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Science for South Africa

Crystals in history fascinating for thousands of years Crystallography brilliant applications in science Crystal Macromolecular crystallography seeing is believing engineering novel adaptations The maths behind crystals ISSN 1729-830X

Volume 10 | Number 3 | 2014

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


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ontents Volume 10 | Number 3 | 2014

Cover Stories 3 Crystallography – a modern science with a rich history

Catharine Esterhuysen explains how crystallography fits into history and science

9 Crystals: the heart of beauty, brilliance,

beasts, better medicines, technology and art

Andreas Roodt explains crystals all around us

12 Crystal engineering

Len Barbour shows how crystals contribute to materials science and engineering

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16 Seeing is believing

Wolf-Dieter Schubert discusses the applications of crystallography to biology and medicine

21 Crystallography matters

RADMASTE shares the excitement about the International Year of Crystallography 2014

27 (Non) sense in crystals

Neil Eddy takes a look at the fascinating maths behind crystals

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Features 32 The wonderful world of worms

Carol Simon tells us why marine polychaetes are exciting

36 A scientist in Namibia

Jan Smit takes a scientific look at a trip to Namibia

40 Failures of technology or human failures?

Jan Smit, Pulane Masoabi and Rufus Wesi look at some of technology's more spectacular failures

Regulars

12 32 21

News

8 Six things to know about Ebola 34 The world’s largest dinosaur 37 World leaders in mineralogy meet in South Africa 38 Simulating a ‘world without birds’ in a major field experiment 39 125-million-year-old Changyuraptor sheds light on dinosaur flight 42 Nanochip in a capsule identifies bacterial infections within minutes 43 Cutting-edge car research at new battery testing lab 47 Not all songbirds sing about love

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44 Books 46 Subscription 48 Back page science • Mathematics puzzle 10| 1 2014

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Science for South AfricA

Crystals in history fascinating for thousands of years Crystallography brilliant applications in science Crystal Macromolecular crystallography seeing is believing engineering novel adaptations The maths behind crystals iSSn 1729-830X

Volume 10 | Number 3 | 2014

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

Images: RADMASTE, Wolf-Dieter Schubert, Andreas Roodt, Jeanet Conradie

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 the 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 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 © 2014 Academy of Science of South Africa

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

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Crystals &

crystallography

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his issue of Quest is devoted to the International Year of Crystallography and we are privileged to have Catharine Esterhuysen, president of the South African Crystallography Association, Andreas Roodt (President of the European Crystallographic Association) and other distinguished colleagues in the field as contributors. We can trace the origin of crystallography in South Africa back to the arrival of Reginald William James at the University of Cape Town in 1937. Two of his ex-students proceeded to win Nobel Prizes in Chemistry and Physiology, and many other students are now leading researchers in this field in the South African scientific community. As you read through the articles in this issue, you will learn that most solid substances are crystalline, not just salt, sugar and diamonds, but also minerals, metals, proteins and even chocolate. Therefore, we can work out what the structures of these molecules are by crystallography. For instance, Watson and Crick worked out the structure of DNA from crystallographic studies performed by Rosalind Franklin. How can we get from knowing that a substance is crystalline to understanding its structure? Scientists work out the structure of molecules using X-ray diffraction: a crystal is exposed to a beam of X-rays which is then bent (diffracted) in specific ways depending on its internal structure. The pattern of diffracted X-rays is then measured and the structure calculated using equations determined 100 years ago by a father-son team, Sir William Henry Bragg and his son, William Lawrence Bragg. This is why we are celebrating the International Year of Crystallography. The younger Bragg was only 25 when he shared the 1915 Nobel Prize in Physics with his father ‘for their services in the analysis of crystal structure by means of X-rays’. While Lawrence came up with all the ideas, his father built the equipment. Most of the world’s important new pharmaceuticals and materials (such as those used in electronic devices) were designed based on knowledge obtained from crystal structures. From this you can see that crystallography is a truly applied branch of science – with importance in almost every area.

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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.


Figure 1. A quartz crystal. Image: ‘Quartz, Tibet’ by JJ Harrison (jjharrison89@facebook.com) Own work. Licensed under Creative Commons Attribution-Share Alike 2.5 via Wikimedia Commons

CRYSTALLOGRAPHY a modern science with a rich history Catharine Esterhuysen takes us into the wonderful world of crystals.

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eople have always loved crystals for their beauty and have been fascinated by their clarity and regular shapes for thousands of years. Crystals have long been used for jewellery because of their beauty, but some other early uses were in medicines and ‘magic formulae’. Plates of very clear gypsum crystals, called lapis specularis, were used as windows by the ancient Romans. These special properties of crystals led the ancient Greeks to use the word ‘κρύσταλλος’ (krystallos), which means ‘cooled drop’ (in other words, hard ice) for clear quartz (see Figure1). This comparison showed particular insight, as ice itself is also crystalline, forming beautiful six-fold patterns as snowflakes (Figure 2). Early understanding The first person to be sufficiently captivated by ice crystals to try and explain why snowflakes always exist

Figure 2. The six-fold pattern in a snow flake. Image: ‘Bentley Snowflake5’ by Wilson Bentley – Licensed under Public domain via Wikimedia Commons.

Figure 3. Johannes Kepler. Image: Licensed under Public domain via Wikimedia Commons

with six corners, never with five or seven, was Johannes Kepler in 1611 (Figure 3). He realised that the external shape of the snowflake had to be the result of the internal packing of the water

Figure 4. Periodic repeating pattern in a crystal with the smallest part of the crystal, the unit cell, shown with black lines. Image: Catharine Esterhuysen

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Figure 7. Häuy’s description of a crystal built up out of repeating units. Image: Licensed under Public domain via Wikimedia Commons

Figure 8. Tartaric acid crystals showing the mirror image relationship between the two forms. Image: Licensed under Public domain via Wikimedia Commons

Figure 5. Two of the many possible sets of layers, shown as planes, within a crystal. The planes are differentiated from each other by their hkl indices, which are ww(a) the (100) set and (b) the (010) set of planes. Image: Catharine Esterhuysen

Miller indices Miller indices are a way of describing the planes of crystal lattices. A family of lattice planes is determined by three integers, h, k and l. They are writen (hkl). To imagine how this is possible, look at the photograph of the D-day cemetery in Normandy, France (Figure 6). It is clear that the crosses are laid out in lines next to one another, but you can follow other lines of crosses each with different repeat units. Planes through each of the layers can be described by a set of numbers, usually given as hkl, which give an indication of how they are orientated in space relative to the unit cell.

Figure 6. D-day cemetery in Normandy showing various planes. Image: Licensed under Public domain via Wikimedia Commons

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molecules into the crystal, and so laid the basis for crystallography. We now know that crystals are made up of atoms, molecules or ions that pack in an ordered way, with the smallest, unique part of the pattern (which we call the unit cell) repeated many billions of times to create the final crystal (Figure 4). This ordering means that the atoms lie in layers, although these layers don’t just lie in one direction but many (Figure 5). Now back to Kepler. In his time the concept of an atom was unknown, so he described the packing in terms of spheres, ideas which we still use today. The effect of this regular packing of spheres was that crystals had regularly defined edges, and it was noted by Niels Stensen in 1669 that the angles between faces on quartz crystals were always the same (look at all the crystals in Figure 1). In fact, in 1783 Jean-Baptiste Romé de l’Isle showed that this is true for many different types of crystals, so that even now geologists use the angles on crystals to identify minerals. The person who laid the groundwork for this method of mineral classification was René Just Häuy, who described crystals in terms of building blocks (Figure 7). Following on from this Johann Hessel, Moritz Frankenheim, Auguste Bravais, Evgraf Fedorov and Arthur Schoenflies successively laid a mathematical basis for the description of crystals in terms of ‘space groups’. They showed that the relative

arrangements of atoms or molecules within a crystal are restricted based on symmetry relationships, which can be described by 230 space groups. These space groups show that there can only be a limited number of molecules within the unit cell of a crystal and that these are related by symmetry. In addition, sometimes if the packing within the crystal is very symmetrical the symmetry involved in a space group restricts the shape of the unit cell. For example, all the sides must have the same length, or all the angles should be 90°. Therefore, knowing what the space group of a crystal is helps in determining its internal crystal structure. In the meantime, progress was being made in the study of biological crystals by a person who would later become famous for his work on microbiology, Louis Pasteur. He was studying solutions of compounds that had been obtained from living organisms, which always rotated the plane of polarised light, when he found that a tartaric acid solution had no effect on polarised light. He then looked closely at a sample of tartaric acid crystals and noticed


Figure 11. X-ray diffraction pattern. Image: ‘X-ray diffraction pattern 3clpro’ by Jeff Dahl – Own work. Licensed under Creative Commons Attribution-Share Alike 3.0-2.5-2.0-1.0 via Wikimedia Commons

Figure 9. Wilhelm Röntgen. Image: Licensed under Public domain via Wikimedia Commons

Figure 10. An early X-ray image taken by Röntgen. Image: Licensed under Public domain via Wikimedia Commons

that they could be separated into two forms that were mirror images of each other (Figure 8). When he made solutions from the two different sets of crystals they both rotated polarised light, but in opposite directions. This was the first identification of a chiral compound, i.e. one that possesses ‘handedness’. Tartaric acid is also a very good example of a compound that has different crystal structures (polymorphs) that have different properties. We now know that many compounds exhibit polymorphism, leading to crystals of the same compound having differences in solubility, melting point and even colour. X-ray diffraction – the breakthrough The next great breakthrough in crystallography came with the discovery of something that we are all familiar with: X-rays. Wilhelm Röntgen (Figure 9) discovered this strange radiation in 1895, using it almost immediately to take an X-ray of his wife’s hand (Figure 10). This is the application of X-rays that most people know today. However in 1912, Max von Laue saw greater possibilities. He realised that since the wavelengths of X-rays are similar in size to the distance between atoms in a crystal it must be possible to diffract X-rays from a crystal. He and two students, Paul Knipping and Walter Friedrich, proved that this was indeed the case by obtaining a diffraction pattern such as that shown in Figure 11.

Each of the spots is formed by a beam of X-rays that has been diffracted from a set of planes in the crystal. The spots are therefore also in the shape of the crystal. This study was extremely important for establishing that X-rays were a form of electromagnetic radiation and so was published rapidly that same year. Bragg’s law However, the real significance of the finding was seen by a University of Cambridge student, William Lawrence Bragg, who realised that there had to be a connection between the internal structure of the crystal and the diffraction pattern that it produced. His father, William Henry Bragg, built the X-ray diffraction equipment necessary to test this theory, while the younger Bragg put together the theory to describe the process. He knew that X-rays must be scattered from the electron cloud surrounding each atom, but under most circumstances the scattered beams would undergo destructive interference. Nevertheless, since the atoms or molecules in a crystal are packed in an ordered manner, that must mean that there is a situation when all of the scattered X-ray beams could be scattered in the same direction and would then undergo constructive interference to form the diffracted beams that were observed on the diffraction pattern (Figure 12). Bragg realised that this would only happen if the beams were at a specific angle with respect to a set of layers in the crystal. He calculated that

Figure 12. X-rays are coherently scattered from electrons in atoms when the distance between the planes and the incoming angle of the X-rays fulfil Bragg’s law. Image: Catharine Esterhuysen

there was a very simple relationship between the wavelength of the X-rays, λ, the distance between the layers in the crystal that the X-rays were diffracting off, dhkl where the hkl index describes the specific set of planes that the X-rays are diffracting from, and the angle of the incoming X-rays, θ, namely: λ = 2 dhkl sin θ This equation is now known as the Bragg equation and is the basis of crystallography as we know it today. What it means is that each of the diffracted beams of X-rays found on a diffraction pattern can be related to a specific set of planes in order to determine the distance between those planes. The second factor that Bragg used was that the intensity (brightness) of a diffracted spot is dependent on how much of the X-ray beam has been diffracted. Since X-rays are scattered by electrons in an atom, the higher the element number, the more electrons and so the greater the scattering, which means that gold atoms with 79 electrons will scatter more X-rays than carbon atoms with only six or hydrogen 10| 3 2014

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with only one. This means that more intense spots come from planes that contain more heavy atoms. Bragg was able to use this information, along with his equation, to determine the first two crystal structures – those of diamond and rock salt (Figure 13). In 1913 he and his father published this information. The use of X-rays in crystallography was an immediate sensation. Max von Laue received a Nobel prize for Physics for his work in 1914, with the Bragg father and son team sharing the Nobel prize for Physics a year later. This made William Lawrence Bragg, at 25 years old, the youngest ever Nobel prize winner. Röntgen himself had been awarded the very first Nobel prize for Physics in 1901. But this was just the start. Crystallographers or scientists using crystallography have won a staggering 24 Nobel prizes since then, mostly in chemistry, but also in physics and physiology or medicine. In fact, of the only four women who have won Nobel prizes for Chemistry two are crystallographers – Dorothy Hodgkin in 1964 and Ada Yonath in 2009 (the other two were Marie Curie and her daughter Irène Joliot-Curie). Chemical bonds One of the first scientists to use crystallography intensively in his research to understand the chemical bonding was arguably the greatest chemist of the twentieth century, Linus Pauling. His seminal work on chemistry The Nature of the Chemical Bond, published in 1939, is still widely read. Although he started his research career studying inorganic compounds he moved on to look at larger, biological molecules, becoming one of the pioneers in this field and determining the structure of the ‘alpha-helix’. He was awarded the Nobel prize for Chemistry in 1954 ‘for his research into the nature of the chemical bond and its application to the elucidation of the structure of complex substances’. In the meantime, although he had developed armaments during the Second World War, he had become increasingly pacifist, and was well-known for his antinuclear weapons stance. He was awarded the Nobel Peace prize in 1962 for his efforts, becoming the only person to win two Nobel prizes unshared. 6

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Figure 13. Crystal structure of rock salt – green spheres: chloride ions, purple spheres: sodium ions. Image: Catharine Esterhuysen

Unfortunately, though, Pauling missed out on the one structure that would have made him legendary. He was working on the structure of DNA at the same time as James Watson and Francis Crick, but failed to correctly identify it, as he was convinced that it was a triple helix. Watson and Crick, in the meantime, had seen the X-ray diffraction pattern of a crystal of DNA taken by Rosalind Franklin of King’s College London. Using this information they came up with the correct double-helix model of DNA that earned them the 1962 Nobel prize in Physiology or Medicine. Although Rosalind Franklin’s contribution was vital to their breakthrough she died before the Nobel prize was awarded, so instead that prize was shared with Maurice Wilkins also of King’s College London for his role in crystallography. In the same year, two more crystallographers, Max Perutz and John Kendrew, shared the Nobel prize for Chemistry for working out the structure of globular proteins. Two years later Dorothy Hodgkin was awarded a Nobel prize for Chemistry. She had made major breakthroughs in the field of medicine by determining the structures of steroids, vitamin B12 and penicillin. However, her work elucidating the structure of insulin, which took nearly 35 years, was probably the most important aspect of her research and led the way to further improvements in insulin research.

