to store digital data in the base sequence of DNA using artifical DNA. This storage system is more compact than current magnetic tape or hard drive storage systems and can also potentially last for tens of thousands of years. In theory, such data storage is ‘apocalypse-proof’ because it would survive a hypothetical global disaster. A paper published in Nature in January 2013 describes the work of a group of scientists from the European Bioinformatics Institute and Agilent Technologies who have encoded 739 kilobytes of data into DNA code, synthesised the actual DNA and then sequenced the DNA and decoded the information back to its original form with 100% accuracy. The Human Genome project The Human Genome Project was completed ten years ago – in its initial form at least. It is an international scientific research project that aimed to determine the sequence of chemical base pairs that make up human DNA and to identify and map the total genes of the human genome. It is the largest collaborative biological project ever. It started in 1990, a working draft of the genome was announced in 2000 and the complete one in 2003. More detailed analysis is still being published. The key findings are: n There are approximately 20 500 genes in humans – the same range as in mice. Once we understand how these genes are expressed we will better understand how disease is caused. n The human genome has significantly more nearly identical, repeated sections of DNA than the genomes of other mammals. These sections may point to the creation of new genes that are specific to primates. n At the time when the draft was published, less than 7% of protein families appeared to be specific to vertebrates. As of now, the Human Genome Project has lead to the

Above: The first printout of the human genome to be presented as a series of books, displayed in the ‘Medicine Now’ room at the Wellcome Collection, London. The 3.4 billion units of DNA code are transcribed into more than 100 volumes, each 1 000 pages long, in type so small that it is barely legible. Image: Wikimedia Commons

Right: X-ray diffraction image of the double-helix structure of the DNA molecule, taken in 1952 by Raymond Gosling, commonly referred to as ‘Photo 51’, during work by Rosalind Franklin on the structure of DNA. Image: Wikimedia Commons

discovery of more than 1 800 disease genes. There are now more than 2 000 genetic tests for human diseases. At least 350 biotechnology-based products have arisen from the Human Genome Project and are currently in clinical trials. A complete sequence of the human genome is similar to having a manual to make the human body. We now need to learn how to read the contents of these pages and understand how everything fits together in health and disease. One step towards this understanding is the HapMap, which was developed in 2005. This is a catalogue of common genetic variation, or haplotypes, in the human genome. In 2010, the third phase of the HapMap project was published with data from 11 global populations – the largest survey of human genetic variation performed to date. HapMap data have accelerated the search for genes involved in common human diseases. The tools that were created in the Human Genome Project are still being used in research to characterise the genomes of important organisms that are used in biomedical research such as fruit flies, roundworms and mice. Q 9| 3 2013

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First human genome sequenced on the African continent

What is DNA sequencing? It is the process of determining the precise order of nucleotides within a DNA molecule. It includes any method or technology that is used to determine the order of the four bases – adenine, guanine, cytosine and thymine – in a strand of DNA. http://en.wikipedia.org/wiki/DNA_sequencing Left: Raw sequencing data before assembly into a genome. Image: Stellenbosch University

Stellenbosch University is at the forefront of DNA sequencing in Africa. Wiida Fourie-Basson explains how.

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hile the world is celebrating the 60th anniversary of the discovery of the DNA double helix this year, few people realise that, to date, DNA sequencing of large genomes such as that of humans and other organisms – requiring highly sophisticated instruments, technical expertise and super computing power – has not been possible on the African continent. In 2011 Stellenbosch University (SU) received a grant from the National Research Foundation to acquire a SOLiD 5500xl Next Generation Sequencer. Nicknamed MegaMind, it was deployed in the DNA Sequencing Unit that forms part of SU’s Central Analytical Facilities (CAF). Earlier this year MegaMind sequenced a human genome – the first time that this has been done on the African continent.

What is a genome? A genome is the entirety of an organism’s hereditary information. It comprises the hereditary instructions for building, running, and maintaining an organism, and for passing life on to the next generation. In most organisms the genome is made of a chemical polymer called DNA. The genome contains genes, which are packaged in chromosomes and affect specific characteristics of the organism. (http://www.genomenewsnetwork.org/resources/whats_a_genome/Chp1_1_1.shtml#genome1)

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Introducing MegaMind In September 2012 SU’s DNA Sequencing Unit launched a small competition during a joint meeting of the South African Genetics Society and the South African Society for Bioinformatics and Computational Biology. The prize? A free next-generation sequence run on MegaMind. Requirements? A good research proposal. PhD candidate Shareefa Dalvie was the worthy winner. She is supervised by Prof. Raj Ramesar at the Human Genetics Research Unit of the Medical Research Council, based in the Institute of Infectious Diseases and Molecular Medicine (IIDMM) at the University of Cape Town. Her research focuses on understanding the genetic factors underlying bipolar disorder. This study involved sequencing the genome of a single individual whose family members’ genomes had previously been sequenced in the United States. According to Prof. Ramesar, technology like MegaMind adds great value to larger-scale continental efforts on studying human diseases. Not so easy to sequence a human genome In 2001 two large consortiums published the first draft of the human genome in two separate papers in Nature and Science. This was the culmination of nearly 15 years of work


Table 1: Comparison of different genomes sequenced at CAF in terms of Gigabases of DNA (Stellenbosch University) Organism

Genome size Number of (basepairs) chromosomes

Homo sapiens (Human) 3 200 000 000

46*

Vitis vinifera (Grapevine)

38*

Mycobacterium tuberculosis (TB) Human papilloma virus * Diploid

487 000 000 4 411 000 7 909

1# 1#

# Haploid

by over a thousand scientists at a total cost of US$3 billion. It signalled the start of the genomics era, where researchers look at the whole genome of an organism in order to understand it instead of just looking at a few genes at a time. By 2005 genomics was taken to another level with the introduction of a new technology called next-generation sequencing (next-gen). With next-gen it was now possible to sequence the whole human genome in a matter of weeks (not years) and at a cost of less than $100 000. Since then this type of high-throughput sequencing has evolved and progressed at such a rate that human genomes can now routinely be sequenced for around US$6 000. Since 2007 several next-generation sequencing instruments have been acquired by South African researchers and used in various projects where smaller genomes – like those of bacteria and fungi – have been sequenced. But while human genomes from all over the world have been sequenced, until now this was not possible on African soil. Several resources had to be in place first: technical expertise, sophisticated instruments and super computing power. How do you sequence a human genome? Before a DNA sample gets even close to MegaMind, there is lots of preparation involved. And in the case of a human genome the process is even more complex, explains Dr Ruhan Slabbert, principal analyst at CAF’s DNA Sequencing Unit. The process starts when the scientist obtains sample material from someone and extracts DNA from the tissue material. The DNA is then sent to an analytical facility such as CAF, where preparation for sequencing takes place. Together Slabbert and the manager of the unit, Carel van Heerden, worked for nearly six days in the lab to complete the first four steps in preparing the sample of the human genome DNA for sequencing. The steps included quality control, fragmenting the DNA into millions of smaller pieces, adding SOLiD-specific adaptors for templating and building a library. Dr Slabbert explains: ‘During templating the DNA molecules are attached to magnetic beads. Each

While the actual sequencing involves preparatory work in the lab involving various complex physical and chemical reactions before the DNA sample gets to MegaMind, the analysis of the subsequent data requires some serious hardware. For this purpose, Stellenbosch University acquired a high-performing computing cluster with over one Terabytes of RAM, more than 200 processors and over 60 Terabytes of storage. Image: Wiida Fourie-Basson

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bead contains a single DNA molecule, which is clonally amplified by means of a polymerase chain reaction’. ‘The beads carrying the DNA fragments are then loaded onto a special glass flow cell for sequencing by MegaMind. During the sequencing process, MegaMind automatically adds various reagents, including special primers containing fluorescent probes. These primers bind to the DNA fragments and emit a fluorescent signal when excited by a laser.’ Each primer has a different wavelength and shows a different colour depending on whether adenine, thymine,

A first for South Africa and Africa: the team from Stellenbosch University’s Central Analytical Facilities (CAF) that sequenced a human genome – Dr Ruhan Slabbert, principal analyst, Anelda van der Walt, bioinformatics analyst, and Carel van Heerden, manager of the DNA Sequencing Unit at CAF. Image: Wiida Fourie-Basson

Bioinformatics analyst Anelda van der Walt and senior systems administrator Charl Möller at one of the high-performance clusters supporting the DNA Sequencing Unit at Stellenbosch University’s Central Analytical Facilities. Image: Wiida Fourie-Basson

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cytosine or guanine (abbreviated as A, C, T or G) are present on that part of the DNA fragment. The arrangement of the letters of this four-letter alphabet generates a ‘sentence’ or ‘genome sequence’. Millions of these fluorescent data points are collected by a microscope lens and interpreted by software, similar to the way the Hubble telescope will interpret data from the stars. ‘In the end all these points are consolidated into a single data file that can be used in downstream analysis’, Slabbert adds. In the case of this specific human genome, it took MegaMind about two weeks to complete the run. According to Van Heerden it is fairly simple to sequence a human genome, in that we know what to do and how to do it – ‘It must just be done correctly, though,’ he explains. ‘It is like playing a piano concerto. You have to read the notes from the paper and do what it says. But just as it is with playing the piano, you have to practise until you get it right.’ However, sequencing a human genome compared to the genome of a virus or bacteria is like playing one of Chopin’s piano concertos versus playing the popular version of Für Elise, he adds. Furthermore, there is very little room for errors when sequencing a human genome. ‘Because it is so huge, you can easily lose large chunks of data. It is the same when analysing the data. It is easier to analyse a small genome than a large genome. It is like piecing a puzzle together: ten pieces are easy, 1 000 pieces nice, but 10 000 pieces border on the insane. While building a 10 000-piece puzzle is still humanly possible, we would not be able to piece the three billion basepairs of human DNA together without the help of computers,’ he says (see Table 1 for a comparison of examples of different sized genomes sequenced by CAF in terms of Gigabases of DNA). Last in line is bioinformatics analyst Anelda van der Walt. While she is part of the team from step one, her task is to piece together this 10 000-piece puzzle in such a way that it will make sense to the researchers. In other words, what has been invisible to the human eye or unknown when it entered the lab in a vial, now leaves the DNA sequencing unit in a digital format that can be used and interpreted by the researchers. Bioinformatics analysts like Van der Walt help researchers to understand what is happening in a cell by converting digital data to biologically relevent information. q Carel van Heerden is the manager of the DNA Sequencing Unit at Stellenbosch University’s Central Analytical Facilities (CAF). He has an MSc in genetics from Stellenbosch University and is currently pursuing a PhD degree in the same field. Dr Ruhan Slabbert is a principal analyst in the DNA Sequencing Unit at Stellenbosch University’s Central Analytical Facilities. He has a PhD in genetics from Stellenbosch University. Anelda van der Walt has an MSc in bioinformatics from the South African National Bioinformatics Institute at the University of the Western Cape. Wiida Fourie-Basson writes about science and the people behind it for Stellenbosch University Faculty of Science. She has an MA in Communications from UNISA.


DNA analysis reveals the true origin of the

chameleon

A major DNA analysis of the evolutionary origin and history of one of the world’s most remarkable invertebrates – the chameleon – has shown that it originated in Africa, and not Madagascar, as was previously thought. Quest investigates.

T

oday most chameleon species are found in Africa and Madagascar, both of which are fragments of the ancient super-continent Gondwana. But the origin of the family Chamaeleonidae dates back 90 million years, after the Gondwana break up which caused Madagascar to separate from Africa. The two have been completely disconnected for at least 120 million years. This last fact is important, because it means that chameleons could have evolved in Madagascar and then dispersed using ocean currents to continental Africa. Up until now most scientists have favoured this idea. However, new evidence from DNA analysis has turned this idea on its head. Dr Krystal Tolley, head of the Molecular Ecology Programme at the South African National Biodiversity Institute, and her colleagues now think that chameleons originated in Africa and then dispersed to Madagascar. According to Krystal Tolley, ‘the original ideas about where chameleons originated didn’t make sense to me. So I was curious, and because I work with DNA of chameleons, I was able to use these modern methods to try and understand chameleon history better’. The main argument for chameleons originating in Madagascar was that there are so many species on the island. But this didn’t feel right to Krystal Tolley – there are in fact more species in Africa (although new species are being discovered all the time in both places, so the final numbers are still not known).

A male Knysna dwarf chameleon (Bradypodion damaranum) in display. All photographs courtesy of Krystal Tolley.

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TRIASSIC 200 million years ago The two super-continents that made up the super-continent, Pangea, 200 million years ago.


Pygmy chameleons (Rhampholeon platyceps) often pose so that they mimic a leaf.

Juvenile Mulanje pygmy chameleon (Rhampholeon platyceps) sleeping on a leaf, Mt. Mulanje, Malawi

Dr Krystal Tolley with a chameleon.

Also, the closest relatives of chameleons are not on Madagascar. But there are related lizards in north Africa and the near East. So it seemed to make more sense that chameleons originated in Africa and then spread to Madagascar. Using the DNA evidence, plus new information on ocean currents, Krystal Tolley and her team were able to put the ideas together and show that chameleons must have originated on continental Africa instead. Phylogenetic analysis The findings come from using modern biogeographical techniques to carry out a phylogenetic analysis of 170 chameleon species, plus 28 other reptiles in the group known as Squamata – or scaled reptiles. This is the most recent order of reptiles and includes all lizards and snakes. A phylogenetic analysis is a way to reconstruct the evolutionary relationships between groups of organisms (species) using molecular DNA sequencing methods. DNA lets you reconstruct an evolutionary history because DNA accumulates mutations in its sequences. Species that have the same mutations have the same common ancestor. These mutations allow you to construct a ‘tree’ of their history – much like constructing a pedigree. Once you work out who is related to who, you can run some probability analyses to work out where they came from. A mutation is a change in the nucleotide sequence in DNA. Mutations are caused by errors during the process of replication of DNA (or RNA), or insertion or deletions of segments of DNA. Mutations may produce changes that can be seen in the outward appearance of an organism. Most mutations are harmless, although some can be harmful.

The real origins of chameleons According to this research, chameleons split away from other lizards around 90 million years ago. These other lizards were probably in Asia or North Africa. At the time, chameleons were

Up close to a male two-horned chameleon (Kinyongia multituberculata) from Magamba Forest in the West Usambara Mountains, Tanzania.

A male two-horned chameleon rests on a branch for the night (Magamba Forest).

mainly ground living creatures and probably only crawled up into low bushes occasionally. This was around the same time that the dinosaurs were ruling the planet. For the next 25 million years, not much happened with chameleons, but starting around 65 million years ago (about the same time that the dinosaurs became extinct), chameleons 9| 3 2013

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The spiny-sided chameleon (Trioceros laterispinis) from the Udzungwa Mountains (Tanzania) gets its name from the modified pointy scales that cover its flanks.

Usambara spiny pygmy chameleon (Rhampholeon spinosus) from the East Usambara Mountains, Tanzania has a modified ‘horn’ for display.

Brookesia Rieppeleon archaius Rhampholeon

Bradypodion Nadzikambia chamaeleo

Furcifer Calumma

Kinyongia

Trioceros

A chronogram for chameleons. The species are colour-coded according to their ancestral area – Africa, green; Madagascar, blue; Europe, pink; Asia, purple; Seychelles, orange; Socotra, lime green. The time scale is included and the maps show the direction of the ocean currents and latitude (S) of Africa and Madagascar (‘Plio', Pliocene; ‘Pleis’, Pleistocene). Image: http://dx.doi.org/10.1098/rspb.2013.0184

Reference Tolley KA, Townsend TM and Vences M. Large-scale phylogeny of chameleons suggests African origins and Eocene diversification. Proceedings of the Royal Society 2013;280: http://dx.doi.org/10.1098/rspb.2013.0184

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managed to do three major things. They first dispersed to both Madagascar and then much later, to the Seychelles from the African continent. During this period of geological time (through the Oligocene Epoch which ended about 23 million years ago) the main ocean currents were flowing toward Madagascar and Seychelles – not toward Africa as they do today, so it's likely that some large rafts of vegetation were washed down a river and floated across the ocean. Given the speeds of the current, the journey would probably have taken less than a month. Once they arrived in Madagascar, they diversified (radiated) into different species. However, they didn’t do this on the Seychelles, because these islands are probably too small to hold many species. The other thing that chameleons did was on the African continent itself. Around 50 million years ago, they started to take over the trees. In Africa, they are really the only lizard group that has successfully colonised the arboreal (tree/bush) habitat. Once they started moving into the trees, they also diversified into many, many species. At the time there were few other species in the same habitat, so it was an open niche for the chameleons and they took advantage of it. Africa was much more forested during these times so there was plenty of habitat. Finally, one of these arboreal chameleons dispersed to Madagascar a second time around 47 million years ago. The currents were still running toward Madagascar, so the dispersal probably took place the same way – on a floating raft of vegetation. There are now two main groups of chameleons in Madagascar, but both of them have their closest relatives on the African continent. In summary, it seems that there were three separate dispersals out of Africa: 65 million years ago to Madagascar (the genus Brookesia), followed by another dispersal 47 million years ago, also to Madagascar (the genera Calumma and Furcifer) and finally a dispersal 34 million years ago to the Seychelles (the genus Archaius). Ocean disperal Krystal Tolley says that the most important thing about this research is that it shows oceanic dispersal is possible. Scientists do already know this because somehow, volcanic oceanic islands like Hawaii are well colonised by species from the Americas. This study shows that oceanic dispersal to Madagascar from Africa is probably relatively common – at least twice here, plus the Seychelles – and that the flora and fauna of these landmasses are linked. Because Madagascar has an almost unique flora and fauna – think of the lemur species – scientists have always questioned where its species came from. Madagascar broke away from Africa 120 million years ago, but much of the species on the island are younger than this. So did these species arrive from Africa? Or did new species evolve there by splitting from species already present? In the end, both are true, but Africa probably plays a much bigger role in populating Madagascar than was originally thought. q Dr Krystal Tolley is a Principal Scientist Specialist: Molecular Ecology Programme, South African National Biodiversity Institute, Cape Town and a Research Associate, Department of Botany and Zoology, Stellenbosch University. Her particular research interest is in understanding the historical processes that generate patterns of diversity which lead to species radiations in African reptiles using biogeographic and phylogenetic approaches.


❚❚❚❙❙❙❘❘❘ Fact file

Geological time

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onstructing the Earth’s history – and that of the organisms living on the Earth – requires an understanding of the geological time scale (GTS). The GTS is a way of describing the timing and the relationship between events that have occurred during Earth’s history. Radioactive dating shows that the Earth is abour 4.5 billion years old. Radioactive dating is a way of determining the age of materials such as rocks, usually based on a comparison between the observed abundance of a naturally occurring radioactive substance and the products that are produced as it decays, called decay rates. The geology or deep time of Earth’s past has been organised into units according to events that took place during each period. Different periods of time on the GTS are usually marked by changes in the composition of the rock strata that correspond to that time. These show major geological or palaeontological events, such as mass extinctions. For example, the boundary between the Cretaceous period (145 - 66 million years ago) and the Paleogene period (66 - 23 million years ago) is defined by the Cretaceous-Paleogene extinction event. This is when the dinosaurs and many other groups of life became extinct. Older periods of time – before the fossil record – are defined by absolute age.

A comparative geological time scale. If you made a geological time scale with one year for every millimetre, the whole list would be about 4 600 km long. Human-like primates showed up in the last 2 - 3 km of the list. In comparison, the dinosaurs lived for about 160 km of the list. Modern humans began to appear about 10 - 15 metres from the end of the list. A 30-year-old person would only have been on the list for the last 3 centimetres. Image: Wikimedia Commons

Units of time The largest unit of time is the supereon which is made up of eons. Eons are divided into eras which are then divided into periods, epochs and ages. Geological units from the same time, but from different parts of the world, often look different and contain different fossils. When geological time was first defined this meant that the same periods were often called by different names in different parts of the world. These names have now been standardised by the International Commission on Stratigraphy.

Representing time There are different ways of representing the GTS graphically. Two examples are shown.

Graphical representation of Earth’s history as a spiral. Image: Wikimedia Commons

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How does sequencing the DNA of the little-known velvet worm aid conservation? Wiida Fourie-Basson explains the work done by Savel Daniels.

The forest floor of the Ngele mistbelt forest is covered with moist leaf litter and fallen and rotten logs. This is home to the pink velvet worm and other endemic and critically endangered species such as the chirping frog (Anhydriophryne ngongoniensis) and the Cape parrot (Poicephalus robustus). Image: Dai Herbert

DNA sequencing, velvet worms

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rof. Savel Daniels, a zoologist at Stellenbosch University, is one of the few scientists in the world studying velvet worms – a fascinating group of ancient, caterpillar-like animals that have changed little over the past 550 million years. He is also the first in over a 100 years to have found several specimens of the critically endangered pink velvet worm. The pink velvet worm (Opisthopatus roseus) was first described in 1945. The original six specimens were found in the Ngele mistbelt forest in KwaZulu-Natal, and to date this remains the only location where pink velvet worms have been found. Another two specimens were collected in 1951, one in 1985 and six in 1995, also from the Ngele forest. In 1996 the International Union for the Conservation of Nature (IUCN) assessed this species as ‘extinct’. Then, in 2010, Savel Daniels managed to find 35 specimens from five different sampling sites. These sites were in the Ngele forest which surrounds the newly built national highway, the

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conservation

N2. The secretive pink velvet worms are notoriously difficult to collect, hiding in decaying logs and vegetation. The IUCN has since revised the pink velvet worm’s status to ‘critically endangered’. But that does not mean this little creature is now home safe and dry – on the contrary. Unlocking the velvet worm’s secrets Simply finding specimens of an animal or a plant is not enough – biologists need to understand the organism’s behaviour and population ecology in order to ensure that different species survive in a changing landscape. This is particularly important in an endangered species because without this knowledge it is impossible to plan conservation strategy. Using DNA sequencing and phylogenetic analysis, Savel Daniels established that groups of individuals collected from within a single log do not come from a single maternal lineage or reproductive unit – ‘The results indicate that the worms disperse from their natal ranges [where they were born] to form loose social aggregations where


Above: Sometimes a zoologist needs to get down and dirty – Prof. Daniels digging for a new species of freshwater crab on the Mpumalanga Highveld. Image: Stellenbosch University

Left: Prof. Savel Daniels in his lab at the Department of Botany and Zoology at Stellenbosch University. Image: Wiida Fourie-Basson

Interesting facts about the velvet worm from the Australian Museum

multiple reproductive females can co-inhabit the same log. This implies that a large number of genetically distinct individuals are found in one decaying log. If that log is removed for fuelwood, or to clear the forest to prevent forest fires, it will mean the loss of a valuable pool of genetic diversity for this already critically endangered and narrow endemic group,’ Daniels explains. The fact that one decayed log is home to a genetically diverse population of this sparsely distributed worm, is particularly important to its consevation. In order to conserve the velvet worm, indigenous trees that have fallen in the forest should be left to decay and not be removed, because they provide an essential habitat for the species. Daniels also found that velvet worms were not found in decaying logs in a nearby plantation of aliens, mainly pines. These logs were much drier and there was little natural vegetation cover, making them unsuitable habitats for the velvet worms. Even more alarming was the apparent lack of male velvet worms – at three of the five sites only a single male was present, and at two other sites only female specimens were present. Further studies of social organisation and behaviour are needed to find out if this is normal or as a result of their low numbers. q Prof. Savel Daniels is part of the Evolutionary Genomics Research Group in the Department of Botany and Zoology at Stellenbosch University. One of the focal points of his research is to understand the interplay between species diversity and historical time in southern Africa. His research covers South African velvet worms, the Afrotropical freshwater crab fauna, limbless skinks and, more recently, tortoises. The main objective of all these studies is to better understand and document the spectacular biodiversity of South Africa to aid the conservation of these groups. He has a BSc and an MSc from the University of the Western Cape, and a PhD from Stellenbosch University.

n Velvet worms have between 14 to 30 pairs of lobe-like, stumpy legs. Their characteristic flowing movement is caused by alteration of fluid pressure in the limbs as they extend and contract along the body. This characteristic movement led to a second common name, peripatus, from ‘peripatetic’, which means ‘wandering’. n Velvet worms are secretive and display ‘photonegative’ behaviour – they hide away from light. n Velvet worms breathe through little holes called ‘trachea’ that are scattered over the body. These pores are permanently open, so water from the body can easily be lost. The porous nature of their cuticle means that velvet worms can easily dry out, so they are restricted to areas of high humidity, such as in logs, under stones, in the soil, or among leaf litter. n The evolutionary history of velvet worms (Onychophorans) has long fascinated scientists. They have been described as a missing link between the arthropods (a group that includes insects and spiders) and the annelids, or segmented worms (which includes earthworms and beach worms). It is now known that Onychophorans are much more closely related to arthropods than to annelids. Source: http://www.australianmuseum.net.au/Velvet-worm#sthash.eAuAJ81R.dpuf

Why study velvet worms? The anatomy of velvet worms has changed little since the Early Cambrian (541 - 485 million years ago), which is why they are important for addressing various evolutionary and other scientific questions, for example: n What are the origins of vision and colour vision? n How are the major arthropod groups related to each other? n What is the developmental basis of animal segmentation? n How did the arthropod head evolve? n What are the origins of the arthropod nervous system? n How did the mitochondrial genomes evolve? n To what extent are velvet worms useful for conservation? n What is the actual species diversity of Onychophora? n Can the velvet worm’s slime be used for bioengineering? Sources: http://onychophora.com/index.htm and http://www.nrmsouth.org.au/uploaded/287/15130505_37v elvetworms.pdf

Did you know? DNA sequence data is increasingly being used by biologists to differentiate between species that were formerly thought to be one species. Biologists call these ‘cryptic species’, meaning hidden or concealed. Certain species cannot be distinguished because of the lack of obvious differences in their outward appearance. DNA sequencing is used to determine whether there are genetic differences between groups. It is particularly difficult to distinguish species of velvet worms because they look so similar. However, using DNA sequencing, several new species were described in 2013. Prof. Daniels described five new species in the Peripatopsis moseleyi species complex (published in Invertebrate Systematics) as well as several new species in the P. balfouri species complex (published in Zoologica Scripta).

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A native fynbos legume, Aspalathus neglecta. Image: Jaco le Roux


GOLDEN WATTLE’S

promiscuous relationships ensure invasion success The invasion success of aliens such as Australia’s Golden Wattle in South Africa’s fynbos biome might have something to do with fraternising with the right kinds of local and imported bacteria. By Wiida Fourie-Basson.