Biological crystals Eighteen years later Aaron Klug, who had grown up in South Africa and learnt crystallography from Reginald James of the University of Cape Town before moving to Cambridge, was awarded a Nobel prize for his contribution to the advancement of crystallography by incorporating electron microscopy. He had become interested in the structures of biological molecules after meeting Rosalind Franklin after completing his doctoral studies, and went on to study the structure of the tobacco mosaic virus. His research allowed him to build up three-dimensional structural information from two-dimensional electron microscopic images in order to determine the structures of complex biological compounds. As a result of the groundwork laid by these scientists, among others, the study of biological compounds is the fastest growing field of crystallography owing to its direct applications in improved drug design. In fact, since Klug’s Nobel prize in 1982, the Nobel prizes for Chemistry awarded in 1988, 1997, 2003, 2006, 2009 and 2012 all involved crystallographically-based studies of biological molecules leading the understanding of complex biological processes. One of the techniques that made this explosion in analysis of biological crystals possible was the development of a technique known


as direct methods, initially developed by Herbert Hauptman and Jerome Karle in the 1950s and 1960s, although they were only awarded the Nobel prize for Chemistry for this work in 1985. Even though Bragg’s equation gives exact information regarding the distance between planes from the angle of a diffracted beam of X-rays, the relationship between the intensity of the spot and the positions of the atoms in the planes is not so clear-cut. The intensity and atomic positions are related by the phase of the X-ray beam that is scattered (see Figure 14). However it is not possible to determine the phase from X-ray diffraction data. This means that in order to solve the crystal structure one needs the phase of the X-ray beam, but one can only work out the phase if you have the structure! Luckily the phase may be calculated reasonably accurately if the positions of just a few heavy atoms are known, so initially elucidating a crystal structure hinged on guesswork. In 1935 the first systematic approach to solving the so-called ‘phase problem’ was introduced by Arthur Patterson, who had learnt crystallography from William Henry Bragg in the 1920s. He derived a function that now bears his name, which yields a map containing vectors corresponding to those between heavy atoms. If the crystal structure contains an element that is much heavier than the rest (i.e. contains more electrons), for instance a gold atom in a compound with carbon and hydrogen, then the position of the gold atom can be identified from the Patterson function. This position can then be used to calculate the phase. The diffraction pattern that would correspond to a crystal structure containing only the gold atom in the identified position is then generated utilising this approximate value for the phase and compared to the experimentally measured pattern. Using an iterative process, the positions of all the atoms in the crystal structure can then be identified and refined until the calculated and experimental patterns give a good fit. In the early days of crystallography this was backbreaking work as each calculation involves adding up a huge number of terms, with all the calculations being

performed by hand, so that single crystal structures could take months or even years to solve. However, with the computational power available nowadays crystal structures can sometimes be solved in a matter of minutes. Returning to the phase problem, although the Patterson function is very effective for solving crystal structures it was no good for dealing with biological compounds such as proteins, which typically only contain carbon, hydrogen, oxygen and nitrogen atoms, i.e. no heavy atoms. This was where direct methods made the breakthrough. Hauptman and Karle realised that there were statistical relationships between the phases and intensities of diffracted beams and generated equations linking the two that could then be solved directly (the ‘direct method’) to determine the phase. Although their method was criticised initially it has since been used extensively, and further improved upon by a number of other scientists to the extent that the structure solution today is generally fairly trivial, even for reasonably large protein structures.

Figure 14. Phase (f) of an X-ray beam. Image: Catharine Esterhuysen

Figure 15. Diffraction pattern of a quasicrystal showing the ten-fold symmetry. Image: ‘Zn-Mg-HoDiffraction’ by Materialscientist - Own work. Licensed under Creative Commons Attribution-Share Alike 3.0 via Wikimedia Commons

Figure 16. Penrose tiling showing that five-fold symmetry is aperiodic. Image: Licensed under Creative Commons Attribution-Share Alike 3.0 via Wikimedia Commons

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Penrose tilings By the time Hauptman and Karle received their Nobel prize it seemed that the crystal structures and how to determine them were largely understood. However, just the year earlier a study by Dan Schechtman had been published that turned conventional thinking about crystallography on its head. Schechtman had been studying an aluminium-magnesium alloy when he noticed that the diffraction pattern that he obtained from the electron microscope showed ten-fold symmetry (Figure 24). The diffraction pattern is usually a reflection of the internal symmetry of the crystal and further investigation showed that the crystal had five-fold symmetry. According to all the rules of symmetry and space groups laid down by Hessel and Schoenflies, etc. this was impossible! None of the 230 mathematically described space groups contain five-fold symmetry since objects with five-fold symmetry, such as pentagons, cannot be packed in any way without leaving spaces. Roger Penrose went on to prove this in the early 1970s, with his so-called Penrose tilings. These tilings (see Figure 16) are clearly ordered, but they are not periodic, i.e. they do not show a repeating pattern, unlike the traditional view of crystals as ordered periodic structures. So when Schechtman published his findings showing that the aluminiummagnesium crystal was aperiodic, calling it a quasicrystal, these were

The International Year of Crystallography Since then crystallography has continued to grow. The over-arching body focused on crystallography, the International Union of Crystallography (IUCr), is continually promoting and encouraging crystallography to the extent that this year has been declared the International Year of Crystallography. For more information regarding the IYCr along with a broad range of documentation about crystallography, including a far more in-depth background to crystallography and its history, video and audio clips, activities and games, please see www. iycr2014.org . There is also a long list of links to educational websites. I particularly recommend the general crystallography teaching resources at http://www.xtal.iqfr.csic.es/ Cristalografia/index-en.html. Huge amounts of fascinating facts and information regarding crystallography can also be found on the IUCr website, www.iucr.org. There are also many interesting details regarding the Nobel prize winners, including

general background to their research, given on the Nobel website, www. nobelprize.org, while the IYCr website shows a timeline with all the Nobel prize winners involved in crystallography (including many more equally important contributions than those mentioned here). An excellent in-depth description of the history of crystallography can be found in the book Early Days of X-ray Crystallography by Andre Authier (International Union of Crystallography, 2013). Q After completing a PhD in crystallography under the supervision of Gert Kruger at the Rand Afrikaans University in Johannesburg, South Africa, Catharine Esterhuysen joined Stellenbosch University as a lecturer in 2000. During her studies she developed an interest in computational chemistry, which she was able to develop when an Alexander von Humboldt fellowship allowed her to join the group of Gernot Frenking of Philipps-Universität Marburg in Germany in 2002. Her main focus is now the study of intermolecular interactions, combining her knowledge of computational chemistry and crystallography to explain unusual interactions. She was co-editor of Acta Crystallographica E (from 2006 to March 2012) and is currently the president of the South African Crystallographic Society. In this capacity she delivered a presentation on crystallography in South Africa at the opening ceremony to the International Year of Crystallography at UNESCO in Paris in January 2014.

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met with derision. Even Linus Pauling weighed in with his opinion that such a thing as quasicrystals did not exist. However, as more evidence in support of the phenomenon was identified by a wide range of scientists, broad acceptance of the concept of quasicrystals was achieved, with Schechtman eventually being awarded a Nobel prize for Chemistry for his work in 2011.

Six things to know about Ebola Sean Whelan, a Harvard Medical School virologist explains the challenges of confronting the outbreak in West Africa. Whelan talked to Harvard Medicine News about the deadly disease. HMN: What is Ebola? It is an RNA virus with what we call a negativesense genome, and that virus, when it infects a cell, makes more virus particles. An infection by this virus causes haemorrhagic fever and massive damage to the internal organs. Basically, the body goes into shock. HMN: What can be done to prevent or treat it? There is no current vaccine or antiviral drug that is approved to treat Ebola virus infection. HMS: What might be in the pipeline?

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There’s a candidate vaccine that’s based on vesicular stomatitis virus (VSV). HMN: What about ZMapp, the experimental serum? It’s an anti-serum that is an antibody against Ebola virus. It is still experimental, although it has been used in a few people. HMN: Why do Ebola outbreaks flare and subside? It’s very difficult to pin down with absolute certainty why an outbreak starts. One source of transmission to people is eating or butchering contaminated monkeys. Some people argue that it’s bats. And then the reason that the outbreaks subside is often because of the isolation of the

people who are infected. People who are infected are very sick and it’s only very close contacts of these people who usually are infected by the virus. So it sort of naturally dies out. HMN: What’s next? I’m optimistic based on the currently available data that one day there will be an effective treatment.

The Ebola virus. Image: CDC


Diamonds. Image: Andreas Roodt

CRYSTALS: the heart of beauty, brilliance, beasts, better medicines, technology and art Andreas Roodt shows us that crystals are more than simply beautiful objects.

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hen one mentions ‘crystallography’, or more simply ‘crystals’, what comes to mind immediately? Yes, you guessed, diamonds. Or if you like, jewellery in general. However, crystals and crystallography are so much more, and are literally all around us and have influenced our lives in virtually immeasurable terms. The study of crystallography has produced almost 30 Nobel Prizes. Fantastic? For sure! Crystals in nature I hope to illustrate with this short article the vast and many applications of this (forgive the pun) ‘brilliant’ science. But let us get back to what I said in the beginning. Who has not yet admired the beauty of a brilliant cut diamond? In general, when we think of diamonds, it is usually around a carat, or at best, a few carats, or even fractions of carats (five carats = one gram). But, large diamonds have been found in the world; and it is no surprise that the famous Cullinan diamond springs to mind almost immediately. This once-in-a-lifetime treasure was discovered on 25 January 1905 at the now famous Cullinan Premier mine, just east of Pretoria in South

Africa. It weighed more than half a kilogram (to be precise, 0.5678 kg); a massive 3 026 carats, and was almost the size of a man's fist. It was cut into a number of smaller stones,

The Cullinan diamond with a man’s fist next to it to show the scale. Image: Andreas Roodt

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Amethyst crystals. Image: Andreas Roodt

Egg shells, glucose and gall stones. Image: Andreas Roodt

Selenite – CaSO4

Liquid crystals used in smartphone displays. Image: Jeanet Conradie

Quartz – SiO2

Image: Ted Baker

Scales in kettles

NaCI

Sodium Chloride Flavoured Table Salt

Sugar

Everyday examples of crystals. Image: Andreas Roodt

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which now form part of the crown jewels of the British Empire. The beauty is further highlighted by other 'simple' crystals which form in nature as minerals, for example selenite and quartz. Other gemstones are equally beautiful; see the amethyst as illustrated. Sadly, diamonds are ‘just’ pure carbon, and are closely related to the lead in pencils: graphite. The only difference is the way the carbon atoms bond. Graphite consists of layers which slide on top of each other. In diamond however, the carbon atoms form a three-dimensional framework, with very strong bonds in three dimensions, as shown. They are formed at very high pressures and temperature. But remember to please be careful: your diamond can burn just as ordinary charcoal does. As I indicated previously, there are many examples of crystals all around us. Some are irritating (the brown scales in kettles, or sand in our shoes) but others are used daily, such as ordinary salt for lamb chops, or sugar for your coffee. Crystals are all around us, in some surprising places. For example, egg shells are crystalline, glucose is also crystalline, as are gall stones. Even chocolate has crystalline properties, which is why its nature and taste change if it melts and becomes solid again. Crystallography is used in the development of insecticides, additives in foods and high quality agricultural products. Crystals in technology Crystallography contributes to the study and development of better LCD displays for different purposes such as high-


Photovoltaic cells used to capture the Sun’s energy. Image: Andreas Roodt

These bright coloured pigments are identified using crystallography techniques. Image: Andreas Roodt

definition television. For social media junkies and sporting fanatics crystallography helps us to constantly improve the designs of cellular smartphones, more effective and secure credit cards, and displays for television. The security chip in your credit card (requiring your PIN code) was developed using crystallographic analysis of the advanced multi-dimensional material from which it was manufactured. Crystallography enables us further to study and design new materials to preserve energy, capture energy from the sun and gives us green energy. Molecular complexes absorb the sun’s energy, convert it into electricity and allow it to potentially be fed back into the energy grids. Crystallography is used in the study of molecular catalysts and their bonds. Better and more robust catalysts produce better petrol and other products with fewer by-products and solvent waste, so allowing greener chemistry from natural gas, crude oil and coal. Crystallography in art and beauty Crystallography is also used in the study and preservation of art. It is the mainstay to identify colour pigments used in paintings from the old masters, and in ceramics and mosaics. Pigments can easily be identified using crystallography, which can indicate if a painting is an original masterpiece or just a cheap copy. Crystals and crystalline compounds are further fundamental in the study of pigments for beauty products such as in nail polish, sunblock lotions, mascara and eye shadow. Crystallography in space Crystallography is currently used by the Curiosity Rover, analysing the substances and minerals on Mars. It is also used to study meteorites. In 1967 a strange crystal was discovered in one of Iscor’s (South Africa’s principal iron producer) high-temperature iron-smelting blast furnaces at Vanderbijl Park. The structure was solved as a complex iron oxo silicate, and called iscorite. This compound had never previously been reported on Earth. But when the moon rocks recovered by the Apollo Programme were analysed, iscorite was found. So this crystal appears to be present on the moon, but not on Earth.

A meteorite. Image: Andreas Roodt

The importance of crystallography It is clear that crystals and crystallography are an important part of our daily lives, and X-ray crystallography is probably one of the greatest innovations of the twentieth century. That is why this discipline is actively studied at nearly all universities and centres of scientific research in South Africa. Crystallography finds application in chemistry, physics, biology, mathematics, geology, engineering and the medical fields. 2014 has been declared by the United Nations as the International Year of Crystallography and celebrates the centennial of the work of Max von Laue and the father and son, William Henry and William Laurence Bragg. q Andreas Roodt is professor and chairperson of Chemistry at the University of the Free State (UFS). He currently serves as President of the European Crystallographic Association and leads the UFS Inorganic Chemistry research group. His prime research focus is on reaction mechanisms in coordination chemistry and chemical processes, with application in industry and medicine utilising X-ray crystallography and spectroscopy. 10| 3 2014

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CRYSTAL ENGINEERING How crystallography contributes to materials science and engineering. By Len Barbour. Materials engineering in nature and human society Scientists know that all plants and animals evolved from unicellular microorganisms (bacteria and archaea) that first appeared on Earth about 3.7 billion years ago. As these organisms gradually increased in complexity, they responded to the various challenges of life by developing ways to support themselves in their environments. For example, plants are supported by cellulose and vertebrate animals by bones. The exoskeletons of insects, crustaceans and shelled molluscs provide protection in addition to support. Indeed, the fossil records show that nature has been engineering functional materials for hundreds of millions of years. This evolutionbased materials engineering is a natural process, involving selection and survival of useful modifications, and ruthless rejection of what doesn’t work. What sets humans apart from other life forms is that we use our intellectual capacity to actively develop and adapt materials in novel ways. In fact, this inventiveness has been so central to the development of human civilisation that we classify archaeological ages in terms of materials: Old and New Stone Ages, Bronze Age, Iron Age and Silicon Age. Over these ages we have learned to extract and process the raw materials from our surroundings to manufacture useful objects such as tools, weapons, clothing, etc. This process involves recognising that different materials have different properties, and that these properties are the reason that materials will be suitable for a particular function. Thus, the history of humanity is closely linked to the invention of tools and processes, i.e. technology, which provides us with the ability to adapt to and control our environments. Certainly, many of the other major endeavours of humanity such as communication, navigation, agriculture, architecture, production of energy, health care, commerce, transport and biotechnology have all involved the development of tools that are inextricably linked to the technology of materials engineering. Over the past century we have made great strides in developing instruments and methods that now allow us to probe the nature of the universe in more detail than our natural senses could ever allow. In particular, we are now beginning to understand the structure-function relationships of materials at the atomic and molecular level.

The two strands of DNA are held together by weak adenine-thymine and guanine-cytosine interactions and can be unzipped for replication. The electrostatic profiles of guanine and cytosine illustrate why these two molecular units recognise each other. Image: ‘DNA Structure+Key+Labelled.pn NoBB’ by Zephyris – Own work. Licensed under Creative Commons Attribution-Share Alike 3.0 via Wikimedia Commons. Zip – www.freepik.com

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Molecular recognition and self-assembly An atom consists of a positively charged nucleus surrounded by an electron cloud. Atoms can be bound together in various ways to form molecules, and the process of modifying molecules by means of making or breaking bonds is referred to as chemical synthesis. A covalent bond is formed when two atoms share their outermost (valence) electrons and the ability of an atom’s nucleus to attract these electrons is called electronegativity; the stronger the attraction, the higher the electronegativity. The periodic table arranges atoms according to common tendencies and it is by understanding these tendencies that synthetic chemists


have made great strides in controlling the organisation of atoms in molecules. In any molecule the distribution of electrons is affected by the distribution of atoms, the atom electronegativities, as well as the nature and direction of each bond. This means that charge is unevenly distributed around a molecule (i.e. there are regions of more negative and more positive charge), and this phenomenon forms the basis of chemical reactivity. However, individual molecules can also interact with one another without reacting (i.e. without forming covalent bonds). That is, the negative region of one molecule can be electrostatically attracted to the positive region of another. Such intermolecular interactions are generally much weaker than the covalent bonds between atoms, but they are certainly no less important. Indeed, much of the chemistry of life depends critically on the existence of weak interactions. We now know enough about electron distributions to create computer-generated colour-coded models of any molecule, where blue represents positive, red negative and green intermediate electrostatic charge. Such electrostatic profile maps allow us to easily understand how two molecules might recognise each other (much like two bar magnets, where the north pole of one is able to seek out the south pole of the other). Of the many examples that exist in Nature, the concept of molecular recognition is most elegantly illustrated by the association of the two individual strands of a DNA molecule. Although the two strands are not chemically bonded to each other, they are held together by many weak intermolecular interactions involving the recognition of adenine by thymine, and guanine by cytosine. Indeed, just by looking at the electrostatic profiles of guanine and cytosine it is easy to see why these two molecular subunits are predisposed to recognise each other. The existence of many weak adenine-thymine and guanine-cytosine interactions between the two strands holds them together when it is necessary to do so. However, the interactions are sufficiently weak such that the two strands can also be separated like the two halves of a zip – this ability is critical for the selfreplication of DNA. A good analogy for the strong covalent intramolecular bonds versus the weak intermolecular interactions is superglue versus the glue on Post-It® notes – each has ideal properties to serve a very specific purpose. Matter can exist in many different states but the three best-known of these are the solid, liquid and gas phases. In the gas phase, molecules have sufficient kinetic energy to move around very rapidly. Although they may occasionally collide with one another, they are generally quite far apart (relatively speaking). In the liquid phase the molecules maintain contact with each other, but still have enough energy to jostle around without assuming an ordered arrangement. However, in the solid state the molecules usually become highly ordered in three dimensions, thus forming a crystal. They take on an arrangement that minimises intermolecular repulsions and maximises attractions. Therefore, the process of crystallisation involves self-assembly of molecules by means of molecular recognition. The result is generally a densely packed arrangement of molecules with little free space (the old saying ‘nature abhors a vacuum’ applies). The ordered three-dimensional internal arrangements of crystals, combined with several important discoveries,

A moving crowd is a good analogy for the gas state – the people are close together, but able to move independently, even though they may sometimes collide. Image: Licensed under Creative Commons Attribution-Share Alike 2.5 via Wikimedia

The ordered movement of a military parade is a good analogy of the solid state. Even though the people are moving, they do so in a very ordered way, giving the appearance of a single body. Image: www.wallpaperso.com

The way that players move in a football game is a good analogy for the liquid state. Image: www.sportsecrets.net

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Lego building blocks are self-complementary and can be connected in different ways. Image: Len Barbour

inventions and ideas, made it possible for scientists to map the positions of atoms in a crystal with a high degree of accuracy. The technique of X-ray crystallography thus allows us to explore molecular space, allowing us to gain deep insight into the factors that influence the process of self-assembly. Once we understand something we can begin to control it, and one of our ultimate aims is to utilise our understanding of intermolecular interactions to engineer designer materials that can perform specific functions – a field called crystal engineering. By engineering materials at the molecular level we will be following the examples in the natural world around us. Given the complexity of natural materials, it is reasonable to assume that we too will be able to increase the complexity of our designer materials with time. X-ray crystallography – our eyes into the molecular world Since our eyes are only sensitive to a very small region of the electromagnetic spectrum, our visual experience of the world has, for most of human history, been limited only to what can be seen with visible light. In practice, when imaging an object using electromagnetic radiation, it is not possible to resolve features smaller than half the wavelength being used. Therefore, in order to ‘see’ atoms and molecules, scientists had to wait for the discovery of X-rays in 1895 by Wilhelm Röntgen (for which he was awarded the 1901 Nobel Prize in Physics). During the almost two decades after Röntgen’s important discovery, physicists were not certain that X-rays formed part of the electromagnetic spectrum. Until 1912 it was generally assumed that crystals consisted of three-dimensional lattice-like arrangements of atoms, molecules or ions – an assumption based on their regular external shapes. In 1912, Max von Laue supposed that X-rays might indeed be part of the electromagnetic spectrum, and with wavelengths comparable to the supposed spacings between the atoms in crystals. In a landmark experiment he showed that a crystal placed in an X-ray beam produced an interference (diffraction) pattern on photographic film, thus proving the wave nature of the new type of radiation and marking the birth of X-ray crystallography (for which he was awarded the 1914 Nobel Prize in Physics). Soon thereafter the father and son team William Henry and William Lawrence Bragg showed that X-ray diffraction could be explained using a simple equation and that it could also be used to deduce the relative positions of atoms in crystals. For their work they shared the 1915 Nobel Prize in Physics. The technique of X-ray crystallography has progressed significantly over the past 100 years, benefitting from many technological innovations that include more powerful X-ray sources, highly sensitive X-ray detectors based on chargedcoupled device technology (a device for the movement of 14

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electrical charge, important in digital imaging), advances in electronics, automation, fast computers and sophisticated algorithms. Since 1912, X-ray crystallography has revolutionised the fields of physics, chemistry, mineralogy, metallurgy, pharmacy, molecular biology and materials science. Crystal engineering Engineers apply knowledge in order to create new technologies, or to improve those that already exist. To create macroscopic structures such as buildings, bridges and machines, civil and mechanical engineers need to understand how to assemble well-defined building blocks in a predetermined way. Fortunately these structural components can usually be manipulated manually or mechanically. However, the intriguing prospect of engineering useful entities at the nanometre scale poses a difficult challenge: how do we control tiny entities (such as molecules) that we can’t handle individually, or even see? The answer is that we can draw inspiration from the natural world, where there are complex structures that span the full scale from the galactic to the nanometre level. Over the past century we have learned that in the natural world molecular recognition and selfassembly are the mechanisms through which highly complex systems are built from the bottom up, using simple molecular building blocks. While engineering an entity as complex as even the simplest living organism is still far beyond our reach, we are beginning to unravel the concepts that govern the selfassembly of molecules to form crystals. Synthetic chemists have developed ingenious methods for constructing an almost limitless array of different molecules with tailored functional groups (i.e. suitable electrostatic profiles) that can serve as recognition sites for self-assembly. We can consider any of these molecules to be a building block that may form a crystal, much like Lego pieces that have studs and stud receptors such that each piece is selfcomplementary (i.e. is designed to connect to another, identical piece). However, like Lego pieces, it is often possible for molecules to recognise one another in different configurations, making it difficult to predict the crystal packing arrangement in advance. The packing arrangement of a crystal’s building blocks gives rise to its properties, and useful properties may include (amongst others) solubility, thermal expansion, photoresponsivity, thermoresponsivity, electrical conductivity and magnetism. q Len Barbour obtained a PhD at the University of Cape Town on thermodynamic and structural aspects of solvate formation and decomposition. He currently holds the South African Research Chair in Nanostructured Functional Materials at Stellenbosch University. Current research includes the study of solid-state phenomena.


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Protein crystals come in many shapes, sizes and colours. Most are colourless, but a cofactor or ligand (smaller chemical entities bound by proteins) may cause them to be coloured. Protein crystals are normally very soft and break easily. They need to stay in their ‘mother liquor’ to be able to diffract X-rays. Nowadays, most crystals are cooled to very low

temperatures in nylon loops (right) to reduce damage from the X-rays. Images: Top left: http://web.chem.ucsb.edu/~kalju/chem112L/public/Crystals_11/crystals_S2.html Top right: http://iss.jaxa. jp/kibo/kibomefc/spcf_e.html Bottom left: http://www.bbsrc.ac.uk/news/industrial-biotechnology/2011/110524-pr-electricityfrom-microbes.aspx Bottom right: http://www.usask.ca/research/100yrsinnovation/1_search_skies.php Large right: https:// biocars.uchicago.edu/page/biology-customized-macromolecular-crystallography

Seeing is believing Wolf-Dieter Schubert explains the science behind macromolecular crystallography.

H

ave you ever wondered how something small like a virus or a bacterium can infect a person and cause anything from minor irritations such as a sore throat, to more severe symptoms like fever and measles, or even kill? Or have you marvelled at the elegant yet intricate double helix structure of DNA? How do we know that these things really exist or how they work? And how do we know what medicines to take to treat a particular disease? Thinking about or answering such questions was way beyond our reach until a few decades ago. Then came the discovery and refinement of crystallography in the first half of the 20th century and its application to biology from the 1950s onward. Slowly this opened our eyes to the wonders of the microcosm, showing us how biology works at the cellular, molecular and even atomic level. We live in a physical, three-dimensional world. We are born with two eyes and two ears set slightly apart. This allows us to perceive the world around us. We not only see the height and the width of any object but its depth too. This in turn allows us to understand how one thing relates to another – is it smaller, thicker, broader, behind or in front of another? Are boxes neatly stacked one on top of the other or are they randomly thrown onto a big heap?

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To analyse a protein normally requires milligram amounts of that protein. This may not sound a lot, but it is not easy to get. Generally bacteria are tricked into making the protein. They are grown in flasks with medium (yellow) at 37°C. Image: Structural Biology Initiative Cape Town 2010 (No longer exists


In the early days of macromolecular crystallography, representations of molecules had to be drawn by hand, as in this historic work of art of phosphorylase domain 2. Since then graphics programs have been improved allowing pictures to be prepared much more quickly. Image: http://commons.wikimedia.org/wiki/File:Phosphorylase_domain2.jpg

Protein X-ray Diffraction: Proteins are large molecules compared with salts and small chemicals. As a result X-ray diffraction images contain many reflections (black spots). To collect a complete data set, the crystal is rotated around an axis that will leave the crystal in the X-ray beam. Many such images are recorded and evaluated together. The white spot in the middle is caused by a ‘beam stop’ that protects the detector from the direct, high-intensity X-ray beam.

Myoglobin was the first macromolecule whose structure was experimentally determined. This was done in Cambridge, UK, in 1956 by John Kendrew and colleagues. Even for this fairly small protein it is difficult to see what is going on because there are too many atoms. Carbon – green, oxygen – red and nitrogen – blue. Image: PDB entry 1MBN in Pymol

Image: http://folk.uio.no/utek/research.shtm

Haem

In the same way, scientists would like to understand how microscopically small objects like molecules and viruses interact with each other. Fortunately, we can now do this for biological molecules with the help of the technique known as macromolecular crystallography. Biological crystallography Exactly when biological crystallography started is open to debate. Many proteins crystallise spontaneously in their natural environment. One example is insulin, which regulates our blood sugar levels and which occurs as tiny crystals before being secreted into the blood stream. Another is alcohol oxidase, which crystallises in peroxisomes inside yeast cells grown on methanol. This allows dense packing of the protein without losing its activity. More frighteningly, protein crystals sometimes form due to genetic mutations. For example, crystalin, a protein found in the human eye, may crystallise and damage the eyes if certain mutations occur. Or haemoglobin may crystallise within red blood cells, preventing them from squeezing through narrow arteries and causing a lot of pain and suffering. Scientists have been able to purify and crystallise proteins since around 1850. Protein crystallisation was seen as proof of protein purity by around 1900. Crystals are neat stacks of millions upon millions of molecules. The fact that proteins crystallise means that they have a defined three-dimensional shape. Before that proteins were assumed to be shapeless colloids similar to jelly. However, the technology to analyse

If we show only the chemical bonds connecting the atoms instead of atoms themselves, things are a little clearer. For example, we can now see where the haeme group is, but it is still too complicated. (Hydrogens are not shown for clarity.) Image: PDB entry 1MBN in Pymol

protein crystals was not yet available. This changed after the discovery of X-rays at the end of the 19th century, the realisation that X-rays could be used to probe the structure of crystals and many, many innovations producing better X-rays, better detectors and, of course, computer soft- and hardware. 10| 3 2014

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Haem Haem

We can take just one central atom from each amino acid making up a protein and connect these up. Now we can see that myoblogin starts at one point (‘N’ for amino-terminal end) and ends at another (marked ‘C’). In between the chain forms spirals called a-helices, which in turn are connected ‘loops’. Overall the chain packs up quite tightly, forming a pocket for the haeme cofactor

Haemoglobin actually consist of four chains. Each chain binds a haeme cofactor (red), allowing haemoglobin to carry four times as much oxygen. Image: PDB entry 2DHB in Pymol

The nature of enzymes Until around 1930, it wasn’t clear whether enzymes (catalysts of biochemical reactions) are proteins. Many people thought that enzymes were chemical things that could bind to proteins but could also leave again. By crystallising the first enzyme urease, which was still active inside the crystal in 1926, James Sumner proved that enzymes are indeed proteins. In fact most of the first protein structures to be solved were those of enzymes. In 1934, John Bernal and his 24-year-old student Dorothy Crowfoot (later Hodgkin) were the first people to demonstrate that protein crystals do scatter X-rays using crystals of pepsin, a stomach enzyme. The secret that had escaped everyone else was to keep the crystals moist and bathed in their ‘mother liquor’, the solution in which they crystallise, during the experiment. 18

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(red), which binds the oxygen (pink sphere). Haeme is dark red in colour, giving blood its red colour. Haemoglobin: Can you spot differences between myoglobin on the left and a single chain of haemoglobin on the right? Although the amino acid sequences are quite different, the fold is essentially the same. Image: PDB entry 2DHB in Pymol

Haemoglobin and myoglobin The first protein structures derived from a full crystal analysis were those of haemoglobin and myoglobin, two molecules involved in oxygen transport and storage. These could be isolated in large quantities from blood and muscle respectively. First understood was the structure of smaller myoglobin solved by John Kendrew and colleagues in Cambridge, England. Two years later the same group worked out a much more detailed myoglobin structure. Around the same time, Max Perutz and colleagues worked out a low-resolution haemoglobin structure. These first protein crystal structures were revolutionary, as we could for the very first time see molecules of life magnified to a level where we can see, feel and understand their properties. Unexpectedly, the fold of the protein chain in myoglobin turned out to be very similar to that of each of four chains in haemoglobin. Clearly the molecules are related, meaning that evolution also applies to molecules. In 1962 Max Perutz and John Kendrew were rewarded for their hard and pioneering work with the Nobel Prize for Chemistry. The structures of haemoglobin and myoglobin immediately made a lot of physical sense. Each protein is like a chain with twenty differently coloured beads or amino acids along the way. Each chain has a single starting point and a single end. In between, the chain folds in a complicated but unique way that leaves no gaps. In haemoglobin and myoglobin the chain wraps around another smaller entity called haeme, which is the actual oxygen carrier. The haeme cofactor is dark red in colour and the reason for that blood is red. Understanding the structure of haemoglobin and myoglobin also allowed the scientists to show that the protein chain is locally arranged as spirals called α-helices that had previously been predicted by Linus Pauling. A second way of efficiently packing proteins, discovered later, is by zigzagging the chain up and down, forming a sheet-like arrangement. These structures are called β-sheets. Individual β-strands are often depicted as arrows (top left figure on previous page).