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ne of the main conclusions of a study published in the Journal of Biogeography recently is that the Golden Wattle – which also happens to be Australia’s national flower (Acacia pycnantha) – is a promiscuous plant, associated with at least six different types of beneficial soil bacteria (called rhizobia), as well as growth-promoting bacteria from the genus Burkholderia. This means the Golden Wattle is getting all the help it needs to literally produce its own fertiliser and grow stronger and more roots, trunks, leaves and flowers. While there have been extensive studies done on alien invasives, this is one of the first literally to go underground, to the roots of the matter. ‘The ability of Australian acacias to nodulate and fix nitrogen must have been a substantial factor contributing to their success in South Africa’s fynbos biome, which is characterised by soils that are generally poor in nutrients, especially nitrogen,’ researchers from the Centre for Invasion Biology at Stellenbosch University and the South African National Biodiversity Institute write in the article ‘Co-invasion of South African ecosystems by an Australian legume and its rhizobial symbionts’. According to Dr Jaco le Roux from Stellenbosch University (SU)’s Department of Botany and Zoology, and one of the lead authors, nitrogen-fixing bacteria are found in the root nodules of almost all legumes studied to date. The nodules can be seen as a swellings on the root structures. Within root nodules nitrogen-fixing bacteria have the ingenious ability to transform atmospheric nitrogen into ammonium that can be easily and directly taken up by the plants. Plants cannot utilise atmospheric nitrogen on its own, but nitrogen is an essential part of those acids (amino acids and nucleic acids) that are vital to all life on Earth. In exchange, the legumes provide rhizobia with a safe haven and nutrients. The study found that the Golden Wattle brought most, if

Root nodules found in legumes. Image: Natasha Mavangere

Within root nodules nitrogen-fixing bacteria have the ingenious ability to transform atmospheric nitrogen into ammonium that can be easily and directly taken up by the plants. Plants cannot utilise atmospheric nitrogen on its own, but nitrogen is an essential part of those acids (amino acids and nucleic acids) that are vital to all life on Earth.

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Fynbos areas around Helderberg, Western Cape, invaded by wattles (Acacia longifolia and Acacia saligna). Image: Jaco le Roux

not all, of its rhizobial symbionts along from Australia. This means that invasive populations of Golden Wattle may also be spreading non-indigenous bacteria in South African soils. Another interesting finding was that both the native and invasive ranges of the Golden Wattle harboured growthpromoting bacteria from the genus Burkholderia. ‘This may indicate that this symbiosis – between this bacteria and the Golden Wattle – is not something new, but that the Burkholderia species may be common associates of acacias’ Le Roux explains. If this is true, it could in part explain the invasion success of acacias all over the world. Unique rhizobia originally discovered in South Africa Not all bacteria have been created equal, though: ‘The difference between conventional rhizobia and Burkholderia species is like comparing a pine tree with a Namaqualand daisy! Conventional rhizobia was originally regarded as the only nitrogen-fixing bacteria that nodulates legumes, until the recent discovery of rhizobia from the genus Burkholderia, coincidentally also from South Africa, in 2001,’ Le Roux says. According to the article, there is a whole bunch of reasons why a close relationship with the Burkholderia species seems like a very good idea, such as larger root systems (thereby offering more opportunities for the rhizobia to form root nodules), more and larger leaf hairs, steadier stems, higher lignin deposits around the vascular system, larger amounts 18

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of chlorophyll, increased levels of those plant hormones that promote the division of cells, and increased levels of resistance against pathogens. Bacterial sex and unintended consequences The mixing of bacterial symbionts from different geographic origins like Australia and South Africa may have unintended consequences. Le Roux explains: ‘Bacteria often have “sex”, strange as that may sound. They carry some genes on little circular genomes known as plasmids. In other words, these do not form part of the core genome. Having sex means they attach and exchange plasmids through a process called conjugation. Symbiotic genes – those responsible for the successful formation of root nodules and fixation of atmospheric nitrogen – are carried on plasmids. In many instances these genes are highly specific for certain legume plants, for example Australian wattles’. According to Le Roux, it is conceivable that Australian bacteria might exchange plasmids with South African bacteria as the invasives come to dominate the landscape. ‘This phenomenon has been documented elsewhere in the world. From an evolutionary perspective it would make sense for South African bacteria to acquire Australian symbiotic genes, so as to survive by utilising the newly abundant host plants, namely Golden Wattles. This, in turn, can lead to novel genetic combinations and may even enhance invasiveness. But this also means that as native bacteria “pick up” Australian genes they lose their native genes, thereby negatively impacting the ability of native


Dr Jaco le Roux. Image: provided by Jaco le Roux

legumes to form successful symbiosis.’ Indigenous fynbos like the honeybush (genus Cyclopia), for example, is nodulated primarily by Burkholderia species, while some Lotononis species are nodulated by Methylobacterium nodulans. Further research will be needed to understand how the introduction of non-native bacteria impacts on these unique associations. Finally, in South Africa, where dense monospecific stands of acacias cover tens of thousands of hectares, it can substantially change the soil’s microbial structure as a result of increased soil nitrogen. But in this instance what’s good for the goose is not good for the gander: ‘The fynbos soils are generally very low in nutrients. This means that the flora of the Cape Floristic Region originally evolved in response to a nutrient-poor environment. It is conceivable that altered nutrients may negatively impact native vegetation,’ Le Roux warns. Q Dr Jaco le Roux is interested in the evolutionary mechanisms and dynamics of small populations, particularly those involved in invasive plant populations. Most of his research focuses on molecular ecology, using population genetic and phylogenetic approaches to better understand the evolutionary processes that underpin biological invasions. He holds a PhD from the University of Hawaii at Manoa. Wiida Fourie-Basson is a media liaison officer in the Faculty of Science at Stellenbosch University. Ndlovu J, Richardson D, Wilson JRU, Le Roux J. Co-invasion of South African ecosystems by an Australia legume and its rhizobial symbionts. Journal of Biogeography 2013;40:1240-1251.


DNA and the complexity of life: infinitely more questions than answers ‘Any discoveries that claim to provide the ultimate answer ... always create more questions than answers’. An interview with Dr Jurie van den Heever by Wiida Fourie-Basson.

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o says palaeontologist Dr Jurie van den Heever on the significance of the discovery of the DNA double helix 60 years ago. From his office at Stellenbosch University, overflowing with books, fossils and, of course, an illustrated edition of Darwin’s original 1859 text of On the Origin of Species, he reflects on the meaning of life and what biology has to offer in understanding humanity and life on Earth. What was the impact of the discovery of the DNA double helix on biology? It was an unbelievable breakthrough. In the early 1950s people believed that the discovery of the structure of DNA would provide us with all the answers. But of course it did

Where we sit in the general scheme of things!

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not work that way. When the entire human genome was worked out we also thought that we knew it all. But, again, it was not the whole truth. Combined with technology, DNA has now developed into a very important piece of equipment for science because it provides strong and conclusive proof of scientific findings. But at the same time we now realise that life on Earth is infinitely more complex than anyone could ever have imagined. What is the current thinking around DNA and evolution in the biological sciences? Complexity – the one thing that biology has contributed to the philosophy of science. In the early 1900s the philosophy of science was dominated by Newton’s laws, physics and chemistry. Biology was not considered part of that debate. It was accepted that you can reduce the complexity of life to chemicals and atoms. But life does not work like that. You can buy all the chemicals needed for ‘life’ at your nearest pharmacy, but to create an organism is much more complex. And even if you can do as Craig Venter and his team did in 2010 when they constructed the first synthetic bacterial cell, you can still not predict how that ‘life’ will be affected by its environment or by culture. Darwin stated in the Origin of Species that the evolution of life depends on its environment as well. There is much more to evolution than just DNA and genes. So what is the next big thing in the biological sciences? Until recently the predominant view was that of Richard Dawkins in The Selfish Gene (1976) – organisms are ‘machines created by our genes’. But that is a very genocentric view, and there are many evolutionary phenomena that cannot be explained within this framework. We now have a whole-organism view and realise that biology consists of complex, interacting networks. This new view is nicely described by Eva Jablonka and Marion Lamb in their 2005 book, Evolution in Four Dimensions. It is mind-


If we continue to see ourselves as being above nature, as ruling Earth and nature, then we find ourselves in a very precarious position. We have to look back at evolution and how animals and plants have become integrated as a system. The moment you do that, your brain makes an about-turn and you reconsider the way you live and consume. boggling to think that changes in the cytoplasm of a cell can inform changes in the gene itself. There is research showing that the sons of smoking fathers have an increased chance of heart disease, even if they do not smoke themselves. Imagine the impact of famines or wars on people’s consciousness and development, a kind of collective scar that needs to be dealt with and understood also on a genetic level. This understanding should become part of our world view and our understanding of life. Today, philosophers of science recognise that the complexity of nature is best represented by biology, and the philosophy of science is being driven by questions raised in biology.

The young Charles Darwin. Image: Wikimedia commons

Will we ever be able to fully understand humankind? What happens when we apply this understanding to our lives today? Take capitalism, for example. Where are we going with capitalism? We are plundering the Earth and its resources. Too many people think the economic system or technology will save humanity. But the economy forms only a subsection of ecology and not a very important subsection at that. Humanity is not in control. We are also not essential to life on Earth. Quite the contrary. If we continue to see ourselves as being above nature, as ruling Earth and nature, then we find ourselves in a very precarious position. We have to look back at evolution and how animals and plants have become integrated as a system. The moment you do that, your brain makes an about-turn and you reconsider the way you live and consume. And today we can do that with the help of science. Or as us palaeontologists like to say, mortui vivos docent – the living are instructed by the dead. Q Dr Jurie van den Heever is a Karoo palaeontologist in the Department of Botany and Zoology at the University of Stellenbosch and is a team member on the programme ‘Hoe Verklaar Jy Dit?’ on the Afrikaans radio station RSG. He is a founding member and past President of the Palaeontological Society of South Africa and in his free time turns wood.

Paleontologist Dr Jurie van den Heever in his office at Stellenbosch University with one of his favourite fossils, Lycosuchus vanderrieti. Described by Dr Robert Broom in 1903 this Karoo fossil is a Therapsid, the group of vertebrates from which mammals evolved. Lycosuchus is approximately 260 million years old and already exhibits incipient mammalian characteristics. Image: Wiida Fourie-Basson

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The Public Understanding of

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he Department of Science and Technology (DST) launched the Public Understanding of Biotechnology (PUB) programme in 2003 following the publication of the National Biotechnology Strategy in June 2001. PUB is a dynamic and innovative public communication programme aimed at increasing broad public awareness and promoting a clear, balanced understanding of the scientific principles and potential of biotechnology. In addition PUB seeks to create meaningful opportunities for public dialogue and debate around biotechnology and its general applications to enable informed decision making. It is essential that people understand and debate the principles around biotechnology – this concept is being promoted and funded by the government. Both the economic and social potential benefits of the technology must be understood, as well as its safety (or otherwise). If people do not understand the technology, it is easy for unbalanced and often incorrect information to be spread by the media – which can lead to confusion. With balanced and scientific information, people 22

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The dynamic team who help to put together PUB messages. Image: SAASTA

can engage in dialogue and debate issues, rather than following a prescribed view. The key message is about the practical applications of biotechnology in different areas, including medical/health, agriculture and industry – and how this technology can positively affect the lives of South Africans. This is where the South African Agency for Science and Technology Advancement (SAASTA), a business unit of the National Research Foundation, comes in. With its unique history, SAASTA (formerly FEST) is the ideal organisation for implementing the PUB programme. Established in 1950, SAASTA has adapted and changed significantly over the years, but the original aim of promoting the public understanding of science still remains. Achievements Since its inception in 2003, PUB, as the most established public engagement programme in the country, has been at the forefront of innovative ways to communicate science to various sectors of society in the following ways. The development and distribution of resources: n Production and dissemination of

resources from fact sheets covering over ten biotechnology focus areas, to careers booklets for learners, cartoon posters, periodic tables as well as resources specifically designed for educators. n Educator resource pack with all resources aligned to the curriculum. n Production of 30-second public service announcements (PSAs) by Jive Media – short cartoon video clips aired on SABC in 2007/8. n The Biotechnology World Touchscreen, created by the Foster Brothers, in which five biotechnology focus areas can be explored in an interactive digital world. Interaction with researchers: n Media round tables (MRTs) aimed at journalists – hosted around the country on various topics such as genetically modified organisms (GMOs) in wine, DNA in forensics, GM potato and biofuels. Numerous biotechnology-related articles have been published in South African print media, reaching thousands of people. n Basic biotechnology (BBT) workshops for educators – held to promote the understanding and teaching of the biotechnology


Biotechnology (PUB) Programme

concepts in the school curriculum. Hundreds of educators have benefited from these workshops. n Critical thinkers’ forums – a relatively new addition to the programme’s activities targeting scientists, content specialists and the general public. ‘Hot’ biotechnology topics (acid mine drainage, stem cells, etc.) are discussed and debated at these events. Five have been hosted thus far. Interaction with learners and the public: n Exhibiting at science festivals (SciFest, Sasol Techno X, etc.) across the country and running forensics and BBT workshops. Promoting biotechnology and related careers sp contributing to nurturing youth talent for SET careers and developing human capital that feed the excellence pipeline. (2012/13 FY; forensics workshops at Sasol Techno X reached 342 learners and 12 educators). n Industrial theatre plays used to disseminate biotechnology information among learners at high schools in Gauteng, KwaZulu-Natal and North West provinces. n Participation in the SAASTA National Schools Debates Competition over the past three years, during which biotechnology has been a provincial or national debate topic. (2012 reach at provincial level: 405 learners and 81 educators). n Interviews conducted in the media through national radio stations highlighting the impact of biotechnology in daily life and career profiling.