X-ray diffractometer: Protein crystals diffract X-rays only weakly. As a result highbrilliance X-ray sources coupled to a very sensitive detector are needed to record the diffraction data. There are currently two such systems in South Africa – one in Cape Town and the other in Johannesburg. Image: Structural Biology Initiative Cape Town 2010

A robot can be employed to optimise the use of purified protein during crystallisation. A robot can dispense much smaller amounts of protein than a human can do by hand. Image: Structural Biology Initiative Cape Town 2010

More and more structures The theories and the methods of solving protein crystal structures developed by Max Perutz, John Kendrew and colleagues allowed many scientists around the world to solve crystal structures of their favourite proteins – a revolution that is continuing to this day. At first enzymes were very popular, as methods had been developed by other scientists to isolate large amounts from the various organisms. As time went by, though, technologies for copying and changing DNA became more established. Now scientists could trick certain bacteria, yeast, plants or other cells into making large quantities of proteins, originally made in entirely different organisms. Over the years, the size and the complexity of crystal structures have increased. First, mainly enzymes were analysed. These could reveal exactly how one molecule is changed into another with the help of the amino acids making up the protein chain. Then more complicated, multimeric proteins started being analysed. These proteins are composed of more than one chain and the arrangement can either be spherical, hollow spherical, tubular, cupshaped and many other shapes. Virus coat structures are among the most complicated structures, made up of tens to hundreds of identical units. Quite a lot of these have been solved, telling us which part of the virus protein is likely to be responsible for infecting human cells.

European Synchrotron Radiation Facility (ESRF): Synchrotrons are very large, custom-built scientific instruments that produce high-intensity X-rays. Hundreds of scientists can simultaneously run many experiments in stations spread all around the ring. South Africa is a participant in the ESRF located in Grenoble, France, as there is currently no synchrotron in Africa. Image: Licensed under Creative Commons Attribution-Share Alike 3.0 via Wikimedia Commons.

The structure of ribosomes Another major achievement was the determination of ribosome structure. Ribosomes are the protein-making factories in cells. The information from a particular gene is fed into the ribosome in the form of messenger RNA. The ribosome reads this genetic sequence and converts the information into a linear sequence of amino acids that then folds into an active protein doing its particular job. The structure of the ribosome allows us not only to think of the processes in broad brushstrokes, but to really understand it in a lot of detail. As a result we can understand why certain drugs work by binding to important places in the ribosome and either slowing or speeding up the process of making a protein. And ideally we can improve those drugs by looking how they bind and whether that binding can be improved. Membrane structure An important class of proteins are those that are embedded in membranes. Membranes are the outer perimeter of most cells. They are made up of particular fat molecules, scientifically called lipids. As fats and oils don’t mix with 10| 3 2014

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X-ray Free Electron Laser (XFEL): SACLA (SPring-8 Angstrom Compact Free Electron Laser) is one of only three X-ray free electron lasers in the world. It is adjacent to the SPring-8 synchrotron (circular building at the back) in Hyogo

Prefecture, Japan (near Kobe/Osaka). Insert: Samples are destroyed by X-ray lasers within femtoseconds (millionth of a billionth of a second), but useful information is still obtained before this happens. Image: http://xfel.riken.jp

water, membranes form a barrier around the cell. Without proteins spanning the membrane, cells would die as very few substances would be able to get either in or out of a cell. Proteins form channels across the membrane, letting through only very specific ions or molecules which the cell needs. On the other hand, membrane proteins also act as the eyes and ears of cells. These proteins are called receptors. Receptors wait around for the right molecule to swim past the outside of the cell. They then grab hold of that molecule and either pass it directly to the other side of the membrane or send the message across the membrane that food, hormones or possibly a poisonous substance is around. The cell as a whole can then respond by either moving in the direction of the signal in the hope of finding more such molecules – or moving away from harm. Improved technology To be able to solve structures of complicated proteins and complexes, much experimental progress was needed over the years. This included better, faster and more automatic laboratory equipment, better crystallisation techniques and, very importantly, much brighter X-rays and much more sensitive detectors. From the 1970s onward, synchrotrons provided more and more intense X-ray beams, allowing smaller and smaller crystals to be used. Synchrotrons are essentially circular pipes with magnets around them. By synchronising the magnets, subatomic particles can be made to move around the synchrotron within the pipes at ever increasing speeds. These speeding particles produce high-intensity electromagnetic radiation including X-rays away from the circular pipe. The radiation can be made to pass through crystals which will then scatter the X-rays. By collecting information on the scattered X-rays, the structure of the molecule making up the crystal can be inferred. More recently X-ray lasers have been built. At present 20

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there are only a few of these lasers in the world and people are still working out exactly what to do with them. X-ray lasers produce beams of extreme brightness, which destroy or evaporate anything in their way. But before evaporating, crystals still briefly scatter the X-rays, allowing crystal structure to be determined. The advantage is that these crystals can be really tiny, allowing much more difficult projects to be attempted. These difficult projects involve very delicate proteins, which generally don’t crystallise easily at all. Macromolecular crystallography has been around for just over 50 years. Many achievements have resulted in Nobel Prizes and countless other awards. Open any modern textbook on biochemistry, microbiology, molecular and cellular biology and you will see numerous pictures describing what molecules look like and how their shape and arrangement of amino acids allows them to do whatever they are meant to. The Protein Data Bank, the international repository of macromolecular structures (www.pdb.org), currently contains a total of 102 720 structures, accounting for around 40 000 unique proteins. While this is a very large number, scientists have really only scratched the surface of all the potential proteins out there. In addition proteins are often modified, bind cofactors, drugs or inhibitors, and are produced as different splice variants. Thus we can expect generations of future structural biologists to continue in the quest of magnifying molecules to make them accessible and understandable to everyone. q Wolf-Dieter Schubert is a professor in the Department of Biochemistry, University of Pretoria, specialising in molecular aspects of infectious diseases using Structural Biological techniques. His undergraduate and postgraduate degrees in Chemistry and Crystallography are from the University of Cape Town, his PhD from the Free University of Berlin.


Coarse salt crystals. Image: images.wisegeek.com

RADMASTE shares activities that it has developed to promote the International Year of Crystallography 2014.

Crystallography matters

I

n this International Year of Crystallography 2014, crystallography matters. Why does it matter and why in 2014? This year was chosen because 100 years ago Max von Laue was awarded the Nobel Prize in Physics (1914) for showing that crystals diffracted X-rays to produce (on a photographic film) a regular pattern of spots. This has led to the exact description of the arrangement of atoms in different crystals and thereby to knowledge of molecular structures. This matters to us all, because it is this knowledge of molecular structure (still evolving) that has allowed huge advances in many fields of science, including medicine and materials, over the last century. The aim of the International Year of Crystallography 2014 is to create awareness of the importance of crystallography (especially X-ray crystallography) among young scholars and the general public. In South Africa, the Department of Science and Technology is participating in this UN-backed programme, and we were asked to design suitable activities to support this, which are described in this article. At the outset we were convinced that awareness and interest are best created by hands-on activities. Furthermore these activities had to be fairly easy to do and be as cost-

effective as possible, so as to make them accessible to all, at least in principle. We have experience of designing kits for school curriculum applications with the same considerations in mind. The specific items of equipment and chemicals, then assembled, support the following four activities, chosen for their links to the science curriculum: 1. Growing crystals 2. Crystals great and small 3. Modelling crystals 4. Diffraction. Growing crystals A good starting point for the novice ‘crystallographer’ is to grow a crystal. Such an activity is very rewarding to anyone who is interested in crystals. Home-grown crystals are common. Sugar and table salt crystals are easily made by putting a solution of sugar or table salt on a sunny window sill for a couple of days until the water has evaporated and nice crystals have formed. We developed an activity to illustrate crystallisation with the aim to grow a single copper sulfate pentahydrate (CuSO4.5H2O) crystal, and not a cluster of crystals. Growing a single crystal is challenging, as it requires effort and skill. Copper sulfate is a well-known chemical that produces beautiful crystals with a deep blue colour and a distinctive rhombus shape.

A copper sulfate crystal that has been growing at the end of a piece of string. Image: RADMASTE

A single crystal of copper sufate. Image: images.wisegeek.com

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seed crystals. In order to determine the mass of copper sulfate that is needed to saturate 100 ml of water at a chosen temperature, one can consult the solubility curve of copper sulfate. The solubility of a substance is the mass of that substance that will dissolve in 100 ml of water at a certain temperature. A saturated solution cannot dissolve any more of the solute at that temperature, i.e. the solute is at its maximum concentration at that temperature.

The challenge of selecting a seed crystal. Image: RADMASTE

This activity was designed to use microscale equipment, which is costeffective, robust and durable and only small quantities of the chemicals are needed. Microscale science is not only a trend in science practices around the world, but is also a means of making science, and in this case, crystallography, accessible to everyone. The seed crystal

The main concept of growing a single copper sulfate crystal is to start with a seed crystal around which the copper sulfate crystal can grow. Starting with a seed crystal ensures large and wellshaped crystals. A saturated copper sulfate solution is needed to grow the A Petri dish full of seed crystals. Image: RADMASTE

Solubility of copper sulfate pentahydrate (CuSO4.5H2O) in g per 100 ml H2O versus temperature (°C). Image: RADMASTE

Right: The set-up, apparatus and steps for growing a copper sulfate crystal. Image: RADMASTE

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For instance, a saturated solution of copper sulfate can be prepared by dissolving 60 g copper sulfate in 100 ml water at 80°C. The warm solution is then transferred to a Petri dish and cooled to room temperature. Evaporation and cooling initiate crystal growth. At room temperature (25°C) only 22 g of copper sulfate can dissolve in 100 ml water (see graph). The extra particles (ions) of copper sulfate that can no longer stay in solution, will arrange into a particular 3D pattern forming a solid with a particular shape, copper sulfate crystals. After a couple of days a suitable seed crystal can be chosen from the crystals in the Petri dish. The slower this process of crystallisation, the better the shape of the seed crystals will be. Growing the seed crystal

The next step is to suspend the seed crystal in a saturated solution of copper sulfate, as shown in the diagram.


Solubility curve showing the best conditions for growing a single crystal. Image: www.analyticjournal.de/downloads_ak_pat_3kolloq2008/schoell_kristallisation.pdf

An amethyst crystal. You can see that the crystal has a hexagonal column and a pyramidal top. Image: Licensed under Fair Use Wikimedia Commons

There are several factors that have to be managed during the crystal-growing period. Firstly, the seed crystal should be left in a place that has a reasonably constant temperature. The solution is sensitive to temperature fluctuations and copper sulfate solubility varies greatly with temperature, as shown in the graph on page 22. Secondly, to obtain controlled growth of the seed crystal, the copper sulfate solution should be kept saturated. This will prevent the crystal from dissolving in the solution. The solubility graph alongside shows the ideal conditions for growing a single crystal. The region above the solubility curve is called the ‘supersaturated’ area. This is an unstable zone where spontaneous nucleation occurs. A crystal suspended in a solution under the conditions of the metastable zone will grow further. Thirdly, the rate at which crystallisation occurs will affect crystal quality. Usually, the best crystals are the ones that grow slowly. Therefore it is essential to avoid excessively rapid growth. This encourages the formation of multiple crystals instead of a single crystal. The crystal growth should be monitored and any bumps on the surface of the crystal or small crystals on the line should be removed. They compete with the growth of the big crystal. The crystal should be allowed to grow undisturbed for several days. The keyword is patience. The longer the crystal is left in the saturated solution, the bigger it will grow. Although crystal growth can sometimes be unpredictable, getting a crystal to grow provides a great sense of achievement. Crystals great and small Crystals v. amorphous solids

A selection of crystalline and amorphous substances for learners to observe. Image: RADMASTE

Everyone knows what a solid is. But when is a solid a crystal and when is it not? Solids may be everywhere, but crystals are not. There are other solids which we call amorphous. The difference is a crucial one for several reasons and so we had to deal with this. To do so we decided to provide some impressive, big crystals of quartz, which could be compared with other solids we encounter on an everyday basis. These other solids included window glass and powders where some powders were in fact composed of very small crystals. 10| 3 2014

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A diagram showing the angles and faces that characterise all crystals. Image: RADMASTE

Stacking beads to show how stacking atoms could account for crystal shapes – the stack of beads on the left is a pyramid and the stack of beads on the right is a cube. Image: RADMASTE

Characterising and measuring crystals

Learners observe crystals great and small with the hand-held microscopes. Image: RADMASTE

Diagrams to show how to build bead models of crystals – cube at the top and square pyramid below. Image: RADMASTE

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The big crystals allow one to see very clearly the beauty and the characteristics we can use to judge other solids by. The characteristic faces, angles and symmetry of crystals can be described and measured, and a simple protractor is provided for measurement of angles. A glass window pane may be a nice flat solid but that is because we have a manufacturing process that makes it that way. Broken glass shatters the illusion one might have that the window pane is a very large crystal! The jagged and curved surfaces look quite different from the orderly faces and angles of a crystal. To study powders we can sometimes decide with the naked eye whether or not there are very small crystals. Otherwise, for challenging cases, use a hand-held microscope (x 40) to help. For many learners this was their first chance ever to use a microscope with this kind of magnification. Through these activities they learnt that crystals may be big or very small, but whatever their size they are not the same as amorphous solids. This lead to a richer understanding of what the concept of crystal means. It identifies for all, what is special about these solids. Modelling crystals The idea that matter is made of atoms is two or three thousand years old. However, hard evidence for the idea was lacking for a very long time. Crystals played a role in strengthening support for the atomic idea, when some four hundred years ago Hooke pointed out that the characteristics of crystals could be explained on this basis. He drew attention to the fact that balls could be stacked or packed together to make neat piles reminiscent of the shapes of crystals. This is not mentioned in school textbooks, which merely plunge into

the particle model of matter as if it is obvious and natural that we should. Beads – and lots of them

Once again it is the hands-on experience of crystal modelling that can make the difference, and be a revelation for learners today, as it was for scientists centuries ago. We provide a lot of little beads and some Prestik, with which to build two models – one a cube and one a square pyramid. We had previously designed a molecular modelling kit with these components, so this was a simple application of the same basic idea. An important general result of this modelling is a better understanding of the relation between what we see on the macroscale and what we imagine on the microscale (or sub-microscopic scale). We learn that as a house may be seen from a distance as a simple red-brown building but close up will be seen to be made of bricks, so too a crystal may be seen as a regularly shaped solid to our eyes but perhaps is also made of ‘bricks’ – that is atoms (or molecules). Diffraction The atoms and molecules in crystalline structures/crystals (but not amorphous solids!) are arranged in regular arrays and planes. The work of crystallographers is to find out exactly how the atoms or molecules are arranged in a crystal. They do this by studying diffraction patterns of X-rays that they pass through a crystal. An X-ray film behind the crystal records the resulting patterns. A typical X-ray diffraction pattern is shown on the next page. The position, symmetry and brightness of the dots in each picture reveal information on the repeating pattern of particles in the crystal that caused the X-rays to diffract. Most International Year of Crystallography publications emphasise


Diffraction pattern from a horizontal wire.

Diffraction pattern from a vertical wire.