A touch screen application used to disseminate information about biotechnology. Image: SAASTA

Interaction with role players in the NSI: n Through the grants system, PUB has managed to work with stakeholders in the sector, for example science centres, higher education institutions (HEIs) and other scientific institutions, increasing the exposure of various target audiences to SET activities such as MRTs, BBT workshops, public lectures and speed-dating scientists, to name a few. Surveys and publications: n A human capital needs analysis (HCNA) study was conducted in the 2009/2010 financial year. One of the significant findings of the HCNA study was that the local biotechnology industry is unable to provide employment opportunities for students graduating with biotechnology degrees and that there may be an issue with the ‘type’ or specific field of biotechnology skills required. n Public perceptions of biotechnology survey conducted by the Human Sciences Research Council (HSRC) in 2004/5 revealed that eight out of ten South Africans have no knowledge about biotechnology and well over half have never even heard the term. Despite this lack of understanding, an average of 57% indicated that varied applications of biotechnology should continue. This national study involved a

sample of 7 000 adults aged 16 and older in households spread across the country's nine provinces, including urban and rural communities. n PUB has participated on an international level in platforms such as biotechnology workshops/ profiling in Japan, Uganda and Mauritius, and in science conferences in Spain, and Egypt. n Science communication workshops have been held at HEIs and scientific institutions across the country and more recently in Zimbabwe. The aim of these workshops is to provide scientists and content specialists with the necessary skills to convey their science knowledge to the public and the media. Going forward In celebration of 10 years of PUB, SAASTA will increase exposure at science festivals and continue basic biotechnology workshops for educators, as well as increasing general public exposure to biotechnology. There will also be a mass survey of public perceptions and attitudes to biotechnology. Individuals who have contributed significantly to the South African biotechnology sector will be recognised and rewarded and a book will be published profiling individuals and institutions who have played key roles in promoting biotechnology. Q 9| 3 2013

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DNA

Profiling 101

DNA (deoxyribonucleic acid) is what makes you, YOU. It's what makes everyone special and unique. And it can help scientists discover all sorts of things like how to diagnose and treat genetic diseases (diseases passed from a parent to a child), or help the police catch a criminal.

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What is DNA?

What is DNA profiling?

Every cell in every living thing (or organism) has DNA, a molecule that contains all the information about that organism. Lengths of connected DNA molecules, called genes, are tiny pieces of a code. They determine what each organism is like in great detail. Almost all the DNA and genes come packaged in thread-like structures called chromosomes (humans have 46). There are 22 almost identical pairs, plus the X and Y chromosomes, which determine if a human is male (one X chromosome and one Y chromosome) or female (two X chromosomes). Genes are passed on from parents to children, and no two organisms (except clones and identical twins) have the same DNA. Many things – the colour of your eyes or hair, whether you're tall or short, your chances of getting certain diseases – depend on the genes you get from your parents. Half of your genes come from your mom and half come from your dad.

The exciting possibilities of the fact that each person has a unique DNA “fingerprint” (scientists call it a profile) was first realised in 1984 by the British scientist, Alec Jeffreys. Two years later, American scientist Kary Mullis developed the PCR (polymerase chain reaction). This is a process that scientists can use to multiply small amounts of DNA so they can study it more easily. For example, let's say that someone has broken into a store and accidentally got cut on a broken window, leaving a very small amount of blood behind (what scientists call “trace elements”). Before 1986 scientists might not have been able to extract any DNA for analysis from the blood on the glass because there was too little blood. But with PCR they can now take that small amount and copy it over and over again, making the extraction of the DNA for analysis much easier. Basically, DNA profiling is the matching up of individuals' DNA profiles. Let's use the above example of the store robber. The police find a suspect and get them to give a DNA sample (this could come from saliva or blood). They then send it to the laboratory where this sample is compared with the sample taken from the window. If the samples match, then it is likely that the suspect is the one who robbed the store; if they don't match, then the police know they've got the wrong person. It is virtually impossible for one person to have the same profile as someone else in the world, unless they are identical twins. So, if a lab matches two DNA samples they can only be from one person.

MiniMag


DNA fact file In South Africa the police's forensics laboratory uses tests, which limit the sequence to one person in a billion who will have that exact pattern. In places like England, forensic scientists use tests which limit the pattern to one person in a trillion.

By: Professor Valery Corfield DNA stands for deoxyribonucleic acid. It is a chemical substance made from building blocks that form long, thin strings.

More uses

The DNA strings, called molecules, are packed very tightly into the nucleus of cells.

DNA profiling doesn't only have to be used to catch criminals. It can also help doctors in finding out if a child might get a disease that their parent has, or for a court to determine whether or not someone is really another person's mother, father, sister or brother. And DNA is not only used for analysis in humans, but also other organisms like plants, animals and even bacteria.

The DNA molecules twist around each other and form a spiral ladder – the DNA double helix. DNA double helixes are organised into 23 pairs of chromosomes in every cell in your body. This set of chromosomes is the instruction manual to make YOU. Each different instruction is called a gene. The gene instructions are written in a DNA code – the genetic code. New coded copies are made when the DNA double helix unzips down the middle and new molecules are added to each unzipped strand.

DNA profiling in the future

DNA can help people in conservation management. In South Africa, many universities are finding ways of using DNA profiling to identify animals and plants for conservation, and in preventing poaching of animals like rhino and elephant. DNA profiling can also help in tracing pollution outbreaks and infectious disease research. In other parts of the world, databases of the DNA of cats and dogs have been set up. These have actually helped to solve criminal cases where, for example, a cat's hair was found at a crime scene and could be linked to its owner. Another use for DNA profiling in South Africa is in looking at the DNA found in the organisms that cause HIV/AIDS and TB. If scientists can understand the DNA better, they might be able to find a cure. 2

Scientists hope that they will one day be able to not only use DNA to match people, but to actually form an “identikit” or “photo” of what that person will look like. But this might still take some time as it is not yet possible for scientists to work out tests to identify with 100% certainty things like eye, hair, or skin colour. Scientists are also hoping that they will one day be able to identify people through the DNA of the tiny bugs that live on our skin. They believe this will help to distinguish even identical twins, as each person has a different kind of bug-population that co-habits with them. The study of DNA and DNA profiling is always growing and improving. And it can help scientists to understand many things about all living organisms that they never knew before.

EasyScience is produced by the South African Agency for Science and Technology Advancement (SAASTA), an operational unit of the National Research Foundation. SAASTA’s mission is to promote the public's understanding, appreciation and engagement with science and technology among all South Africans. Visit the website: www.saasta.ac.za for more information.

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The odd couple Scientists from South Africa, Australia and France have discovered a world-first association while scanning a 250 million-year-old fossilised burrow from the Karoo Basin of South Africa. Quest takes a look.

This 3D image shows the mammal-like reptile Thrinaxodon nestling up to the amphibian Broomistega. Image: Wits University 9| 3 2013 26


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The two fossils. Image: ESRF/V Fernandez

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any land animals burrow – for brooding, to avoid predators and as protection from extreme climates. Scientists call this burrowing activity fossorialism and the large number of fossilised burrow casts that have been found immediately after the Permo-Triassic boundary in southern Africa suggest that this behaviour was widespread in many tetrapods more than 250 million years ago. The Permo-Triassic boundary is the period of geological time during which the Permian-Triassic extinction event – known as the Great Dying – took place around 250 million years ago. This is the Earth’s most severe extinction to date, with 96% of all marine species and 70% of terrestrial vertebrates becoming extinct. It is the only known mass extinction of insects. Some 57% of all families and 83% of all species became extinct and it probably took around 10 million years for life on Earth to recover.

The Karoo contains a particularly large number of burrow casts, suggesting that the animals of the time used burrows extensively to escape the particularly harsh climate that characterised this period of geological time. A few of these burrow casts contain fossils that provide scientists with important information about vertebrate evolution and ecology. There are quite a few different types of burrows found in the Karoo rocks, which suggests that the burrows were

An artist’s impression of Broomistega seeking shelter in Thrinaxodon’s burrow. Image: Wits University

excavated for different reasons. Over the past few years several fossil therapsids have been found curled up in burrows – the most important being the Early Triassic cynodont Thrinaxodon, which was found curled up in a posture that suggested a period of aestivation – becoming dormant for a particular season to escape food and water shortages. This adaptation – aestivating in burrows – may have allowed some mammal-like reptiles to survive the Permian-Triassic extinction. Therapsids are a group that contains the early ancestors of mammals. The Karoo is particularly rich in therapsid fossils.

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Thrinaxodon. Image: Wits University

Non-destructive excavations Fossilised remains are usually excavated by scientists in a way that means that the rock surrounding the fossil is effectively destroyed. However, new developments in synchrotron imaging have allowed scientists to essentially X-ray these burrow casts without destroying them. After many impressive results when using synchrotron imaging to investigate fossils, the use of the technique has led to revived interest in studying the numerous fossilised burrows found in the Karoo Basin, dated to 250 million years ago. The first attempt to investigate one of these burrow casts surprisingly revealed a world-first association of two unrelated animals. In this study, local and overseas scientists found that the burrow revealed two unrelated vertebrate animals nestled together and fossilised after being trapped by a flash flood event. Facing harsh climatic conditions subsequent to the Permian-Triassic (P-T) mass extinction, the amphibian Broomistega and the mammal forerunner Thrinaxodon cohabited in a burrow. Scanning shows that the amphibian (Broomistega), which was suffering from broken ribs, crawled into a sleeping mammal-like reptile’s shelter for protection. Unearthing the past The fossils were recovered from sedimentary rock strata in the Karoo Basin. It dates from 250 million years ago, at the beginning of the Triassic Period. At that time, the ecosystem was recovering from the Permian-Triassic mass extinction that wiped out most of life on Earth. In the 28

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Pangea Supercontinent context, what is now South Africa was an enclave in the southern half called Gondwana. It was the scene of pronounced climatic warming and increased seasonality, marked by monsoon-like rainfall. To survive this harsh environment, many animals, including the mammallike reptiles, turned to burrowing, demonstrated by the numerous fossilised burrow casts found in the Karoo Basin. These casts have long been thought to enclose fossilised remains. Early this year, an international group of scientists started to investigate the contents of these burrows using X-ray synchrotron computed microtomography. Two burrow casts were selected from the collection at the University of the Witwatersrand (Wits) to be scanned using the state-of-the-art facility at the European Synchrotron Radiation Facility (ESRF). Using the unique properties of the X-ray beam which allows non-destructive probing, the scan of the first burrow started to reveal the skull of a mammal-like reptile called Thrinaxodon, an animal previously reported in another burrow. As the scan progressed, the three-dimensional reconstruction displayed results beyond expectations – the mammal-like reptile was accompanied by an amphibian Broomistega, belonging to the extinct group of Temnospondyl. ‘While discovering the results we were amazed by the quality of the images’, says lead author Fernandez, ‘but the real excitement came when we discovered a second set of teeth completely different from that of the mammal-like reptile. It was really something else’.


Comparison of results from a traditional laboratory microtomograph and X-ray images obtained at the ESRF. Image: ESRF/V Fernandez

Besides the almost perfect preservation of the two skeletons, the team focused on the reasons for such an unusual co-habitation. Fernandez explains: ‘Burrowsharing by different species exists in the modern world, but it corresponds to a specific pattern. For example, a small visitor is not going to disturb the host. A large visitor can be accepted by the host if it provides some help, like predator vigilance. But neither of these patterns corresponds to what we have discovered in this fossilised burrow’. The scientists gathered all the information to try to reconstitute the events that led to this incredible fossil aggregation, testing scenarios one after another. ‘It’s a fascinating scientific question: what caused the association of these two organisms in the burrow? One of the more obvious possibilities is a predator-prey interaction, but we inspected both skeletons looking for tooth marks or other evidence implying predation, ultimately finding no support for one having attempted to feed on the other,’ says Fernandez’s co-worker Kristian Carlson. His colleague, Della Collins Cook, adds that the consecutive broken ribs resulted from a single, massive trauma. The amphibian clearly survived the injury for some time because the fractures were healing, but it was probably quite handicapped. According to Fernandez this Broomistega is the first complete skeleton of this rare species that has been discovered. ‘It tells us that this individual was a juvenile and mostly aquatic at that time of its life,’ he says. The scientists eventually concluded that the amphibian crawled into the burrow in response to its poor physical condition but was not evicted by the mammal-like reptile. Numerous Thrinaxodon specimens have been found in South Africa, many of them fossilised in a curled-up position. Another Wits scientist on the team, Fernando Abdala, says: ‘I have always been fascinated by the preservation of Thrinaxodon fossils in a curled-up position that show even tiny bones of the skeleton preserved. It’s as if they were peacefully resting in shelters at the time of death’. The shelters prevented disturbance of the skeletal remains from scavengers and weathering. ‘We also think it might reflect a state of torpor called aestivation in response to aridity and absence of food resources,’ Abdala says. Piecing all the clues together, the team finally worked out the strange association, concluding that ‘the mammallike reptile, Thrinaxodon, was most probably aestivating

‘It’s a fascinating scientific question: what caused the association of these two organisms in the burrow? One of the more obvious possibilities is a predatorprey interaction, but we inspected both skeletons looking for tooth marks or other evidence implying predation, ultimately finding no support for one having attempted to feed on the other.’ in its burrow, a key adaptation response together with a burrowing behaviour, which enabled our distant ancestors to survive the most dramatic mass extinction event. This state of torpor explains why the amphibian was not chased out of the burrow,’ says Bruce Rubidge, Director for the Centre for Excellence in Palaeosciences. Both animals were finally entrapped in the burrow by a sudden flood and preserved together in the sediments for 250 million years. Paul Tafforeau, of the European Synchrotron Radiation Facility, Grenoble, France, says: ‘Thanks to the unique possibilities for high-quality imaging of fossils developed during the last decade at the ESRF, these unique specimens remain untouched, protected by their mineral matrix. Who knows what kind of information we’ll be able to obtain from them in the future and which would have been completely lost if the specimen had been prepared out of its burrow cast?’ Q The international team of scientists was led by Dr Vincent Fernandez from Wits University, South Africa and the European Synchrotron Radiation Facility (ESRF) in Grenoble, France. The other authors from Wits University include Prof. Bruce Rubidge (Director of the newly formed Palaeosciences Centre of Excellence at Wits), Dr Fernando Abdala and Dr Kristian Carlson. Other authors include Dr Della Collins Cook (Indiana University); Dr Adam Yates (Museum of Central Australia) and Dr Paul Tafforeau (ESRF). Fernandez V, Abdala F, Carlson KJ, Cook DC, Rubidge BS, et al. Synchrotron Reveals Early Triassic Odd Couple: Injured Amphibian and Aestivating Therapsid Share Burrow. PLoS ONE. 2013;8(6): e64978. doi:10.1371/journal.pone.0064978

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The sting and pincers of the new scorpion species. Image: Wits University

The oldest scorpion A Wits scientist has discovered the oldest known land animal in a remote part of the Eastern Cape. Quest takes a look.

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odern scorpions are an abundant group of invertebrates and are usually found in tropical and warm temperate regions around the world – although there are some at altitude in Patagonia, South America. Scorpions are found in the fossil record from the early Silurian period (443 419 million years ago). Understanding the fossil record from a period of geological time allows scientists to draw conclusions about climate, movement of continents and the ecology of the time. A new species Dr Robert Gess, from the University of the Witwatersrand, discovered a new fossil species of scorpion from the Witpoort Formation, Waterloo Farm near Grahamstown.

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The new species is called Gondwanascorpio emzantsiensis. The Witpoort Formation rocks at Waterloo Farm were deposited in the Late Devonian period, about 360 million years ago. At that time, Waterloo Farm was part of the shoreline of the Agulhas Sea, within 15 degrees of the south pole. The Agulhas sea lay between Laurasia (the single northern landmass then comprising what is today North America and Asia) and the more southerly Gondwana. Gess found fragments of the scorpion sting and pincers. Early land animals Gess’s find is the first record of a Palaeozoic scorpion from Gondwana. It is very unusual because the specimen was found in rocks that appeared to have been deposited at far higher latitude than that at which modern or fossil


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scorpions are known to have occurred. This is significant because the find may suggest improving climate conditions towards the end of the Devonian period. The other significant factor is that the presence of this scorpion in Gondwana – a species that is similar to those found in Laurasia – is more evidence for the idea that terrestrial ecosystems around the world at the end of the Devonian periods were very similar. There is evidence for this already from the different genera of plants such as the pro-gymnosperm tree Archaeopteris, which has also been described from Waterloo Farm. The increasingly similar ecosystems are probably as a result of Laurasia and Gondwana moving closer together during this period. Gondwanascorpio emzantsiensis is the oldest known land animal from Gondwana. The next oldest records of terrestrial animals from southern Africa are insects from the Early Permian Whitehill Formation, which was deposited about 90 million years later. This is a large gap in the fossil record – accounted for by the geological events that occurred as southern Africa passed over the south pole during the Carboniferous period (358 - 298 million years ago), which was followed by most of Gondwana being covered in ice – glaciation. Gess explains that early life was confined to the sea and the process of terrestrialisation – the movement of life onto land – began during the Silurian period. The first wave of life to move out from water onto land consisted of plants, which gradually increased in size and complexity throughout the Devonian Period. This initial colonisation of land was closely followed by plant and debris-eating invertebrate animals such as primitive insects and millipedes. By the end of the Silurian period, about 416 million years ago, predatory invertebrates such as scorpions and spiders were feeding on the earlier land animals. By the Carboniferous period, early vertebrates – our four-legged ancestors – had in turn left the water and were feeding on the invertebrates. Although we knew that Laurasia was inhabited by diverse invertebrates by the Late Silurian and during the Devonian, this supercontinent was at the time separated from the southerly positioned Gondwana by a deep ocean – the Agulhas sea. ‘Evidence on the earliest colonisation of land animals has up till now come only from the northern hemisphere continent of Laurasia, and there has been no evidence that Gondwana was inhabited by land-living invertebrate animals at that time,’ says Gess. ‘For the first time we know for certain that not just scorpions, but whatever they were preying on were already present in the Devonian. We now know that by the end the Devonian period Gondwana also, like Laurasia, had a complex terrestrial ecosystem, comprising invertebrates and plants which had all the elements to sustain terrestrial vertebrate life that emerged around this time or slightly later,’ said Gess. Q Dr Robert Gess is a postdoctoral fellow at the Evolutionary Studies Institute at the University of the Witwatersrand. Additional material for this article was supplied by Erna van Wyk, Communications Officer, University of the Witwatersrand.

Dr Robert Gess doing field work at the site near Grahamstown. Image: Wits University

Archaeopteris is an extinct genus of tree-like plants with fern-like leaves. It is an index fossil – one that is used to define and identify geological periods.

A fossil Archaeopteris showing the fern-like leaves. Image: Wikimedia Commons Gess R. The earliest record of terrestrial animals in Gondwana: A scorpion from the Famennian (Late Devonian) Witpoort Formation of South Africa. African Invertebrates. 2013;45(2):373-379.

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Short tails, hind limbs evolution in birds

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Early birds had long bony tails – they had to lose these before the variety of specialised hind limbs that we see in modern times could evolve. Quest looks at recent studies on bird evolution.

Two bird fossils. Image: Wits University

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irds originated around 152 million years ago from within the theropod dinosaurs. Today there are almost 10 000 species of birds. This might look like a clear example of adaptive radiation driven by the main characteristic of modern birds – powered flight. There is fossil evidence of adaptive radiation among bird species present in the Mesozoic period (252 - 66 million years ago). However, studies of the evolutionary splitting events – called cladogenesis – in birds, a process that leads to the development of great varieties of sister species, suggest that the main burst of speciation (formation of new species)

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came after the origins of flight by up to 85 million years ago. This speciation occurred well within what is called the ‘crown group’ – all the taxa descended from a major splitting event. A taxon (plural: taxa) is a named group of organisms that are linked by shared physical or genetic characteristics. There are, however, few fossils that have been used in the study of bird evolution, which leaves two main questions: (1) did the earliest birds undergo significant radiation compared with their non-avian relatives (other groups that descended from the dinosaurs) and (2) whether flight,


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A size comparison of selected giant theropod dinosaurs and a human. Image: Wikimedia commons

Theropod dinosaurs The theropod dinosaurs were bipedal dinosaurs belonging to the order Theropoda. They were mainly carnivorous, although some groups ate plants and insects. They first appeared during the Late Triassic period, about 230 million years ago and included the only large terrestrial carnivores from the Early Jurassic until at least the close of the Cretaceous, about 66 million years ago. During the Jurassic, birds evolved from small specialised coelurosaurian theropods. There are several features that link theropod dinosaurs to birds including the presence of a wishbone (furcular), air-filled bones, brooding eggs and in some cases, feathers. The best-known theropod dinosaur is probably Tyrannosaurus, but several other giant carnivorous dinosaurs have been described. All known theropods are bipedal with short forelimbs that were specialised for a wide variety of tasks. Benson BJ and Choiniere JN. Rates of dinosaur limb evolution provide evidence for exceptional radiation in Mesozoic birds. Proceedings of the Royal Society. B. 2013;280:1780.

Irritator, a spinosaur theropod. Image: Wikimedia commons

and related new features, had any role in promoting the formation of new species and changes in the physical makeup (morphology) in the earliest birds. Adaptive radiation is the evolution of a wide range of species that occupy and exploit many different types of available habitat from an ancestral organism. For example, mammals show adaptive radiation into many different forms and habitats from a single ancestor.

Controlling flight Birds are unique in that their ability to fly is controlled mainly by their wings (equivalent of forelimbs) and tail – independently of their hindlimbs (legs). In their ancestors – the theropod dinosaurs and the earliest birds – the form of the hindlimb was controlled by the way that the hindlimbs were linked to a long, primative tail. The earliest birds are found in the Jurassic (201 - 145 million years ago). Scientists working on bird evolution have hypothesised that if the hindlimb and the tail became independent units functionally, then evolution of the hindlimb could have resulted in the diversity that we see in modern birds. Birds have been able to exploit many different environments as a result of their different hindlimbs – diving, perching, wading and climbing. Roger Benson and Jonah Choiniere thought otherwise. In their search for the origins of bird diversity, Benson and Choiniere analysed the cladogenesis and limb evolution for

the entire tree of Mesozoic theropods. They documented the transition from dinosaur to bird and the immediate origins of powered flight. They compared measurements of the main parts of the legs of early birds – upper leg, shin, and foot – to those of their dinosaur relatives. By doing this Benson and Choiniere were able to work out whether the speed and diversity of bird leg evolution was exceptional compared to leg evolution in dinosaurs. Their analysis included fossils from China, North America and South America. What they found was that the long bony tail characteristic of the theropod dinosaurs and their early bird relatives, was lost after flight evolved. This means that birds evolved a short bony tail and then the extremely diverse variety of hind limbs found in modern birds. It was this ability to adapt the hindlimbs independently of the tail that resulted in the explosive adaptive radiation leading to diverse early bird species. ‘These early birds were not as sophisticated as the birds we know today – if modern birds have evolved to be like stealth bombers then these were more like biplanes,’ said Benson, who led the research. ‘Yet despite some still having primitive traits, such as teeth, these early birds still display an incredible array of leg shapes.’ Q Dr Roger Benson is at the Department of Earth Sciences, University of Oxford, UK and Dr Jonah Choiniere is at the Evolutionary Studies Institute and NRF/DST Centre of Excellence in Palaeosciences, University of the Witwatersrand, Johannesburg. 9| 3 2013

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TINY TECHNOLOGY reaching for the stars Nanotechnology is moving into space. Helen Henninger explains how.

The boundaries of our solar system. Image: adapted from http://www.dragoart.com/ tuts/3666/1/1/how-to-draw-the-solar-system.htm

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hen supercomputers become reality and massive accelerators and microscopes probe the smallest objects on earth, tiny nanospacecraft – very small low-cost satellites or space vehicles – travelling at close to the speed of light will be bringing us information on the secrets of deep space and probe the interstellar void that separates our planet from the stars. Since the space-age began in the late 1950s humankind has explored space in the regions of every planet, about the sun, asteroids and comets. We have put man on the moon and rovers on Mars, but one thing we have never done is to send a craft far beyond the boundaries of our solar system. We have never reached the stars, even our closest star, Proxima Centauri.

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The reason? The distances are just too great. Voids in space are the result of the way gravity causes matter in the universe to ‘clump together’, and the interstellar void is the void between our solar system and the rest of the universe. The boundary of our solar system is about 11 billion kilometres from Earth. Very few probes have touched this boundary, such as the Voyager 1, which was released by NASA in 1977 and made world news as it approached the boundary – this year. This journey took 36 years because the Voyager travels at only 0.00006 per cent of the speed of light, while our closest star is 4.2 light years away from the centre of our solar system. This means it takes a beam of light from that star more than four years to travel to Earth – and the only way to reach that star in the same time is to travel as fast as light does.


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The Voyager 1 space craft. Image: NASA/JPL-Caltech

The only way we could build a spacecraft which could travel near the speed of light, would be to make it as small and as close to massless as possible. Light is made up of elementary particles called photons, which are known by physics to be massless. So the only way we could build a spacecraft which could travel near the speed of light, would be to make it as small and as close to massless as possible. Until now, this has not been possible; the Voyager 1, which in 1977 was the newest technology, weighs 722 kg – not even close to massless! Its mechanisms and engines, designed to control and power all aspects of its flight, are the major contributors to its weight. Guided flight Since a spacecraft is subjected to many forces during postlaunch flight, such as drag, gravity and solar pressure (the ‘force’ of the sun's rays pressing against an object in space), it needs to be controlled to keep it on its planned flight path. There are two kinds of control – motion control and attitude control. Motion control is applied to maintain a chosen path, while attitude control dictates how the craft is positioned at each point along that path. Correct position is extremely important, for example if the spacecraft uses

A newspaper headline about the first person on the Moon. Image: London Herald

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cameras to record images of the planet which it orbits. Motion control is carried out mainly by engines, while attitude control is more complex and achieved in many ways. First, sensors are required to feed in information about how the spacecraft is orientated (relative to its initial position or an immovable object) at a given time. These can be gyroscopes, horizon sensors (which detect light or warmth of the atmosphere), sun sensors (which analyse light rays to detect the position of the sun) or earth sensors. This information must be gathered and translated electronically to the actuators, where the attitude control is carried out. These are also diverse, from basic thruster engines to solar sails, which produce thrust in reaction to reflected sunlight. These attitude control methods are especially important to nanospacecraft which, says Dr J. Biggs of the Strathclyde space laboratory, UK, have a tendency to tumble post-launch. But nanospacecrafts’ small size means that they need less equipment to sense and interpret these changes in position, and limited propulsion systems to correct them. New strategies are needed to overcome these limits.