Image: RADMASTE

Image: RADMASTE

X-ray diffraction because it is an important aspect of crystallography. However, X-ray diffraction can only be done in scientific laboratories and is not accessible to learners in schools or the public. In addition, it is a topic that is not easily understood. The diffraction of waves, and especially light, is a relatively challenging topic. Consequently we developed a hands-on activity to simulate X-ray diffraction. The activity focuses on the production of diffraction patterns with visible light, as well as their relationships with the workings of X-ray crystallography.

Lasers were chosen for their suitability to produce visible diffraction patterns. Lasers produce monochromatic, coherent and collimated beams of light. For the activity, a red laser pointer with a wavelength of 640 nm and a green laser with a wavelength of 532 nm are used.

The light source

X-rays and visible light are both electromagnetic radiations, but X-rays have much smaller wavelengths than visible light. Crystallographers shine X-rays on crystals, because their small wavelength enables them to diffract from the regular pattern of atoms and molecules. This is because the size of their wavelength is comparable to the size of, and distances between, atoms in a crystal. However, for the activity a more suitable light source was needed to produce significant diffraction patterns. The Sun or a light bulb is not a suitable light source. The white light emitted from a bulb or the Sun is made up of many different colours (with different wavelengths) which diffract differently. In addition, the Sun and a bulb do not produce coherent and collimated beams of light. In fact, the light of a bulb spreads in all directions around the bulb and its intensity decreases very quickly with distance. A beam of light is coherent when the light waves from the light source are in phase. In a collimated beam of light all the light waves propagate in the same direction. Monochromatic light consists of only a single colour with a particular wavelength.

Wires, threads, pantyhose and more

To introduce the phenomenon of diffraction, wires and fine threads of materials are used together with a laser pointer. When the laser pointer shines on a vertical wire, a horizontal pattern appears on a dark wall behind the wire. The centre of the line is much brighter. The bright and dark fringes make the line look dotted rather than continuous. This pattern is more pronounced for the thinner wires or finer threads. The fringes are more difficult to see with the thickest wire. Even a strand of hair can be used to produce diffraction patterns, because of its fineness. The hair can be used to show the differences in the distance between dark and bright fringes using the red laser and the green laser. The fringes on the green pattern are closer together, since the green light has a smaller wavelength. Fabrics with different weaves can then be used to represent crystals with different structures. Organza has a simple weave of perpendicular threads, which produces a diffraction pattern in the shape of a cross, where the bright and dark fringes can easily be observed (vertically and horizontally) due to the very fine threads (see pattern (A)). This is because the threads in the fabric are perpendicular to one another. These regular patterns are produced by the regular arrangement of the threads. Pattern (B) shows the two crosses on top of each other. Here the organza fabric has been folded diagonally. Other fabrics, such as tulle and pantyhose, have different weaves, which result in different diffraction patterns, when the laser pointer shines on them. The diffraction patterns that

An X-ray diffraction pattern from a zinc sulfide crystal (ZnS). Image: Licensed for Fair Use, Wikimedia Commons

A

B Diffraction patterns of organza fabric. Image: RADMASTE

appear on the wall or a surface behind the material can give us an idea of the weave or structure of a fabric. In fact, measurements of the distance between the fabric and wall and between dark spots along diffraction lines could even be used to calculate the thickness of the strands. These are all very basic steps also followed in X-ray crystallography, though the patterns can be far more complex. X-ray diffraction by DNA crystals Perhaps the most famous X-ray diffraction picture is that from DNA crystals taken in the early 1950s by Rosalind Franklin. It suggested that the structure of a DNA molecule was helical. 10| 3 2014

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A

B

A X-ray diffraction pattern of crystallised DNA suggesting that DNA is helical; B A model of a DNA molecule, showing its double helix structure. Image: Licenced for Fair Use by Wikimedia Commons

Diffraction patterns of green laser light diffracted by a lamp filament. Image: RADMASTE

A common and spectacular demonstration that simulates an X-ray diffraction pattern of DNA can be produced by shining a laser pointer on a slightly stretched lamp filament. A striking similarity between the two patterns,is the formation of an 'X' made up of fringes (laser light pattern) or dots (X-ray pattern). This indicates that two objects (that caused light or X-rays to diffract) are crossing one another in an X formation. The lamp filament is shaped into a coil. If the coil is stretched a bit, the front and back parts of the coil form 'X's. Considering that if one shines the laser beam at any part along the length of the lamp filament results in roughly the same pattern, it means that this ‘X’ pattern repeats along the length of the filament. If we did not have a picture, we could predict that the lamp filament must be shaped like a coil, simply because of the X pattern. The same would apply to the X-ray pattern of DNA. Further reading RADMASTE (2014): RADMASTE IYCr Facilitator’s Guide. A manual for teachers and facilitators to be used with the RADMASTE™ Facilitator’s Crystallography Kit. http://www.radmaste.org.za/ provides some information about research, teaching and community engagement activities of the RADMASTE Centre. http://www.microsci.org.za/ provides more information about the microscience concept and the various RADMASTE™ microscale resources available for hands-on practical work, including the crystallography kits as shown on the RADMASTE price list. http://www.iycr2014.org/participate/crystal-growing-competition, provides information for a crystal growing competition. http://www.rsc.org/learn-chemistry/collections/online-experimentation/ collaborative-chemistry/global-experiment-2014, provides information about IYCr2014 and the global crystallography competition. http://www.nstfawards.org.za/ShowProperty?nodePath=/NSTF%20Repository/ NSTF%20Awards/files/Winners2013/CrystallographyPresentation.pdf - a valuable slide show on crystallography and the evolution of X-ray crystallography.

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Conclusions These four activities have been combined into a Crystallography Kit with a Facilitator’s Guide and worksheets and there are plans to use them at several science centres around the country to promote the International Year of Crystallography. In addition, they featured at National Science Week events in Bloemfontein and in Orange Farm near Johannesburg. More and more learners will be made aware of the importance of crystallography and hopefully some will be encouraged to become crystallographers. And all who see and participate in the handson activities will perhaps view crystals in a new light for the rest of their lives. We thank the Department of Science and Technology for the initiative and for giving us the opportunity to help in achieving these goals. We also thank three volunteers from the SAASTA/NRF National Youth Service Programme (Katlego Malesa, Jabulile Malindi and Anastesia Mayimela) who have helped with the development and trialling of the four activities. (Read their profiles at www. radmaste.org.za.) q This article was provided by R Basson, B Bell, J Bradley, M Lycoudi and C Roberg all from RADMASTE, Wits School of Education, Johannesburg. RADMASTE is a self-funding unit of the University of the Witwatersrand, Johannesburg, falling within the School of Education. It was founded at the end of 1990 with the aim of improving the accessibility, relevance and quality of mathematics, science and technology education. (RADMASTE stands for Research and Development in Mathematics, Science and Technology Education). There are approximately 20 mainstream staff, of which 14 are academic graduates with some further

qualification or degree. During RADMASTE’s 23 years, the educational environment has undergone many major changes, but the aims have remained the same. One consistent emphasis has been on teacher and teacher educator development (formal and non-formal) in the mathematics and science subject fields. Another has been on development of teaching and learning resources for these subjects, notably the microscale science kits. These have gained international recognition and substantial application, especially in developing countries. They address the lack of science equipment for practical activities that is a common problem in these countries. RADMASTE engages in projects of varying duration with funds from government, private corporations, international organisations and assorted donors. Although most work has been conducted within South Africa, projects and contacts in other African countries have also been a regular feature. In this connection a UNESCO-associated Centre for Microscience Experiments was established at RADMASTE. For more information on RADMASTE and the Microscience resources, please see www. radmaste.org.za and www.microsci.org.za.

SAASTA Volunteers Anastesia, Katlego and Jabulile. Image: RADMASTE


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(Non)sense in crystals Neil Eddy explains the maths behind crystals. True artists and true physicists know that nonsense is only that which, viewed from our present point of view, is unintelligible. Nonsense is nonsense only when we have not yet found that point of view from which it makes sense. Gary Zukav in The Dancing Wu Li Masters

S

tories abound of scientists and mathematicians whose ideas were thought to be nonsense, later being hailed as heroes when everybody else caught up with their way of seeing things. Sometimes theory follows experiment, while sometimes it is the theory that comes first. Paul Dirac, a British physicist, predicted the existence of anti-matter, because he trusted the beauty of his mathematical equations, but he was ridiculed for these thoughts for decades, until experimentation gave evidence for the truth of his theories and he was awarded a Nobel Prize. Dan Schechtman, an Israeli chemist, found evidence in his experiments for the existence of crystals that theory said could not occur. This time it took a decade for the mathematical theory to link up with the experiments. But we are a little ahead of ourselves, so let us step back and look at some mathematics that is useful in working with crystals. Five ideas could help in following the story of Schechtman: n Covering a 2-dimensional surface n Symmetry n Filling a 3-dimensional space n Polyhedra n Group theory Covering a 2D surface If we are able to cover a surface completely (with no overlaps or gaps) with pieces that are all the same shape, we can say that this shape tessellates. Probably the easiest tessellation is made with squares and is the origin of the word (from the Latin tessara for congruent squares). If we want our pieces to be 'regular',

Circle Limit III by MC Escher. Image: Licensed under Fair use of copyrighted material in the context of Circle Limit III via Wikipedia

Dan Schechtman, a chemist. Image: Holger Motzkau - Own work. Licensed under Creative Commons AttributionShare Alike 3.0 via Wikimedia Commons

a mathematical word meaning that all angles are equal and all sides are equal, then we have only three shapes to choose from – triangles, squares and hexagons. If we are prepared to sacrifice regularity slightly we may use a rectangle, a rhombus, a parallelogram, etc. The Dutch artist Maurits Escher made himself famous with the ingenuity with which he created tessellating shapes. But back to regularity – why can we only get tessellations of 3-, 4- and 6-sided figures? To work out (in degrees) the inside angles of a regular n-sided figure we can use the formula:

Regular shapes – three to choose from.

A = 180 (n – 2) 6 In a regular hexagon, each angle would be: 180 (6 – 2) n which is 120°. A pentagon would thus have angles of 108°. When we place them

Fitting regular pentagons together.

around a point we find we cannot fill up space in this way (i.e. with no overlaps or gaps) – only angles that are factors of 360 will work. 10| 3 2014

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The butterfly – a classic example of symmetry. Image: ‘Simetria-bilateria’ by Bea.miau - Own work. Licensed under Creative Commons Zero, Public Domain Dedication via Wikimedia Commons.

Symmetry The study of symmetry is currently a very fashionable pursuit and many fields are being re-imagined in terms of various ideas around symmetry. In a very simple sense symmetry is present if something is done to a shape and the new shape looks exactly the same as the original shape. The classic example of symmetry is a butterfly – the two halves are mirror images of each other (they are not perfect in reality, so maybe it is a bad example, but carries the general idea). This is a form of symmetry where we reflect in a line. Of much greater interest to the crystallographer is rotational symmetry – if we rotate a crystal around an axis, do we get to a point where the crystal looks exactly the same as before? Of course if we rotate through 360° this will be the case, but we are speaking about amounts less than that. Let us take a 2D example of a regular pentagon. Rotate it 72° in either direction and the new shape will look exactly the same as the previous shape. This can be done

A regular pentagon has 5-fold rotational symmetry.

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Filling space.

five times before we are back to our starting point, so a regular pentagon has 5-fold rotational symmetry. In an algebraic sense an expression can be symmetrical. If we exchange x and y in the expression x²y + xy² – x – y we end up with the exact same expression, so we can say that it is symmetrical. The expression x² + y² – 5x + 4y is not symmetrical. An equation such as a + b = 9 can be said to have symmetrical pairs of solutions. For example a = 5 and b = 4 is a possible solution; but so is a = 4 and b = 5. Crystallographers have taken symmetry into a far greater number of dimensions than our usual three and it is these symmetries that are used to categorise them and often, therefore, to identify unknown crystals. Filling a 3D space Let us concern ourselves, for the moment, with just three dimensions. As crystals grow they fill space. To understand how, we are going to look at billiard balls and soap bubbles. How many billiard balls, that have a diameter of 5 cm, can be packed into a box with dimensions 50 cm × 50 cm × 25 cm? It may surprise you to find out that the answer is not 500. A better packing gets close to 600 into the box. Most people think of packing spherical things into a rectangular

box directly on top of each other, but a better method, in most cases, places spherical objects in a pyramidal/ hexagonal format. Mathematicians are often concerned with ‘best’ solutions to a problem. To measure this they make use of a concept of density of packing that is the ratio between the volume of the objects and the total volume of the packing space. The higher the density of packing, the better is the solution. In the problem above the density is about 75% for the hexagonal case. Many problems of packing variousshaped objects into various-sized containers are still unsolved. What if the object being packed can change its shape slightly? You may notice this effect with oranges that have been squashed into a box for a while. Another well-used way of exploring this is through experiments with soap bubbles. Soap will form into a spherical shape. Why does it not form into a cube? Experimenting with simply-shaped wire frames dipped into a soapy solution can lead to the greatest nonsense. If 2 soap bubbles were pushed against each other, what would happen? How about 3? Now try to imagine 4 soap bubbles fitting together into a pyramidal form – how will they change their shape?


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Experiment with nonsense Make a cube with edges formed by wire. Add an extra piece of wire from the one corner to act as a handle. Then make a soapy solution (1 litre of water with 2 tablespoons of dishwashing liquid works quite well). Dip the cube into the soapy solution and draw it out carefully (the effect works best if you pull it out vertex first.) How do you think the soap bubbles will cover the wire frame? You may be in for a nonsensical surprise! Experimenting with wire frames.

Polyhedra So our next question can then be: Are there any rigid 3D shapes that fill space with 100% density of packing? Let us go back to our case of the three pentagons that do not quite fit together. Cut this out of a sheet of paper and then pull the two red sides together. What happens? Suddenly we have a 3D shape. Now what happens if we keep adding pentagons? Will everything eventually close up into a solid shape? Plato, an ancient Greek thinker, claimed correctly that only five regular polyhedra can be made from faces that are all identical. The Pythagorean Brotherhood revered these shapes and believed that they were what made up the four elements of the universe and the universe itself. These Platonic solids are listed, along with their elements. The secret to understanding why there are only 5 possibilities is to look at the number of faces meeting at a point. The sum of the angles must be less than 360°. So 4 triangles can meet, because this gives 240°; 3 pentagons are fine, because this gives 324°; but 3 octagons gives 405° and it is not possible that a Platonic solid can be formed with octagons (or any other regular shape with more than five sides). It is obvious that cubes packed together will completely fill space. What about the other four Platonic solids? Will they fill 3D space in a similar manner to the way certain shapes tiled 2D space? Look carefully at the picture of the icosahedron – do you notice what appears to be a pentagonal form when you look at any vertex where the 5 triangles join? This was important for Schechtman quasicrystals. Of course numerous 3D shapes can be made if we again remove our requirement of regular faces. The icosahedron and dodecahedron would not work very well as soccer balls,

Three badly fitting pentagons.

because they would be too wobbly, so soccer balls, until very recently, were made out of a combination of pentagonal and hexagonal pieces of leather – how many of each? In geometry we are concerned with what stays the same when everything else changes. So is there some rule that is true, no matter how contorted the polyhedron? Leonhard Euler (pronounced ‘oiler’), a Swiss mathematician, was the person to find the rule. Let us take a simple Platonic solid such as the cube – it has 6 faces, 8 vertices and 12 edges. Euler showed that the rule F + V – E = 2 will always hold. If we now truncate (hack off parts of!) the cube – does this still hold? You should find that it is still true: 14 + 24 – 36 = 2. If you view each corner that gets cut off, you will see why – we add a face and 3 vertices . . . but we also cut off a vertex . . . and we add 3 edges

Truncated cubes.

The Platonic solids.

Name of shape

Composed of

Number of faces meeting at a vertex

Element

Tetrahedron

4 triangles

3

Fire

Cube

6 squares

3

Earth

Octahedron

8 triangles

4

Air

Icosahedron

20 triangles

5

Water

Dodecahedron

12 pentagons

3

Universe

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Isometric/cubic – 6 squares

Tetragonal – 2 squares, 4 rectangles

Orthorhombic – 6 rectangles

Monoclinic – 2 parallelograms, 4 rectangles

Rhombohedral – 6 rhombi

Triclinic – 6 parallelograms

identity element exists: 5 × 1 = 5. But it is not invertible: the solution to the equation 5 × b = 1 is not a part of the set. So the natural numbers under multiplication are not a group. How about the integers under subtraction? Closure is fine; an identity element exists; it is invertible, but associativity does not hold. For example: (10 – 5) – 3 ≠ 10 – (5 – 3). So the integers under subtraction do not constitute a group. For the integers under addition, all four properties hold, and so this constitutes a group. The set { – 1; 0; 1} under addition is also a group. The categorisation of crystals is related to point groups involving symmetries in numerous dimensions.

Hexagonal – 2 hexagons, 6 rectangles

. . . so everything balances out in the equation F + V – E = 2. Check Euler’s Law for some other 3D shapes – start with the other Platonic solids and then get more adventurous. Group theory A ‘group’ in mathematics is a set of things (let’s call it {a, b, c, d, . . .}) along with an operation (let’s call it ) that has 4 specific properties: Closure: For all a and b in the set: a  b must also be in the set Associativity: For all a, b and c in the set: (a  b)  c = a  (b  c) Identity For all a in the set, there element: must be an element, e, in the set for which ae=a Invertibility: For all a in the set, there must be an element, b, 30

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in the set for which ab=e It is easiest to understand what a group is by taking examples from arithmetic, though the work for crystals involves geometry. Let us see whether the numbers {0, 1, 2, 3, 4, 5, 6} and the operation of addition form a group: to do this we have to show that all four properties hold. Closure clearly breaks down because 3 + 5 = 8, which is not an element of the set. We need go no further – this is NOT a group, but let’s look at the other properties. Associativity seems to hold: (1 + 2) + 3 = 3 + 3 = 6 and 1 + (2 + 3) = 1 + 5 = 6. There is an identity element: 3 + 0 = 3. But it is not invertible, because the value of b in the equation 3 + b = 0 is not a part of the set. So this set of numbers under addition does not constitute a group, because closure and invertibility do not hold. How about the natural numbers {1, 2, 3, 4, 5, . . . } and multiplication? Closure holds – if we multiply any two elements together, we get another element of the set. For associativity take the numbers 3, 5 and 10 for example: (3 × 5) × 10 = 15 × 10 = 150 and 3 × (5 × 10) = 3 × 50 = 150, which means that associativity holds for these 3 numbers, and does in fact hold true for all triples of numbers in the set, although proving this requires a little bit more work. An

Crystal systems Using all of this, crystals are categorised into seven lattice systems. In the first three all edges are at right angles to each other. In the monoclinic and hexagonal cases, the vertical edges are at right angles to the base, but the edges of the base are not at right angles to each other. In the final two cases, no edges are at right angles to each other. Back to the nonsense So while on sabbatical in 1982, what did Dan Schechtman and his collaborators find that was so worrying? They were busy looking into the crystal structure of an


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aluminium and manganese alloy using X-rays. Their results showed evidence of 5-fold point group symmetry, but, as we have seen, crystals can only exhibit 2-, 3-, 4- or 6-fold symmetry. Sometimes icosahedrons can show 5-fold symmetry, but Schechtman’s results indicated that this was not such a case. He thus proposed quasicrystals, things that did not fit into the definition of crystals at the time, but which he was convinced were crystals. He was maligned for this, fellow researchers ridiculed him and he lost his position in his research group. ‘For a long time it was me against the world.’ Mathematics to the rescue During the next decade the work of crystallographers and the work of mathematicians came together to vindicate Schechtman. A decade before quasicrystals, Roger Penrose, a mathematician at the University of Oxford, proposed an interesting way of filling 2D space with what have become known as Penrose tiles. Two differently shaped rhombi – one fat and one thin – are used. Each rhombus has 2-fold symmetry, but when they tile the plane in a Penrose tiling, 5-fold symmetry emerges. Look carefully at the picture of the tiling and you will see groups of five fat rhombi grouped around a point. Making sense of nonsense A decade after the initial discovery, quasicrystals were accepted and the definition of what constitutes a crystal was changed to incorporate these new structures. Three decades later, Daniel Schechtman’s work was honoured and he received the 2011 Nobel Prize for Chemistry. So remember – fame belongs to

Penrose tiling. Image: Licensed under Creative Commons Attribution-Share Alike 3.0 via Wikimedia Commons.

Each of these rhombi has 2-fold symmetry.

those researchers who are willing to recognise nonsense, to seek it out, to wrestle with it, to accept it for what it is – an opportunity. So let us finish where we started, with Gary Zukav: ‘Those scientists who establish the established lines of thought, are those who do not fear to venture boldly into nonsense, into that which any fool could have told them is clearly not so. This is the mark of the creative mind, this is the creative process. It is characterised by a steadfast confidence that there exists a point of view from which the “nonsense” is not nonsense at all – in fact from which it is obvious.’ q Neil Eddy is a mathematics teacher at Wynberg Boy's High School in Cape Town, involved in teaching 13 to 18 year olds. He has co-authored a series of text books and is involved with the Association for Mathematics Education of South Africa.

References Schechtman D, Blech I, Gratias D, Cahn JW. Metallic Phase with Long-Range Orientational Order and No Translational Symmetry. Physical Review Letters 1984;53(20): 1951-1953. Webb J. Quasicrystals and Penrose Patterns. Mathematical Digest 2012;167:10-11.

5-fold point group symmetry.

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The wonderful world of worms Carol Simon explains her passion for marine worms.

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hen I tell people that I work on polychaete worms, I usually get one of two responses. The less polite people laugh like drains as they can’t imagine why anyone would want to work on worms. The more polite will say ‘Oh, that’s interesting’, and sometimes they actually mean it. The truth is that polychaete worms are interesting. They are mostly marine or estuarine segmented worms with many bristles or chaetae, separating them from their relatives the oligochaetes (earthworms) and hirudinea (leeches), which are mainly terrestrial or freshwater species which have a few chaetae and a clitellum.

Variation in polychaete bristles. A) Copulatory spines of Capitella. B) Comb spines of Ctenodrilus. C) Modified spines and D) hooded hooks of Pseudopolydora dayi. Image: Carol Simon

A clitellum is a thickened glandular secretion of the body wall found in earthworms and leeches that secretes a sticky sac into which eggs are deposited.

They make up a significant proportion of animals in most marine habitats from the nearly dry sand of upper intertidal beaches to great depths where they live around very warm (≥30°C) hydrothermal vents or even on whale bones. They have varying feeding habits and can be filter feeders, bacteriovores, herbivores, carnivores, omnivores or scavengers. They can be mobile or sedentary, free living or parasitic. As a consequence they can be just a few millimetres short to more than a metre long with very variable body forms from simple and ‘worm-like’ to having elaborate structures. They can have exotic names such as feather duster-, paddle-, tangle-, spaghetti- or scale worms (and do yourself a favour, please do an internet search for ‘Bobbit worms’). Many have economic or ecological importance, and many are important alien species around the world.

Polychaete diversity. A) Paddle worm. B) Spaghetti worm. C) Scale worm. D) Tangle worm. E) Capitella. F) Feather duster worm. Image: Carol Simon

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Economically important polychaetes I work mainly on polychaetes, which are pests of aquaculture. My research focuses on a group of shell-boring mudworms belonging to the Polydora complex, mostly in the genera Polydora and Boccardia. Their larvae settle on the outer surface of the shell of, for example, abalone (perlemoen) and usually bore into the shell. Larger species will bore right through and eventually penetrate the inner surface of the shell. When this happens, the host covers the worm with shell, forming an unsightly blister that contains the worm and accumulated mud. In natural conditions these borers assist with the breakdown and eventual recycling of shells, but when they infest farmed abalone or oysters in high numbers they can deform the shells, inhibit body growth because the host is using all its


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energy to repair its shell and, in extreme cases, kill the mollusc. These worms have been recognised as pests since at least the 1880s, but we have not yet found an effective treatment against them because often the host is at least as sensitive to treatment as the worms. The best that farmers can do is to keep their farms and animals clean. Recently colleagues and I described a syllid worm, Syllis unzima, which was found as a pest of sea cucumbers in an experimental farm in Hermanus. The association between sea cucumbers and syllids is not uncommon – the worms usually occur in the grooves between the plates of the skeleton of the host, and when they are threatened will crawl into the mouth or anus of the sea cucumber. We don’t know what S. unzima feeds on. The digestive tract includes a muscular proventriculus or tube and a toothed pharynx, which the syllid can push out of its mouth. It is thought that they pierce the skin of their host or prey with the tooth, and then suck out its body fluids with the proventriculus. However, it is also possible that they just steal the hosts’ food which they suck up with the pharynx and proventriculus. The success of these worms in marine farm environments can, in part, be attributed to the way in which they reproduce. In all cases, the mothers invest a lot of energy into looking after their young. Polydora-complex worms lay their eggs in their burrows where they are fertilised. Here the larvae develop in relative safety during this vulnerable stage of their lives. When they are ready, they will leave their burrows and usually settle nearby. Syllis unzima takes parental care to the extremes, and gives birth to live young at a very late stage of their development. While some polychaetes have a negative impact on aquaculture, others are very useful. Fish love polychaetes, so the group is used extensively as bait for fish feed. Internationally there are many companies that farm larger species, such as blood- and ragworms, for a lucrative bait industry. Locally, one of the abalone farms grows bloodworms, Arenicola loveni, in the nutrient-rich effluent from the farm. This is an ingenious way of farming – the worms reduce the level of nutrients released from the farm into the environment, and are used as feed in fish farms. This farming is still at a relatively small scale, and does not yet produce enough worms to sell to the public. Consequently, local fishermen still catch their own bait, which includes the mussel-, blood- and wonder worms. Alien invasives Polychaetes form a significant component of marine alien species that are transported around the world. An examination of the ballast water of ships travelling from Japan to Oregon, USA, identified the larvae of 42 polychaete species, making them the most species-rich group after the crustaceans. A recent article identified 292 polychaete species recorded as aliens around the world. In South Africa, there are currently eight recorded alien species. Ship fouling and ballast water are considered the most probable means of transport, but hitchhikers on translocated farmed molluscs should not be ruled out. This tally is, however, probably an underestimate, as most of the polychaete species recorded locally by the late 1960s are considered to have a wide distribution. A consequence of alien invasions is that they can negatively affect the communities that they invade. Polydora oplura, originally described from Italy, is an important

Pest polychaetes and their offspring Boccardia proboscidea A) adult and B) brood capsules containing larvae and eggs in tube with mother. Boccardia pseudonatrix C) adult, D) brood capsule with larvae and eggs, E) pre-competent larva. Syllis unzima F) adult with orange juveniles in posterior half of body and G) juvenile removed from mother’s body cavity. Image: Carol Simon

Bait worms. A) Nereidid (mussel worm) species. B) Estuarine wonderworm, Marphysa elutyeni. Image: Carol Simon

pest of oysters and abalone in South Africa, New Zealand, Australia, and probably also Japan and Chile. Boccardia proboscidea, originally described from California, has been recorded as a pest of farmed oysters and abalone in Hawaii, South Africa and Australia, but it has also caused significant impacts on the coast of Argentina, where it has completely displaced indigenous mussels in areas affected by sewage. Another important invasive polychaete in South Africa is Ficopomatus enigmaticus, which forms dense beds of calcareous tubes in estuarine environments. This worm is thought to have originated in Australia, and occurs locally from Table Bay to Kosi Bay. These worms are filter feeders, and may out-compete the indigenous species for food while the increased faeces production may contribute to the increased concentration of pesticides, heavy metals and other pollutants in the benthic environment. 10| 3 2014

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Ecological importance Polychaete worms have a wide range of environmental tolerances and habitats, making them important on many ecological levels. Many species may be used to estimate levels of pollution. Some Capitella species can tolerate polluted or stressful conditions, particularly where oxygen levels are low. When they are present in high densities, pollution levels are usually high. Others are very sensitive, so when their densities are high pollution levels will be low. Others behave like earthworms; Naineris leavigata burrow through sand as they ‘eat’ it, leading to bioturbation. In other words, the worms mix the sand so that oxygen is transported to the deeper sand. The taxonomic impediment Underlying all the fields of polychaete study that I’ve outlined is taxonomy, a field of science dating back to Aristotle, and which involves the discovery, description and identification of species. Unfortunately, taxonomy is often regarded as the poor country cousin of more ‘relevant’ popular scientific fields like biological invasions, ecology, molecular phylogenics and evolution, physiology, neurobiology and even pollution studies. And so what is called the taxonomic impediment developed – the contributions made to science by taxonomists don’t get the recognition they deserve, and less and less money is available to conduct taxonomic studies, which are becoming increasingly difficult to publish in the more prestigious scientific journals. Consequently fewer young taxonomists are being trained to replace those who are retiring. But herein lies the irony – it is very hard to compare, with any confidence, how different organisms are affected by their environment, or how they are related to each other, if you haven’t identified your study organism properly. This was famously shown with Capitella capitata, a popular and widespread indicator species used in many ecological studies. It turns out that C. capitata is in fact a complex of very similar species, making it almost impossible to compare the results from different studies, as no one really knew which species had been used and it cannot be assumed that different species in the same genus will respond to the same conditions in the same way. By 2010, there were at least six species recognised within this complex. In South Africa, the discovery of the alien B. proboscidea on abalone farms was delayed by the fact that farmers thought of these

Dr Carol Simon is a lecturer in the Marine Research Group, Department of Botany and Zoology, Stellenbosch University. Her love of worms started during her PhD at Rhodes University where she worked on a sabellid (featherduster) polychaete that is a pest on farmed abalone. She now lectures in animal diversity and invertebrate biology. Her research focuses mainly on the biology and taxonomy of alien and pest polychaetes, but she will examine any polychaete that comes her way. Her current research team consists of one 4th-year, two MSc and one PhD student, but is growing. If you want to know more about these worms, go to http://www0.sun.ac.za/polychaete/. If you want to know more about marine research at Stellenbosch University, go to http://academic.sun.ac.za/botzoo/marine/index.htm. Internet references http://www.ccar.um.maine.edu/worm.html https://www.capetown.gov.za/en/EnvironmentalResourceManagement/publications/Documents/ Coastcare%202C-Tourism%20and%20Recr%20Activities.pdf

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shell-borers simply as Polydora species. As a consequence they did not realise that their abalone were infested by more than one genus and that the worm on the surface of the shells, and therefore considered harmless, was actually the same species causing significant shell damage. These are just a few examples in the literature. In South Africa, polychaete taxonomy was a prominent research field from about the 1930s to late 1960s. It is only now experiencing a comeback, and seven new species have been described by scientists working locally since 2008. This is because of the gradual realisation that we really do need to know what is out there if we want to get a true idea of our biodiversity. With new and exciting diagnostic techniques being developed, taxonomy is very much like being a detective or a forensic scientist. We want to know who Species A is, where it came from, how it got here and how it may be related to Species B. To determine this, we use the same techniques that Grissom and Abby use in CSI and NCIS: ‘identikits’, molecular sequencing, scanning and transmission electron microscopy, light microscopy (and all the variations thereof), and finally, endless literature, internet and database searches. It just takes us longer, and I wish I could turn a pixelated picture into a clear image, as is so often (misleadingly) shown on television shows. q

The world’s largest dinosaur Fossils of a new species of titanosaur have recently been found in Argentina and it is the largest animal ever to walk the Earth, according to palaentologists. Fossilised thigh bones suggest that it was 40 m long and 20 m tall and weighed 77 tonnes. The creature was a herbivore and walked the Earth during the Late Cretaceous period. A local farmworker came across the remains in the desert near La Flecha in Patagonia. The fossils were excavated by a team of palaeontologists from the Museum of Palaeontology Egidio Feruglio, which was led by Dr Jose Luis Carballido and Dr Diego Pol. They found partial skeletons of seven individuals – about 150 bones in total – all in ‘remarkable condition’. ‘Given the size of these bones, which surpass any of the previously known giant animals, the new dinosaur is the largest

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Scientists work at the site where the dinosaur was found. Image: BBC News

animal known that walked on Earth,’ said the researchers. ‘Its length, from its head to the tip of its tail, was 40 m. Standing with its neck up, it was about 20 m high – equal to a seven-storey building.’