A typical motion and attitude control plan for a drifting satellite. Image: Adaptation, using the satellite image NASA Marshall Space Flight Centre (NASA-MSFC)

Power source for satellite

Positively-charged plate Negatively-charged plate

Fluid containing nanoparticles

Liquid reservoir Structure of a nanoparticle thruster. Image: Adapted from http://nextbigfuture.com/2009/07/nanofet-nanoparticle-field-extraction.htmlCentre (NASA-MSFC)nextbigfuture.com/2009/07/nanofet-nano-particle-field-extraction.html

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Meeting the challenges The technology which made the Voyager 1 so heavy also gave it advantages of computational power and engine capacity. For example, it is powered by three large radioisotope thermoelectric generators which each provide 157 watts of power. How can the tiny nanospacecraft compete? One option, suggested by the Strathclyde team and others, is a zero-propellant mission. In this kind of mission, re-orientation of the spacecraft after launching is achieved by setting the spacecraft on a special attitude trajectory that allows the position to be corrected as a natural response, without the need of thrusters. This method uses the kinematics (literally ‘motionstudy’) and dynamics of the whole spacecraft system (which means the spacecraft itself as well as potential ‘hazards’ to its planned motion in its environment, such as gravity or solar pressure) to create a natural or free motion that still sticks to a clearly defined flight path. As a result, the torque demands are low or zero, since the correction of position uses the natural motions of the spacecraft within its environment. This special attitude trajectory is produced by expressing the whole system as a problem that can be solved using mathematical techniques, which use the symmetry of the spacecraft system. This special trajectory can be programmed into the spacecraft pre-flight and can


Besides the ability to finally investigate the depths of interstellar space, nanospacecraft also give us a chance to lay the groundwork for human planetary exploration. be simply tracked as the flight progresses. This does not require much on-board equipment. Another method being explored by Prof. B. Gilchrist of Stanford University and his team uses engines, but tiny engines which use nanoparticles – objects one billionth of a metre small – as a propellant. While these engines, like the zero-propellant techniques, cannot be used to launch the spacecraft, they are equally useful for controlling the position. The engine is filled with a liquid containing nanoparticles between two charged plates. The charge on the plates accelerates the nanoparticles to break the upper boundary of the liquid, causing a thrust in reaction to their motion – on the small scale! The liquid chambers are etched onto 1 cm sized pieces of silicon using technology currently used in the semiconductor industry. Millions of these tiny engines fit on 1 cm2. Since these powerhouses come in such small packages, a thrust source can be built up from watts to megawatts in a tiny space, allowing engine design to be carried out independently of spacecraft design. What do we gain? Besides the ability to finally investigate the depths of interstellar space, nanospacecraft also give us a chance to lay the groundwork for human planetary exploration. Sending humans to different planets means we need close-proximity information about these planets, for example details about the surface and the precise chemical makeup of the planetary atmosphere. The accuracy of these measurements is currently limited by the lack of observational approaches that can fit within mission cost requirements. Nanospacecraft may be used to access these sites and help us to obtain close-proximity information about planets across the solar system. Closer to home, nanospacecraft could be used in arrays – arrangements of several spacecraft together – to monitor the development of solar winds and solar flares, which interfere with our satellite communication systems. Nanospacecraft could also be used in arrays to capture multiple viewpoint pictures of asteroids, giving us precise information about their structure, which would help us to assess the risk of such asteroids becoming unstable and colliding with the Earth – and to take steps to prevent this. While the development of these spacecraft is still beginning, at least compared to giants like the Voyagers, one thing is certain – from reaching the stars to defending our planet, these tiny tots have a huge potential. Q Helen Henninger currently studies details of the optimal satellite transfer problem in the McTao research team at INRIA Sophia-Antipolis in France. She qualified at Rhodes university, Grahamstown, SA with a research interest in geometric control theory.

Images of asteroid Itokawa taken by the Hayabusa satellite. Itokawa has a moderate earth-impact risk. Nanospacecraft will greatly improve the accuracy of photographs like these. Image: Japan Aerospace Exploration Agency (JAXA)

The actual size of a nanospacecraft. Image: Japan Aerospace Exploration Agency (JAXA)l

References McLean C, Pagnozzi D and Biggs J. Computationally light attitude controls for resource limited nano-spacecraft, In Proc. 62nd International Astronautical Congress 2011. pp. 1258-1263. Cape Town. Musinski, L. Liu, T, Gilchrist, B, Gallimore, A. Electrostatic charging of micro-and nano-particles for use with highly energetic applications. Journal of Electrostatics 2008;67:54-61. Gilchrist B, Gallimore A, Keidar M, Musinski L, Liu T. United States Patent 7,516,610, Scalable flat-panel nano-particle MEMS/NEMS thruster http://en.wikipedia.org/wiki/Attitude\_control http://en.wikipedia.org/wiki/Voyager\_1

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Emerging leaders: Seven South African women take on Silicon Valley and STEM

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ith science, technology, engineering, and mathematics (STEM) widely regarded as critical to national economies, expanding and developing the STEM workforce is a critical issue for many governments, industry leaders, and educators. Despite the tremendous gains that women have made in education and the workforce during the past decades, progress has been uneven, and certain scientific and engineering disciplines remain overwhelmingly male. While statistics show that the number of women in science and engineering is growing, men continue to outnumber women, especially at the upper levels of these professions. (Why so few? Women in STEM, AAUW, 2010) Great strides are constantly being taken across the globe to elevate and promote women in STEM, and TechWomen is one such initative.

Emerging leader countries.

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TechWomen TechWomen (www.techwomen.org) is an initiative of the US Department of State’s Bureau of Educational and Cultural Affairs, formed under Former Secretary of State Hillary Clinton’s leadership. TechWomen is managed by the Center for Women’s Leadership Initiatives (WLI) at the Institute of International Education® (IIE). TechWomen empowers, connects, and supports the next generation of women leaders in science, technology, engineering, and mathematics (STEM) from Africa and the Middle East by providing them the access and opportunity needed to advance their careers, pursue their dreams, and inspire women and girls in their communities. Through a five to six week mentorship and exchange, TechWomen strengthens participants’ professional capacity, increases mutual understanding between key professional networks, and expands girls’ interest in STEM careers by exposing them to female role models. Over the last two years, TechWomen participants hailed from Algeria, Egypt, Jordan, Lebanon, Morocco, the Palestinian Territories, Tunisia, and Yemen. The 2013 TechWomen programme has expanded to include women from Cameroon, Kenya, Libya, Nigeria, Rwanda, Sierra Leone, South Africa, and Zimbabwe. From arrival, emerging leaders are immersed in the innovative, constantly evolving culture of Silicon Valley and the San Francisco Bay area. emerging leaders work closely with their professional mentors to design meaningful projects while exploring the San Francisco Bay area with their cultural mentor and fellow programme participants.


Who are the South African-based emerging leaders? For 2013, out of over 1Â 800 women who applied, a total of 78 emerging leaders have been selected to participate in the TechWomen programme. Seven ladies will leave Johannesburg for the magical Silicon Valley on 30 September 2013 in the first cohort of South African-based emerging leaders to participate in TechWomen. 9| 3 2013

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A brief introduction to each of the seven South Africa-based TechWomen emerging leaders’ ‘STEM credentials’ University of Natal and has recently completed her MBA with GIBS. She currently heads the Electrical Engineering department at Eskom’s Hendrina Power station. She serves as a Non-Executive Director of Zenzele, an incubator of SEDA. In San Francisco, she will be hosted by Pacific Gas and Electric company, one of the largest utilities in the US, whose primary business is the transmission and distribution of energy.

Ngwana Matloa – IT entrepreneur

Ngwana Matloa is a Business Development Manager at ABOT Technology, a technology company providing information management services and products to SMMEs and educational institutes. She started her ICT career as a software developer and has a BSc Information Technology (Honours) degree. She is also a certified ITIL v3 and Microsoft Dynamics CRM Implementation Consultant with a Diploma in Business Analysis. During the TechWomen programme she will be based at Disney Interactive and learning about Big Data and its effective application to businesses.

With a food industry background in product development, quality assurance and process improvement, Sandra currently works as a Certification Auditor focusing on food safety management systems at Bureau Veritas. Sandra will be hosted by her professional mentor at Impact Hub Oakland in downtown Oakland, an innovation collaboratory and co-working start-up for community leaders, change-makers and social entrepreneurs. Nomso Kana – nuclear/radiation scientist

Nomso has a pure and applied chemistry postgraduate background and currently works at the South African nuclear energy corporation (NECSA) as a Scientist. Her work specifically involves determining purity of radio isotopes used for medical purposes, through various radiological analytical assays and development of techniques used to measure radiological nuclides in environmental media. She has been professionally matched with a mentor from Ericsson, who will work with her on a collaborative project during the four-week stay in San Francisco. Sandra Tererai – food technologist

Makgola Makololo – electrical engineer

Makgola graduated with a BSc in Electrical Engineering from the 40

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Sandra holds a BSc in Food Science and Technology from the University of Zimbabwe and a postgraduate Honours in Technology Management from the University of Pretoria.

Chioniso Dube-Hachigonta – robotics engineer

Chioniso has a BSc in ElectroMechanical Engineering and an MSc in Electrical Engineering, both from the University of Cape Town. She currently works as a Robotics Researcher with the Mobile Intelligent


THE ROAD TO BECOMING A 2013

TECHWOMEN EMERGING LEADER

Autonomous Systems group at the CSIR, developing robotic systems for various applications such as mine safety inspection robots and humanoid robots that work as human assistants. Chioniso will be hosted at Juniper Networks by her professional mentor Lisa Ramirez, who has extensive experience in the delivery of technology products and processes.

Total sumitted applications:

1 870 Percentage increase in applications received in 2013 vs. 1012:

330 Number of people directly involved in the selection process:

University of Cape Town. Sibaliso will be hosted by her professional mentor, Susan Hollingshead, at Sungevity in San Francisco, one of the leading designers for solar home systems.

125 Countries, across Africa and the Middle East represented by the applicants:

16 Number of applicants invited to participate in the 2013 programme:

78 Zimkhita Buwa – SAP Business Intelligence Consultant

Zimkhita studied at Universiti Teknologi Petronas, Malaysia, majoring in Information Systems. She is currently part of the SAP Business Intelligence team at the City of Cape Town and is a data geek. She is a SAP Mentor and heads up the Business Analytics Special Interest Group for African SAP User Group. She also serves on the Executive Board of SiliconCape. She will be hosted by her professional mentor at Autodesk, a world leader in 3D design software for entertainment, natural resources and engineering. Sibaliso Mhlanga – Scientist

Sibaliso studied for an Honours in Applied Physics and her major study was on Renewable Energy Resources, specifically implementation of solar systems for homes and industries. She is currently studying for a Masters in High Energy Physics with the

Miles participants will travel to reach San Francisco:

126 500

The TechWomen experience doesn’t end in California or Washington, D.C.! After participating in the programme, emerging leaders are expected to use the networks established and knowledge and skills gained to help develop entrepreneurship and innovation in STEM within their home countries. Emerging leaders also act as role models for and inspire the next generation of young girls interested in STEM. The South African TechWomen emerging leaders are keen to share the knowledge and insights that they will gain from the TechWomen programme focusing on how these can be used to help foster female innovators and entrepreneurs in STEM within South Africa, and the sub-Saharan region (why not?!). The South African STEM ambassadors to Silicon Valley leave with high hopes and expectations including: n Professional development and accomplishing learning goals n Acquiring business skills for upcoming start-ups and long-term professional relationships n Gaining technological and entrepreneurial skills that will help maximize the enthusiasm for learning science, technology, engineering and mathematics in their communities n Gaining insight to facilitate creation of a multi-layer STEM programme for professional, graduate students and high school learners tailored to the South African region.

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Diver Peter Timm, who originally discovered coelacanths in Jesser Canyon at a depth of over 100 m below sea level.

iSimangaliso’s Coelacanths

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Sodwana Bay within iSimangaliso Wetland Park is rated as one of the top ten dive destinations in the world. The coral reefs contain over 1 200 species of fish as well as a variety of underwater seascapes and marine flora and fauna, including the extremely rare coelacanth.

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eventy-five years after the first coelacanth was trawled off East London and thirteen years after their discovery in the Sodwana Bay section of iSimangaliso Wetland Park, an international research collaboration under the auspices of the iSimangaliso Wetland Park Authority is underway. It is one of 148 research projects currently being undertaken in iSimangaliso, South Africa’s sole marine and terrestrial World Heritage site. With only 46 marine World Heritage sites globally iSimangaliso is considered one of the ‘Jewels of the Oceans’. On the recently completed coelacanth research expedition, scientists worked alongside experienced Trimix divers, including Peter Timm, who discovered the coelacanths in Jesser Canyon off Sodwana Bay and awardwinning underwater photographer, Laurent Ballesta, Director of Andromede Oceanology in France. Laurent raised the finances for the expedition and catalysed new research links between South African scientists and coelacanth researchers from the Natural History Museum in Paris. The South African Institute for Aquatic Biodiversity (SAIAB) and the South African National Biodiversity Institute (SANBI) are leading the research effort, building on previous research undertaken through the African Coelacanth Ecosystem Program. The collaborating Parisian scientists have had few opportunities to study living coelacanths and will now be able to combine field data with the results from detailed anatomical and other laboratorybased work on the coelacanth specimens from the National Museum’s collection.


The 'giraffe' enables three-dimensional videography with a high-tech camera.