A petrified tree in Namibia. Image: Jan Smit

A scientist in Namibia Just over a year ago Jan Smit was able to tour interesting places in Namibia. Interesting to a scientist.

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hat a wonderful experience it was and to discover how science is captured in the wonders of nature out there in this country of desert.

South-easterly wind in the Cape You may ask what the Cape south-easter has to do with Namibia. We started out from South Africa with a few kilograms of frozen sardines. The intention was to use the sardines as bait to fish in the cold Atlantic on the west coast of Africa. I wasn’t sure how good our chances of landing fish

The famous Sossusvlei dunes. Image: Jan Smit

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actually were. Why? The south-easter had been blowing fiercely for days. This strong wind blew the hot water from the Indian Ocean south from Mozambique north along the Namibian Coast. This same warmer water blown past Cape Point would increase the temperature in the cold Benguela current that heads north, coming from the Antarctic. Because fish, from the tiny sardines to the gigantic whale fish, love cold water they would go deeper in the ocean to the colder water. That was what I thought would happen. Why do fish love cold water? Cold water contains more air than hot water. So cold water has abundant nitrogen and oxygen. The nitrogen feeds plankton, a tiny organism that marine animals feed on, from the little sardine to the huge whale. Oxygen is vital to life. In cold water there is abundant oxygen dissolved in the water filtered through the gills of moving fish and whales. You can do a simple experiment to show how much air is dissolved in cold water. Take a clear glass beaker, fill it with cold tap water and heat over a flame. You will see that long before the water boils, bubbles collect at the bottom and sides of the beaker. Why? Lots of air is dissolved in cold water. The cold water is saturated with dissolved air. When the temperature rises the water becomes oversaturated with air. The abundant air molecules in the hot water are detached from the water molecules and accumulate as bubbles at the bottom and sides of the beaker. Note the difference between air and solids like sugar or table salt dissolved in water. The solubility of a solid increases with increase in temperature while that of air in water decreases. (Try to work out why? There is a simple scientific explanation.) This explains why our fishing was not successful. Not a single fish was landed during four lengthy fishing sessions. I was right! The dunes at Sossusvlei Another experience was at Sossusvlei. The dunes at Sossusvlei are famous for the sharp contrast between red and black at sunrise or sunset. Where the sunlight falls on a dune it looks red. In the shade it is black. Why this sharp contrast?


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World leaders in mineralogy meet in South Africa Raleigh’s scattering law provides the explanation. This law states that the scattering of light in the Earth’s atmosphere is proportional to the fourth power of the frequency of the light. Consider sunlight. At the one extreme end of visible light is blue light with a high frequency. At the other end is red light with a low frequency. At sunrise and sunset light from the Sun travels a long way through the atmosphere – a much greater distance than at noon, for example. As a consequence of the long distance at sunrise or sunset blue light with high frequency is scattered according to Raleigh’s Law. This also explains why the atmosphere is blue. Red light is scattered much less. Where the light reaches the sand of a dune the red light is reflected and it appears red. The colour of the dunes is red in broad daylight – its natural colour. In the shade no red light reaches the dune – so nothing is reflected – therefore the black. The contrast between the red where sunlight reaches the dune and the black shades is remarkable. It is artistic. Dune 45 at Sossusvlei is one of the most photographed dunes in Namibia. Petrified forest Deep in northern Namibia, in Damaraland, near to the town of Khorixas, is the petrified forest. Trees with year rings, bark and remnants of branches lie on the surface of the sand. As a scientist I know that the dominant element in any tree is carbon. But I could immediately see that the fossil trees were composed of silicon. How did it happen? Were the trees growing millions of years ago based on silicon? Carbon and silicon are both in group four of the Periodic Table. Silicon is just below carbon. The valence of both elements is four. Was that maybe the reason for the presence of silicon and not carbon in these petrified trees? The explanation is that in the distant past, part of the massive continent of Gondwana was forest and that major climatic changes occurred about 300 million years ago. During the Gondwana Ice Age a large part of Gondwana was covered with ice and glaciers. Eventually the ice melted, causing floods so severe that the trees in the forest were snapped off and carried away by the water, glaciers, rocks and other debris that flushed through it. The trees were buried deep under debris, sand, rock and other material. In their air-tight graves the wood could not decompose normally. No decomposers could reach the wood and the normal decomposing processes in air was not possible. The immense pressure exerted by the rocks, sand and other debris was such that the quartz, composed mainly of silicon, dissolved and diffused into the wood. The acidity, temperature and other chemical conditions favoured the replacement of carbon atoms in the cells by silicon atoms. The trees consequently petrified. It is interesting to know that scientists are nowadays able to petrify wood in about two days in the laboratory. Why should they do that? Petrified wood is in demand for ornaments, just as diamonds are. q Dr Jan Smit is the manager of the North-West University Science Centre, Potchefstroom Campus. He is a nuclear physicist by training and specialises in physics education. He has a keen interest in the world around him and how it can be interpreted scientifically.

South Africa remains a global leader when it comes to rich mineral resources such as platinum, chromium, manganese and vanadium, but one of the biggest challenges facing the country is how to extract these elements efficiently. The country also hosts some of the oldest rocks in the world, as well as the largest known meteorite impact structure. This is why South Africa’s hosting of the 21st General Meeting of the International Mineralogical Association (IMA2014) in September 2014 could not have been better timed. More than 800 of the world’s top scientific minds in various branches of mineralogy converged at the Sandton Convention Centre from 1 to 5 September for the conference – the first time a general meeting of the IMA has taken place in Africa. Conference co-organiser, Professor Johan de Villiers of the University of Pretoria’s Department of Materials Science and Metallurgical Engineering, said international collaboration on efficient extraction mechanisms, among other things, is crucial for South Africa – which remains one of the biggest sources of mineral commodities in the world. The conference was particularly relevant as it took place during the International Year of Crystallography and featured a number of sessions covering mineralogical crystallography. ‘Besides being a showcase of our fantastic mineral wealth, this conference is also a wonderful opportunity to collaborate with other top global scientists,’ De Villiers said. ‘What we need in South Africa is a new perspective on ways of extracting these minerals more efficiently. Mineralogy is central in assisting a higher efficiency of extraction. De Villiers said countries leading the way in efficient extraction mechanisms include Australia, Canada, Chile and China. ‘There has been a big decline in research in this area from the traditional European and American countries which are now into advanced materials, like photovoltaics and superconductors,’ he said. ‘But for countries like ours, the “bread and butter” issues still remain. We have to produce commodities like primary metals, steel and cement … and we have to produce them efficiently.’ ‘A key interest for us is to benefit from access to the advanced research facilities of our colleagues from other countries who share these concerns. There are new methods and equipment that need to be tested in SA. At present, much of this is developed overseas, so that collaboration with other countries is crucial. We also need access to large research facilities such as synchrotrons and neutron sources for advanced crystallographic and mineralogical research.’ De Villiers said South Africa, as a significant contributor of CO2 into the atmosphere, needs to encourage research and to draw on collaborative research in this and other areas. ‘We also need to encourage the use of crystallography and mineral chemistry in the mineral sciences – and this conference is a way to do that.’ Scientists ranged from experts in the characterisation and properties of minerals, to the behaviour of minerals in earth processes. ‘For instance, the measurement of what happens to minerals during weathering, reheating during metamorphism, or volcanism …. and what happens when minerals are subjected to extreme pressures during diamond formation or meteorite impact. These are some of the issues which the top minds in our mineralogical community all over the world are applying their minds to,’ De Villiers said. The technical sessions of the conference reflected the ‘traditionally most important topics of the field’ and included Mineralogy of the Deep Earth (aimed at understanding the behaviour of minerals under extreme pressure); Economic Mineralogy (the study of the occurrence and properties of economically important minerals); Critical Metals and Rare earth elements (an evaluation of sources of rare metals that affect people’s daily lives when access is restricted); Environmental Mineralogy (how to treat and immobilise deleterious pollutants); Geochemistry and Petrology (the chemistry and constituents of rock types on earth, the moon and on planets such as Mars). The legacy of such a conference, De Villiers concluded, is a crucial combination of scientific collaboration in the name of advancing science. De Villiers said that South Africa, as a country with a large mining and mineralogical industry, as well as strong mineralogical, geological and geochemical research initiatives, was able to showcase its own ‘excellent research’ in the field of mineralogy, ‘while simultaneously providing South African scientists with exposure to cutting-edge research from the rest of the world’. Additionally, it served to expose young scientists and students from southern Africa to both the local as well as the international mineralogical environment. International collaboration in the field remained excellent, he added. ‘No scientist is an island … we all rely on information from other sources … and it is crucial to build on the edifice of previous and current work so that we can understand minerals and mineral constituents better. International collaboration is extremely important, not only for mineralogy, but for the whole of science.’ Provided by: Lynne Smit, HIPPO Communications

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Netted exclosures in Jonkershoek Nature Reserve. Image: Anton Pauw

Simulating a ‘world without birds’ in major field experiment Ecologists from Stellenbosch University (SU) are undertaking an unprecedented field experiment to simulate ‘the world without birds’. Six netted cages or ‘exclosures’ of 400 m2 each have been erected in the Jonkershoek Nature Reserve outside Stellenbosch, known for its rugged mountains and rare endemic plant and animal species. Prof. Anton Pauw, an evolutionary ecologist at SU who specialises in plant-pollinator interactions, says the global decline in pollinators highlights the question of how plant communities and their interacting animals will respond when an important pollinator is taken out of the system. ‘Many theoretical studies predict that the loss of an important pollinator species will trigger a cascade of linked extinctions throughout the community. Others argue that pollination is of little ecological importance because, in the absence of their primary pollinator, many plant species can compensate by self-pollinating or switching to other pollinators. ‘All in all, real evidence for community-level impacts is lacking. We hope that this community-level study will help to provide the insight needed to conserve and restore plant-pollinator interactions,’ he says.

Pieter Botha working outside a netted exclosure. Image: Anton Pauw

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The focus of the experiment is on the interaction between South African nectar-feeding birds, the iconic sugarbirds and sunbirds, and bird-pollinated plants, particularly proteas, in a community context. Although there are only four species of birds that only rely on nectar for food, they pollinate about 350 plant species. One of Prof. Pauw’s MSc students, Pieter Botha, has been studying the effect of bird exclusion on the pollination network since last year, when the first three exclosures were erected. He is also comparing the seed production of plants inside the cages to that of plants visited by bird pollinators in the control sites (which are not covered by nets). ‘We have already observed that the pincushions inside the cages have more nectar than those in the control sites outside where birds are actively feeding. In some cases we have also observed more ants visiting these pincushions,’ Pieter says. Other possible changes in the community they are investigating include the potential local explosion of planteating insects, as well as spiders. Apart from feeding on nectar, birds are also predators and consume hundreds of insects every day. These exclosures will allow the researchers to determine how important birds are in controlling the numbers of plant-eating insects. Prof. Pauw explains that the effect of more insects on plants is not easy to predict: ‘It is also not at all clear to what extent plants rely on their own defenses, such as tannins, to protect themselves against leaf-eating insects, and to what extent they depend on predators, like birds, to act as their bodyguards.’ After three years of excluding birds the veld will be burned, as natural fires are the trigger for germination in most fynbos plants. ‘If the lack of birds caused a meaningful reduction in seed production, we expect to see that the new veld will lack bird-pollinated plants, and will instead be dominated by insect and wind-pollinated plants, including aliens. All in all, we hope to be able to give a definitive answer to the question, from an ecological perspective, of whether birds really matter,’ he concludes. Issued by: Wiida Fourie-Basson, media: Faculty of Science, Stellenbosch University.


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A newly discovered dinosaur helps us to understand how dinosaurs could fly.

125-million-year-old Changyuraptor sheds light on dinosaur flight

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n international team of experts, including Professor Anusuya Chinsamy-Turan from the University of Cape Town (UCT), has discovered a new predatory dinosaur with very long feathers that sheds light on how dinosaurs flew. The animal has a long, feathered tail that is believed to have been useful in decreasing descent speed and assuring safe landings. The international research team was led by Dr Luis Chiappe, a palaeontologist from the Natural History Museum of Los Angeles County, USA. Their findings, which were published in Nature Communications on 15 July 2014, show that with a weight of 4 kg, the 122 cm-long Changyuraptor was the biggest of all fourwinged dinosaurs. Analysing the bone microstructure of Changyuraptor, Professor Chinsamy-Turan, a palaeobiologist and Head of the Department of Biological Sciences at UCT, said: ‘It shows that the animal was fully grown and that it had experienced at least five years of growth.’  The fossil of the 125-million-year-old dinosaur, named Changyuraptor yangi, was found in the Liaoning Province of north-eastern China. The location has produced a high number of discoveries in feathered dinosaur fossils over the last decade. The newly discovered dinosaur has a full set of feathers cloaking its entire body, including the extra-long tail feathers. According to Professor Chinsamy-Turan these microraptorine dinosaurs are known as the ‘four-winged’ dinosaurs, because the long feathers attached to the legs have the appearance of a second set of wings. ‘As we know, birds have wings on their forelimbs. However, about 10 years ago

predatory dinosaurs were discovered with wings on both their forelimbs and hind-limbs,’ said Professor ChinsamyTuran. ‘These recent discoveries pose an enigma as to how these microraptorine dinosaurs used their four wings to fly. Our new microraptor, Changyuraptor, is quite large, and we propose that its unusually long tail (30 cm in length) helped to keep it airborne and could have assisted with landing.’ The long feathers attached to both foreand hind limbs of these ancient predators have led researchers to conclude that the four-winged dinosaurs were capable of flying. Dr Alan Turner from Stony Brook University in New York, one of the paper’s co-authors, said: ‘Numerous features that we have long associated with birds in fact evolved in dinosaurs long before the first birds arrived on the scene. This includes things such as hollow bones, nesting behaviour, feathers and possibly flight.’ Although it remains uncertain how well these creatures flew, the discovery does explain the role that the tail feathers played during flight control. For larger flyers, safe landings are of particular importance. ‘It makes sense that the largest microraptorines had especially large tail feathers — they would have needed the additional control,’ added Dr Michael Habib, a researcher at the University of Southern California, USA, and another co-author of the paper. The discovery of the Changyuraptor consolidates the notion that flight preceded the origin of birds, being inherited by the latter from their dinosaurian predecessors. ‘The new fossil documents that dinosaur flight was not limited to very small animals but to

An illustration of Changyuraptor yangi showing the long, feathered tail. Image: S Abramowicz, Dinosaur Institute

dinosaurs of more substantial size,’ said Dr Chiappe. ‘Clearly far more evidence is needed to understand the nuances of dinosaur flight, but the Changyuraptor is a major leap in the right direction.’ Article from: Mologadi Makwela, Media Liaison Officer, Communication and Marketing Department, University of Cape Town, South Africa

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A 1:10 scale model of the ship on display at the Vasa Museum. The sculptures are painted in what are believed to be the original colours. Image: Peter Isotalo - Own work. Licensed

A model showing a cross-section of Vasas hull, illustrating the shallow hold and two gun decks. Image: Peter Isotalo - Own work. Licensed under

under Creative Commons Attribution 3.0 via Wikimedia Commons

Creative Commons Attribution 3.0 via Wikimedia Commons

Failures of technology or human failures? The history of science is full of experiments that did not work. Jan Smit, Pulane Masoabi and Rufus Wesi discuss some failures of technology. The double-barrel cannon The front lawn of the Athens City Hall, Georgia, in the US is adorned with a double-barrelled cannon facing north. This cannon was built around 1862 by John Gilleland, a Southerner, during the height of the American civil war between North and South. The concept was to connect the cannon balls in the two barrels with a chain. When the barrels were fired simultaneously the expectation was that the chain would mow down the enemy in the way that a scythe would cut down wheat. However, when the cannon was tested, the unexpected happened – the connected cannon balls flew erratically and instead of hitting the target, they ploughed into surrounding areas and tore down objects they were not intended to hit, causing considerable damage in the process. During one of the tests, the chain broke and the two balls flew in opposite directions. The aftermath of all these tests included a torn chimney, mowed down cornfields and saplings and a dead cow.