'The expedition represented an important opportunity to build the knowledge base on coelacanths and marine ecosystems with new opportunities for science and deepsea research capacity. This knowledge will be used to inform the iSimangaliso Authority’s conservation and protection strategies for this flagship species' said Park CEO Andrew Zaloumis. The research is multi-disciplinary and involves bathymetric mapping, population and genetic research, behavioural studies and a broader exploration of biodiversity in the deep-water habitats of iSimangaliso. iSimangaliso Wetland Park was listed as South Africa’s World Heritage site in 1999 in recognition of its unique ecosystems and high biodiversity. The Park forms one of only two marine World Heritage sites within the Indian Ocean region. With increasing impacts on marine World Heritage sites from climate change, pollution, habitat destruction, overfishing and invasive species, international research collaborations like the coelacanth expedition are becoming more important. The research expedition was linked with a deep mixed-gas diving team and the production of a science documentary. Trimix divers documented the first three coelacanths in iSimangaliso in 2000 and have added at least six new coelacanths into the catalogue that showcases the distinct spot patterns of each individual. They have also improved on the photographs of several known coelacanths and have made a valuable contribution to the understanding of South Africa’s coelacanth population. The divers are more manoeuvrable than either submersibles or remotely operated vehicles (ROVs) and are able to use new and advanced technology to capture imagery of the coelacanths to study their unique features and behaviour. This included three-dimensional videography with a high-tech camera affectionately known as 'the giraffe'. As part of the research expedition, divers attempted to feed a coelacanth to assess the role of the coelacanth’s inter-cranial joint in

The team preparing for a dive to the depths of Jesser Canyon at Sodwana Bay.

feeding. Divers placed a hydrophone in a cave where most coelacanths have been observed in the hopes of finding out whether coelacanths made any noises. A low-light camera was also positioned at the entrance to document the presence of fish at set intervals. These data are still being processed. The expedition also used an ROV which undertook a wider search for coelacanths in the Park. iSimangaliso Wetland Park has an extensive marine protected area and the ROV completed dives from Island Rock Canyon in the north to Chaka Canyon in the south. No new coelacanth locations were found. Highlights of the ROV dives included sightings of a thresher shark on the canyon margin, a onemetre long red steenbras, a first sighting of a ‘seventy four’ fish in the canyons and other new records and potential new species. Q 9| 3 2013

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One of the big things in bioinformatics is visualisation. This image, published in the journal Cell, shows a vast gene regulatory network in mammalian cells that could explain genetic variability in cancer and other diseases. Image: http://www.bioquicknews.com/node/600

Bioinformatics

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he is crazy about her work and never has enough time to do all that can be done! The job also comes with some serious hardware – like a highperformance computing cluster boasting over one Terabytes of RAM, more than 200 processors and over 60 Terabytes of storage. Meet Anelda van der Walt, a bioinformatics analyst in the DNA sequencing unit at Stellenbosch University’s Central Analytical Facility. What is a bioinformatician? Bioinformaticians are scientists who work on some aspect of Life Sciences research with computers as their main research tools – they either analyse data, develop software, or develop algorithms to deal with complex problems. Bioinformaticians can work in a laboratory and perform their own experiments or they can use data generated by other laboratory specialists to work on. But being a bioinformatician also means thinking out of the box and having fun! Take the Facebook game Fraxinus, for example. Researchers at a lab in Australia are trying to get to the root of the ash tree’s susceptibility to a fungus that infects and kills the tree. They are now relying on crowd-sourced analysis by asking Facebook users to help analyse the genomes of the ash tree and the fungus.

Anelda van der Walt. Image: Wilda Fourie-Basson

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What did you study to become a bioinformatician? My career started with a BSc degree at the University of Pretoria, and then Honours at Stellenbosch University with


❚❚❚❙❙❙❘❘❘ Careers

Some cool links to explore: https://apps.facebook.com/fraxinusgame/ http://circos.ca/intro/published_images/ http://jmol.sourceforge.net/screenshots/ http://human.brain-map.org/static/brainexplorer

Genetics and Biochemistry as majors. I then completed an MSc in Bioinformatics at the South African National Bioinformatics Institute at the University of the Western Cape. I am now working as a bioinformatics analyst at Stellenbosch University’s Central Analytical Facility. But you can come to bioinformatics from basically any field. One of my colleagues studied actuarial sciences, another applied mathematics, and another microbiology. Even medical doctors and engineers can move into the field of bioinformatics. As far as I know there are no undergraduate degrees in bioinformatics in South Africa at the moment, but there are several institutes offering postgraduate courses such as Honours, Masters, and PhDs in bioinformatics. Describe a typical day in the life of a bioinformatician Sitting behind my computer! There are various ‘flavours’ of bioinformaticians. If you enjoy protein work, you might be looking at three dimensional (3D) modelling of protein structures. If you are more mathematically inclined, you can develop new algorithms to improve the way 3D modelling is done, or you could be writing software that can be used by biologists to perform 3D modelling of your protein molecule. Some bioinformaticians might be more closely associated with the biology and you may prepare your own samples in the laboratory and perform your own data analysis and even do some minor scripting (writing little programs). It really can be whatever you want it to be, with as much or as little programming as you like. Why do you think this kind of work is important? Over the past few years technological advances in the genomics field have led to huge increases in the data volume that can be produced in laboratories. Biologists and medical scientists cannot find important clues in data any more by making use of traditional analysis methods only. Bioinformaticians support biological and medical research by finding ways to move, store, analyse, and interpret these large datasets. Without bioinformatics the human genome would not have been sequenced and Angelina Jolie would not have known that she is at risk of developing cancer later in life. What kind of research can be done using bioinformatics? If you are in a Life Sciences-related field and you are generating data and analysing it on a computer, you are using tools and algorithms developed by bioinformaticians (excluding of course Microsoft Excel). Some of the projects currently running in South Africa that are making use of bioinformatics include human genome sequencing to look

Image: http://genome.ucsc.edu/cgi-bin/hgTracks?hgHubConnect.destUrl=..%2Fcgi-bin%2FhgTracks&clade=mammal&org=Hu man&db=hg19&position=chr11%3A12%2C399%2C026-12%2C556%2C903&hgt.positionInput=enter+position%2C+gene +symbol+or+search+terms&hgt.suggestTrack=knownGene&Submit=submit&hgsid=344717807

What is Bioinformatics? Bioinformatics is to conceptualise biology in terms of the physical and chemical characteristics of molecules and then applying informatics techniques (derived from disciplines such as applied math, computer sciences and statistics) to understand and organise the information associated with these molecules, on a large-scale. Source: Luscombe NM, Greenbaoum D & Gerstein M. What is Bioinformatics? A Proposed Definition and Overview of the Field. Method Inform Med 4/2001:346-358. Accessed online on 14 August 2013 at http:// bioinfo.mbb.yale.edu/what-is-it/omes/

at genetic causes of various genetic diseases and cancers; genomics analysis of interesting animals such as sharks; biodiversity studies; food scarcity-related projects; and development of software for data analysis. But these are only the tip of the iceberg. How do you stay up-to-date with what is happening in this field? I read articles published in academic journals, follow blogs of experts and attend national and international conferences. Did I mention read, read, and more reading? What do you like the most about your work? I love most aspects of my job. But what I like the most is the opportunity to be part of a very diverse group that gets to work on unbelievably interesting and challenging projects. I also enjoy working with people who are very passionate about their research. What do you dislike the most about your work? The fact that I do not have enough time to do everything there is to do. Where do you see this field going in the future? There are no limits. The ‘big data’ problem has only recently arrived in the biological sciences domain. There are uncountable unsolved problems related to health, population and food scarcity, to name but a few. Bioinformatics is definitely here to stay. Would you recommend this career path to a student? Yes absolutely. If you enjoy problem solving and interesting challenges, bioinformatics is a phenomenal field to get involved in. There are several career paths open to you – you can stay in academia, work for industry or even start your own consulting or software development company. q 9| 3 2013

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ASSAf News

ASSAf Member wins coveted prize Prof. Alan Morris of the Department of Human Biology, University of Cape Town, has won the 2013 WW Howells Book Prize in Biological Anthropology of the American Anthropological Association with his book Missing and Murdered. The Howells Prize was inaugurated in 1993 in honour of Prof. Emeritus William White Howells of the Peabody Museum at Harvard. He is a past president of the American Anthropological Association and a distinguished scholar who has published several landmark books in physical anthropology. The prize is annually awarded to a book in the area of biological anthropology. Books may be single or multiply-authored, but not edited. They should have been published within the last 3 - 4 years, and once nominated will remain on the list for 3 - 5 years depending on their date of publication. Nominated works should represent the highest standard of scholarship and readability. They should inform a wider audience of the significance of physical/biological anthropology in the social and biological sciences, and demonstrate a biocultural perspective. ASSAf Member and Associate Editor of the South African Journal of Science, Prof. Alan Morris. Image: ASSAf

SciELO-South Africa open access platform launched The first open access site for scholarly journals on the African continent, the newly certified SciELO-South Africa, was launched by Dr Khotso Mokhele, on behalf of the Minister of Science and Technology, Mr Derek Hanekom, on 22 July 2013. Dr Mokhele is the founding President of the Academy of Science of South Africa (ASSAf). The open access platform (free to publish and free to read), established

From left: Mr Abel Packer, Director of the SciELO Network and Dr Khotso Mokhele, keynote speaker. Image: ASSAf

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in 2009 when ASSAf pioneered the implementation of online journals in the country, culminated with the certification of the platform as a fully operational collection indexed in the SciELO Network Global Portal in April 2013. Since January, all SciELO journals also appear on the Web of Knowledge (WoK) platform as the SciELO Citation Index. The WoK interface enables subscribed users to access the journal collection Web of Science (WoS) and SciELO together. Thomson Reuters is the leading source of intelligent information for businesses and professionals and the world's most powerful search and discovery platform. Open access publishing allows research literature comprising academic peerreviewed articles and journals, conference papers and theses to be placed in an online portal from which they can be downloaded for use. SciELO-South Africa indexes high-quality South African scholarly journals, extending beyond the Web of Science (WoS) Thomson Reuters Inc indexed titles, and provides free worldwide electronic access to the content of these journals. Very few people in developing countries have access to traditional peerreviewed academic journals in printed form. Publishing in scientific journals is a common and powerful means to disseminate new research findings, and visibility and credibility in the scientific world require publishing in journals that are included in global indexing databases. Limited access leads to a low rate of usage of these publications and thus to the phenomenon known as ‘lost science’. The creation of an open access platform

for these journals will assist greatly in overcoming the obstacles of price and accessibility, and will enhance the international visibility of South African research. Open access does not equates to ‘selfpublishing’ – all articles conform to the traditional process of journal publishing, entailing critical reading by several peer reviewers who ensure that a rigorous standard of research is upheld. Each journal considered for inclusion on SciELO-SA is required to conform to stringent quality control standards, ensuring that only the best journals are published online. Actual usage by scholars and scientists is monitored by the indexing system in various ways, including journal impact factors and article citation and download statistics. The South African Journal of Science, published by ASSAf, was the first peerreviewed journal to be fully open access on the SciELO-SA platform. Currently there are 26 journals available on the SciELO platform and it is expected that at least 180 journals will eventually be published on the platform. These include titles such as the South African Medical Journal, South African Journal of Education, Water SA, and the South African Journal of Animal Science. Since its inception in Brazil, the SciELO indexed platform has been successfully implemented in eight countries, mostly in Latin America, with others being in the developmental phases. For more information about SciELO-SA, visit www.scielo.org.za/ For more information about Web of Knowledge, visit http://wokinfo.com/


❚❚❚❙❙❙❘❘❘ News

Science as art: It’s a beautiful world under the microscope by Mike Fricano This beautiful image is not an artsy photo of a pink flower. It’s a picture of an electrically conductive molecule captured with a scanning electron microscope. This image, titled ‘Tetraaniline in Full Bloom’, won first place in the Materials Research Society’s ‘Science as Art’ competition this spring for UCLA inorganic chemistry PhD candidate Yue Wang. In addition to being beautiful, this molecule has potential for sensors and organic supercapacitors because of its shape and electrical conductivity. The ‘flower’ in the upper right is actually aggregated sheets of doped aniline oligomers and the black and white leaves are flexible sheets. Who knew the microscopic world could be so spectacular? Source: UCLA Image: UCLA

Power of populations Population genetics unravels mysteries of both biology and natural history Two recent studies from Harvard Medical School researchers demonstrate the power of population genetics for probing not only human biology but human history as well. One study describes the discovery of 20 million ‘missing’ base pairs of the human genome sequence. The other shows that the population makeup of modern-day India is the result of recent population mixture among divergent demographic groups. In the Latino Genomes Study, researchers used a mathematical modelling system that analysed data from the genomes of Latinos to find previously unaccounted-for genetic material. The findings in the Indian Population Mixture Study shed light on present-day Indian populations and suggest that the current structure of the caste system came into being relatively recently in Indian history.

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

Source: Harvard University

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

This illustration shows that between 4 000 and 2 000 years ago, intermarriage in India was rampant. Image: Thangaraj Kumarasamy

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


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Books

Adventures in conservation Saving the White Lions: One Woman’s Battle for Africa’s Most Sacred Animal. By Linda Tucker. (Cape Town. Struik Nature. 2013) A broken steering column while on a moonless night ride in the Timbavati bushveld changed the course of Linda Tucker’s whole life. She and her husband, along with the other passengers, were rescued from a pride of angry white lions by a Shangaan Medicine Woman, Maria Khosa, also known as the Lion Queen of Timbavati. Three years later Linda gave up her career in the European fashion industry and returned to South Africa as a pupil of Maria’s. She learned that her destiny was to be the Keeper of the White Lions and with the birth of Marah in the town of Bethlehem on 25 December, 2000 she dedicated her life to saving the white lions from the trophy-hunting industry. This is an autobiography, but to quote Andrew Harvey in his foreword, ‘Saving the Lions can be read as a thrilling adventure story.’ It is one of those ‘unputdownable’ books. A joy to read and a yearning for ‘more’ when you reach the last page. (Review by Margaret Aldridge.)

colour-coded headings which help in identifying the subject matter required. There are an abundance of excellent drawings and photographs and the print is easy to read. Each section also gives a little guide to ‘places to see’ which are relevant to the content and give scope and encouragement for further study and exploration. (Review by Margaret Aldridge.)

Who we are All About South Africa: Our country, its people, history, cultures, economy and wildlife. (Cape Town. Struik Lifestyle. 2013.) This fully updated 7th edition gives a historical picture of South Africa from ‘long, long ago’ to the 21st Century, covering all aspects of life in South Africa. The people, the community, the wildlife, and so on. The contents are well laid out under clear,

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Wild vet Bushvet: My hidden battles to save wildlife. By Clay Wilson with Tony Park. (Cape Town. Umuzi. 2013.) Clay Wilson started life in Johannesburg, but moved to Mexico when he was two. Although he started out at university in Florida he finished his studies at Onderstepoort, where he qualified as a veterinarian, so Africa was in his blood. After practising in Floria for 18 years he moved to Botswana to work as a wildlife vet in Kasane – which was the inspiration for this book. Just about anyone who loves animals probably has dreams of becoming a vet at some stage. Becoming a wildlife vet is even more exciting – although also often heart-rending, as Clay found when confronted by the ravages of poaching, accidents and disease. Across Africa, the tension between the needs of people and the needs of the indigenous wildlife leads to potential conflict, and this followed Clay through his adventures as a wildlife vet in Botswana. An unputdownable read, this book will inspire many in the fight to save Africa’s wildlife.


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Pocket trees Pocket guide to trees of southern Africa. By Piet van Wyk. (Cape Town. Struik Nature. 2013.) Pocket guides are enormously useful if you want to know about the world around you. There are many large and beautiful tree guides available for southern Africa, which are lovely to have on your shelves, but this small volume is the one that you will keep in your backpack when you are hiking, or visiting a park. Southern Africa has a particularly rich variety of tree species, both indigenous. This little guide is an excellent introduction to the trees of the region, describing and illustrating 132 species. Each species account shows the key characteristics used for identification as well as outlining the commercial and medicinal use of the plant. The photographs are clear, showing the tree itself and the leaves and fruits separately for ease of identification. The introduction outlines the vegetation regions of southern Africa and there is a useful glossary and a good index, making this an easy book to use.

Summer in the desert

Kalahari Summer in photographs and oils. By Robert Grogan. (Cape Town. Struik Nature. 2013.) This is a coffee table book with a difference. The illustrations are made up of wonderful oil paintings, complemented by magnificent photographs. The landscapes and wildlife are all of the summer – a particularly rich season in this desert region. It is the transformation of the landscape that attracts Robert Grogan and his wife Lee – the summer cloud banks and the startling local transformation caused by heavy rains. His photographs are not only of the big cats and the raptors, but also of the less obvious butterflies and wildflowers. This beautiful book brings the lush Kalahari summer season vividly to life – encouraging a visit to the area.

Renewable energy Is Chernobyl dead? Essays on energy: renewable and nuclear. By CM Meyer. (Muldersdrift. EE Publishers Ltd. 2011.) According to Chris Meyer, to understand what happened at Fukushima after the Japanese tsunami in March 2011 and how it may affect the future, we need to go back to the Chernobyl, Three Mile Island and Kyshtym accidents. Nuclear energy is one of many potential sources of renewable energy and this is what Meyer starts with, not least because of the fears that surround the use of this form of energy. Meyer outlines the questions that are facing us – are we running out of oil? Is mass transport possible without oil? Should we be switching to electric vehicles? What about biofuels? Is wind energy the answer? And of course – what about the safety of nuclear power stations – particularly pertinent in the light of the continuing problems at Fukushima. This book contains well-written, easy-to-read accounts of the various sources of renewable energy, outlining the pros and cons of the various technologies in a way that is understandable to the lay person. The historical accounts are particularly interesting, putting the whole issue of alternative and renewable energy into perspective – many ideas are far from new! 9|3 2013

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❚❚❚❙❙❙❘❘❘ Astronomy News

Multi-wavelength view of HXMM01. Image: University of Western Cape

Galaxies merge to form star factory By Yolana Makosi, University of the Western Cape Do big star-rich galaxies form slowly over long periods of time, with slow absorption of smaller galaxies and stately formation of stars? Or do they form swiftly when smaller galaxies crash together in a furious burst of star formation? Astrophysicists from the United Kingdom, America, France and South Africa – including the University of the Western Cape's (UWC) Astrophysics Group – may have the answer in a recent paper published in the 22 May online issue of Nature. When the source HXMM01 was first identified by the Herschel Space Observatory as part of the Multi-tiered Extragalactic Survey observing programme, it seemed to be just one massive, sub-millimetre-bright galaxy. Such a strong sub-millimetre emission (that is, with wavelengths of under a millimetre but larger than visible light) is often due to a single distant galaxy forming stars at a high rate, and possibly to the gravitational lensing of a background galaxy by intervening (foreground) galaxies. However, further observations by several telescopes on the ground and in space as part of a coordinated multi-wavelength campaign showed that it was actually composed of two smaller (though still massive) colliding spiral galaxies, connected by a bridge of material. A careful analysis of the various images showed that the gas from the two galaxies is rapidly coalescing into stars, at a rate of about 2 000 Sun-sized stars formed per year – more than a thousand times the rate of star formation in our own Milky Way Galaxy. By measuring the rate of star formation in the two merging galaxies, as well as the amount of gas that still remained in them (about 200 billion solar masses each, or enough to form 200 billion Sun-sized stars), the researchers determined how long it would take before the gas resources were exhausted and the galaxies settled down into one big (super-giant, in fact) elliptical galaxy – around 200 million years.

And while that may sound like a very long time, it's really very short when compared to the age of the universe as a whole (around 14 billion years) or even of our own Sun (around five billion years). And since HXMM01 is 11 billion light years away, this merger happened during a time when our galaxy was only about three billion years old ‘Largely thanks to the launch of two long-wavelength satellites, NASA’s Spitzer in 2003 and ESA’s Herschel in 2009, one of the most important astrophysical quests over the last ten years has been to try and map these processes as we look back in time,’ said Dr Mattia Vaccari, study co-author and SKA Postdoctoral Fellow at UWC's Astrophysics Group, part of the Physics Department within the Faculty of Natural Sciences. ‘Because light takes time to reach us, observing galaxies far away in space allows us to look back into the past phases of galaxies’ lives. We can use the sensitive instruments at our disposal to probe faint distant galaxies and thus see the various stages of their formation.’ These findings may help explain a persistent astronomical mystery – why are there so many large and reddish ellliptical galaxies in the young universe? For years, scientists have debated how these elliptical galaxies formed from smaller spiral galaxies (such as the Milky Way our solar system inhabits). One hypothesis has it that spiral galaxies slowly grew into ellipticals by slowly absorbing many other galaxies with low star formation rates. Another holds that powerful collisions between galaxies led to increased star formation rates. This work provides powerful support for the merger/ collision idea: it seems that when it comes to star formation, the big galaxies of the early days of the universe grew up very quickly – and the biggest galaxies may be the result of smash-ups rather than slow accumulation. 9| 3 2013

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

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

Choose your area of study from:

Biological and Life Sciences: These include the micro and macro study of life. Courses range from the biochemistry of molecules such as DNA, RNA and proteins, and the molecular structure and function of the various parts of living cells, to evolution and the physiological and behavioural study of plants and animals. Earth Sciences: The Earth Sciences study the processes that shape the complex interactions between the solid earth, the oceans, the atmosphere and the organisms that have evolved on Earth. Fields of specialisation include the exploration for, and mining of minerals, the prediction of weather and earthquakes, the evolution of species through time, the state of our natural environment and how we can best manage the environment. Environmental Sciences: This involves the preservation and rehabilitation of our natural resources and can be studied under the Earth or Biological Sciences. Environmental Science studies the importance of the physical, biological, psychological, or cultural environment as factors influencing the structure or behaviour of animals, including humans. Mathematical Sciences: Pure Mathematics is a developing science. Mathematical Statistics and Actuarial Science are important in industrial and governmental planning and to the insurance industry. Applied Mathematics has applications in banking, finances and industry. Computer Sciences offers the understanding of computer hardware and software, in all its applications. Physical Sciences: Areas of study range from nuclear, particle, solid- and liquid-state physics, electricity, electronics, magnetism, optics, acoustics, heat and thermodynamics, to the synthesis of new compounds and the changes that take place during chemical reactions. New options exist at Wits for the study of Materials Science and Chemistry with Chemical Engineering. Scientists in Materials Science develop new ways of working with materials in responding to the challenges facing industry such as energy-fuels and environmental concerns, while in Chemistry with Chemical Engineering they use their knowledge of chemistry to design, operate and construct processes useful in the chemical industry.

Is a career in science right for you? If you have a natural curiosity about the world we live in, care about conservation and the use of our natural resources, enjoy solving problems and are good at mathematics, then a career in science could be an excellent choice for you.

Need to know more? Contact the Student Enrolment Centre, Tel: 011 717-1030, E-mail: admission.senc@wits.ac.za

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❚❚❚❙❙❙❘❘❘ Back page science

The Milky Way’s big brother Big Brother to the Milky Way The image below from NASA's Galaxy Evolution Explorer shows NGC 6744, one of the galaxies most similar to our Milky Way in the local universe. This ultraviolet view highlights the vast extent of the fluffy spiral arms, and demonstrates that star formation can occur in the outer regions of galaxies. The galaxy is situated in the constellation of Pavo at a distance of

about 30 million light-years.

orbiting red dwarfs – the most common type of stars – by considering how clouds affect those planets. The finding means that in our Milky Way galaxy alone, 60 billion planets may be circling these faint little stars at distances suitable for life, astronomers say. The new study doubles that number because it indicates clouds act as a temperature-stabilising ‘thermostat’, whose effects are most pronounced where it would be otherwise too hot. The simulations found that if a planet has surface water, clouds result. These will cool down planets in the inner portion of the habitable zone, where it is relatively hot, enabling planets to sustain surface water much closer to their sun than otherwise. ‘Most of the planets in the Milky Way orbit red dwarfs,’ said co-author Nicolas Cowan of Northwestern. ‘A thermostat that makes such planets more clement means we don’t have to look as far [from the star] to find a habitable planet.’ Because red dwarfs are faint, planets need to orbit them much closer than the Earth does our sun to get the requisite warmth. Thus, estimates show the year on a red-dwarf orbiting, habitable planet would last a mere month or two in Earth time.

‘Your peripheral nerves, the ones in the arms and the face, have an inherent ability to regenerate, but only under ideal circumstances,’ says University of Florida biomedical engineer Christine Schmidt. With support from the National Science Foundation (NSF), Schmidt and her team are working to restore nerve function when injuries are more complicated. Surgeons can sometimes move a nerve from one part of a patient's body to another. Schmidt has developed a method that grafts cadaver tissue onto the damaged area to act as a scaffold for nerves to re-grow themselves. Schmidt and her team are also looking at other approaches to stimulate nerve growth directly using as building blocks the natural sugar molecules found in the body. That would eliminate the need to transplant tissue. While the ultimate goal in nerve regeneration is reversing paralysis, Schmidt says intermediate successes, such as improving lung or bladder function, can be invaluable to patients and their families. Source: National Science Foundation Institute of Technology

Source: World Science, http://www.world-science.net

NGC 6744 is bigger than the Milky Way, with a disk stretching 175 000 light-years across. A small, distorted companion galaxy is located nearby, which is similar to our galaxy's Large Magellanic Cloud. This companion, called NGC 6744A, can be seen as a blob in the main galaxy's outer arm, at upper right.

On 28 June 2013, NASA turned off its Galaxy Evolution Explorer (GALEX) after a decade of operations in which the venerable space telescope used its ultraviolet vision to study hundreds of millions of galaxies across 10 billion years of cosmic time. Image: NASA/JPL-Caltech

The Andromeda galaxy… Could planets’ clouds make life more likely? Image: World Science

Source: NASA

Are we alone in the universe?

Helping the body re-grow nerves

By Megan Fellman/Northwestern University and World Science staff A new study doubles the estimated number of potentially habitable planets

by Miles O'Brien Combat, cancer and accidents – all can cause devastating nerve injuries. Sometimes the body heals on its own.

Bone cells, magnified many, many times. Image: Hongjun Wang, Stevens

MIND-BOGGLING MATHS PUZZLE FOR Quest READERS Q uest Maths Puzzle no. 26

A brick weighs 4 kg. If you wanted to make a new brick that was double the old brick’s length, double its width and double its height, how much will the new brick weigh?

Answer to Maths Puzzle no. 25: It does not matter what value C takes on, the number will always be odd!

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, 1 November 2013. 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. 26’ and send it to: Quest Maths Puzzle, Living Maths, P.O. Box 195, Bergvliet, 7864, Cape Town, South Africa. Fax: 0866 710 953. E-mail: livmath@iafrica.com. For more on Living Maths, phone (083) 308 3883 and visit www.livingmaths.com.

The winner of Maths Puzzle no. 25 was Marlie Muller.

9| 3 2013

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SCIENCE IS THE GLUE

e

THAT HOLDS EVERYTHING TOGETHER verywhere you look, you’ll see science hard at work, making society a better place in which to live. From the food you eat to the clothes you wear; from the battery in your cell phone to the mp3 files in your music player, it’s all about the science. South Africa needs more scientists if it is to compete on a global scale; people who are enthusiastic about finding solutions to today’s challenges and pushing the frontiers of the future. If you want to make a real difference, consider a career in science.

Bringing

science

and

learners

together

to

build

the

f u t u r e.

w w w. s a a s t a . a c . z a

Quest 9(3) sept oct 2013  

Quest, Science for South Africa

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