The double-barrelled cannon. Image: Bloodofox - Own work. Licensed under Public domain via Wikimedia Commons

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Although John Gilleland never conceded that his invention was a failure, it was ruled unfit for the purpose and eventually ended up as a museum piece and tourist attraction in front of the City Hall at Athens, Georgia. But why was the double-barrelled cannon a failure? The reason is simple: The two barrels could not fire at exactly the same moment because the combustion rates of the gunpowder inside the barrels were slightly different. The balls would thus exit the ends of the barrels split seconds apart. Consequently one ball would pull on the other, resulting in erratic movement and an unpredictable trajectory. The Vasa ship The year 1618 saw the beginning of a war between Sweden and Poland that lasted 30 years. As control of the contested Baltic sea was of vital importance to the two countries, the then King of Sweden, Gustavus Adolphus, drove efforts to increase the fleet of warships. The prime ship he ordered built was the Vasa. The king was so interested in the construction of this warship that he was personally involved in its design and frequently changed the building plans. The Vasa would have been an intimidating ship. Its main mast stood 190 meters high and three more masts carried 10 sails. The warship was heavily decorated with wooden lions and cannon decks, carrying 64 heavy cannons and 300 soldiers. One can just imagine how intimidating it would be to the enemy if the large ship appears on the horizon with the white sails bulging in the breeze, the lions and cannons high above sea level.


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Opening day of the Tacoma Narrows Bridge. Image: Licensed under Creative Commons Attribution 3.0 via Wikimedia Commons

The steam generator imported to Johannesburg from Scotland. Image: Sci-Bono Discovery Centre

oscillating, the cables snapped in a wind of about 60 km/h. This was the result of a resonance effect that was so large that the bridge twisted by about 450 degrees in two waves and oscillated up and down, forming nine waves of one meter. Although the bridge was flexible it could not withstand such severe deformations and collapsed. People on the bridge crawled to safety just in time before the collapse. The only casualty was a cocker spaniel dog. Although the investigation team found no faults in the design and construction of this suspension bridge, the failure of the tie-down cables caused the collapse. Had these cables been stronger the bridge would not have collapsed. Tacoma Narrows Bridge as it collapsed. Image: Licensed under Creative Commons Attribution 3.0 via Wikimedia Commons

The 69 meter long Vasa warship started its maiden voyage on 10 August 1628 in Stockholm harbour. It capsized and sank after 1 300 meters of its journey. Why did it sink?

One must bear in mind that in the seventeenth century people did not use plans in the design of constructions. The shipbuilder carried everything in his head and relied heavily on previous experience. The key reason for the disaster was that the centre of gravity of the ship (and everything on it) was higher than the point where the buoyant force (Archimedes force) acts on. In ideal circumstances, the two lines of force (one up and the other down) should coincide, resulting in a zero torque. If, however, the ship tilts slightly to one side the torque would cause it to capsize. This is exactly what happened. Why was the centre of gravity higher than the point of buoyancy? The answer lies in the fact that the weight of the ballast in the lower deck was too little. Furthermore, the 64 heavy cannons on the two upper decks, the heavy wooden structure, decorations and the high masts added to lifting the centre of gravity. It would have taken only a slight wind blowing sideways on the sails to cause the ship to capsize. Tacoma Narrows Bridge Built in 1940, the Tacoma Narrows Bridge connected Seattle and Tacoma in the US state of Washington. The bridge was suspended on steel cables from two masts. Tie-down cables anchored to the ground on both sides of the bridge were used stiffen it during windstorms. On 7 November of the same year (barely four months after it was opened to traffic), following violent twisting and

The steam generator Early in the nineteenth century, the fast-growing city of Johannesburg was in need of more electricity, mainly due to the added demand of the trams that criss-crossed parts of the city. One attempt to meet this challenge was to build a new electricity-generating plant in President Street, which later became known as the Electric Workshop. The building at present houses the Sci-Bono Discovery Centre. A large steam generator was imported from Scotland and installed in the Electric Workshop. Unfortunately no-one checked the suitability of the local coal to fuel the generator. The heat produced by the South African coal was insufficient to power the generator. As a result the imported steam generator was never used and never served the purpose for which it was imported. Today this impressive steam generator is on display in SciBono. To think about It remains for the critical reader to decide: Were the failures of the double-barrelled cannon, Vasa ship, Tacoma Narrows Bridge and steam generator failures of technology or were they human failures? q Dr Jan Smit is the manager of the North-West University Science Centre, Potchefstroom Campus. He is a nuclear physicist by training and specialises in physics education. He has a keen interest in the world around him and how it can be interpreted scientifically. Pulane Masoabi is a final year mechanical engineering student at NWU, Potchefstroom, and holds a prestigious Hexagon bursary. Rufus Wesi is the programme manager at Sasol Inzalo Foundation. He has a PhD in physics education. 10| 3 2014

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News

Nanochip in a capsule identifies bacterial infections within minutes A microbiologist and an electronic engineer from Stellenbosch University have developed a proof-of-concept nanowire biological sensor that can identify any of the major disease-causing bacteria such as Escherichia coli, Salmonella species or Vibrio cholera within ten to fifteen minutes. In the not too distant future, this combination of nanotechnology and microbiology could make the diagnosis of patients during an epidemic or outbreak an order of magnitude faster, more accurate and more affordable. Prof. Leon Dicks, an internationally acclaimed microbiologist, joined forces with Prof. Willie Perold, the electronic engineer. Together they conceptualised the idea of a nanochip that would be able to detect bacteria and viruses in the patient’s stomach within a few minutes after being swallowed. Deon Neveling, a postgraduate student in the Department of Microbiology at SU, was given the task to put this concept to the test as part of his research for a Master’s degree in microbiology.

Zinc oxide nanowires with antigens at the end bend as soon as antibodies adhere to them. The movement then generates a piezoelectrical signal. Image: Deon Neveling

Prof. Leon Dicks and Prof. Willie Perold in front of the building where they first shared ideas about the possibility of adapting the newly developed nanogenerator for detecting pathogens. With them are the two students involved, Deon Neveling and Dr Stanley van den Heever. Image: Wiida Fourie-Basson

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Zinc oxide nanowires as observed with an electron microscope. Image: Deon Neveling

The result? From the engineering side, Prof. Perold and one of his doctoral students, Stanley van den Heever, developed a zinc oxide nanogenerator which generates electricity the moment the nanowires are disturbed. This is the first time that it has been done in South Africa. Then Prof. Perold bumped into Prof. Dicks after a research meeting and they shared thoughts: ‘We came up with the idea to combine the sensor with “biological bait” to selectively attract bacteria. The idea was that the movement would generate an electrical signal which can instantly be picked up,’ he says. In order to prepare the nanogenerator for biological use, the engineers constructed a silicon chip of 1 cm by 1 cm in size. They then stacked zinc oxide molecules on top of each other to form a nanowire (only visible with an electron microscope). Thousands of these nanowires are positioned in such a way that the slightest disturbance of their structure will lead to, what engineers call, piezoelectric energy. This energy is converted to electrical energy and then amplified to produce a voltage reading. Enter the microbiologists. The concept was tested by attaching lysozyme molecules (small disease-fighting proteins present in our saliva) to the tip of each nanowire. As soon as antibodies specific to the lysozyme adhered to the nanowires, it caused a shift in the alignment of the zinc oxide molecules. This was observed as a change in electrical output and proof that the concept works. The reverse of the concept also holds true. That is, by attaching specific antibodies to the nanowires, they will detect the antigens characteristic of a specific pathogen (disease-causing microorganism) and report the presence of the pathogen within seconds. The key to the concept is linking the correct antibody to the nanowires to form a perfect, ‘one and only’, match with the antigen. Prof. Dicks says the concept can best be explained by comparing it with fishing. ‘We use bait (in the form of an antibody) to fish for antigens in the patient’s gastrointestinal tract. In our case the bait is attached to

thousands of zinc oxide nanowires cast on a silicon chip. In real life the chip will be constructed small enough to be encased in a capsule. Ten minutes after swallowing the capsule, the nanochip is released and the fishing trip starts. ‘Our dream is to transfer the electrical signal, which is selected to be unique to each pathogen, to a receiver such as a smartphone,’ he adds. This part of the concept still has to be developed. But, says Prof. Dicks, the important thing is that the nanochip concept works. ‘Instead of prescribing a broad-based antibiotic, or waiting 48 hours for the lab tests to come back, a doctor will be able to immediately prescribe the correct antibiotic to target the pathogen, and by doing so, put less stress on the body’s immune system.’

Could this concept work for identifying deadly viruses like Ebola? ‘Certainly’, he says, ‘as long as you have antibodies specific to antigens that are unique to the Ebola virus.’ Antigens are usually proteins located on the surface of cells. These proteins act as a ‘signature’ of that specific cell. This ‘signature’ is then recognised by specific antibodies. At present it is difficult and timeconsuming to diagnose a patient with the Ebola virus. This is because the early signs and symptoms of Ebola resemble those of several other potentially fatal diseases, such as malaria, typhoid fever, shigellosis, cholera, leptospirosis and meningitis. In the short term, Prof. Dicks plans to work with a group of French scientists to develop a nanochip biosensor implant that would report secondary infections: ‘The idea is to incorporate the biosensor into a patient during, for instance, a hip transplant. This would then allow the surgeons to detect the slightest form of secondary infections that may develop during the recovery phase,’ he explains. The results of the research were recently published in the journal Sensors and Actuators B: Chemical. Issued by: Wiida Fourie-Basson, media: Faculty of Science, Stellenbosch University.


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Cutting-edge car research at new battery testing lab South Africa’s second-biggest battery testing lab – based at NMMU – is leading national research on batteries for electric cars, ‘stop-start’ vehicles and renewable energy traffic and street lights. By Nicky Willemse.

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ressure to reduce CO2 emissions in cars has led to the development of a ‘stop-start’ system, which automatically switches off a car’s engine when it comes to a standstill in traffic jams or at traffic lights, and restarts it as soon as the driver presses the clutch pedal or releases the brake. A number of new cars on South Africa’s roads boast this new system – but they are dependent on advanced lead-acid batteries, which are currently only produced overseas and imported by the automotive manufacturers. Replacing these batteries is expensive and there is pressure for local manufacturers to use locally manufactured components – two good reasons why the production of these batteries is one of the many energy storage projects on the go at Nelson Mandela Metropolitan University’s (NMMU's) newly launched battery testing laboratory. The facility is the second independent battery testing laboratory of its kind in the country, the other being the South African Bureau of Standards (SABS). In addition to the conventional testing of commercial lead acid batteries, which ensures that the battery in your new car, or a replacement battery, complies with the minimum requirements of specified performance, NMMU’s laboratory will also be pioneering national research into new battery technology that will include the testing of lithium-ion batteries for electric vehicles. ‘We are the first laboratory in South Africa that will be equipped to do lithium-ion battery testing,’ said NMMU battery electro-chemistry expert Prof. Ernst Ferg. ‘Lithium-ion battery compliance testing is not a simple thing. Due to the nature of the battery and the chemicals involved in its manufacturing, a testing facility must meet stringent safety requirements. ‘When the performance of these batteries is tested under extreme conditions of, for example temperature, or when damaged or punctured during a simulated accident, every precaution needs to be taken to ensure that the resulting fires can be safely extinguished.’ Also in the pipeline at the lab is battery testing and research for the renewable energy field. This includes off-the-grid energy storage, and stand-alone traffic lights, street lights and electric vehicle charging stations. The laboratory, which opened in May this year, is linked to the university’s uYilo e-mobility programme (sparked via the government’s Technology Innovation Agency [TIA] initiative), which focuses on national electric vehicle research and development, and is run by NMMU’s engineering technology institute eNtsa. ‘When the government gave NMMU the go-ahead to establish the uYilo e-mobility programme, it was decided in that exercise to include the battery testing laboratory, as batteries are a key component of electric vehicles,’ said Ferg. The lab has been set up to conduct standard and specialised simulated battery testing, according to various international battery manufacturers’ and users’ criteria, in collaboration with the local automotive industry. The lab is also conducting research and development with the local battery-manufacturing industry.

Joining the uYilo battery research leader Prof. Ernst Ferg (right) are student Natasha Erasmus and Dr Nico Rust. Image: NMMU

‘With the ever-increasing competitiveness of the automotive industry, the demand for component suppliers to comply with stringent specifications is increasing. In addition, imported components for the local industry are increasingly available. To be able to compete, local manufacturers need to provide new battery types that adhere to a range of international testing standards in the shortest possible time, and yet be able to make these batteries cost-effective within their manufacturing environment.’ The lab’s testing equipment includes a 16-channel 100A 18V tester and a high-rate 2 000A discharge tester with four temperature-controlled water baths and a freezer unit to allow for variable temperature testing. It also has a battery vibrational tester that can evaluate a battery’s performance under a simulated vibrational frequency similar to that typically experienced in a driven car. By early next year, several more testing units will have been installed to allow for higher voltage testing and bi-directional testing. The research side of the facility, which is located in the university’ s chemistry department, has additional battery testing equipment, along with analytical equipment used to study the materials used in the building of batteries. The lab has a number of collaborative research projects with the international Advanced Lead Acid Battery Consortium (ALABC), whose members include battery manufacturers worldwide. ‘They are funding research projects that look at new materials, chemistries and applications of the lead acid battery that can make it more efficient to survive the demands of today’s automotive industry and competition with other energy storage systems.’ Ferg said there were currently very few pure electric vehicles on the roads in South Africa, with most local automotive manufacturers focusing on producing hybrids that include an efficient fuel engine with an electric battery. ‘The lab will be looking at the international testing requirements for batteries in such applications and will eventually be able to work with batteries that are used in stop-start, mild-hybrid, plug-in hybrid and full electric vehicles. Under the uYilo programme, a number of pure electric vehicles are being evaluated. These include the Nissan Leaf and the Joule, South African Optimal Energy’s prototype vehicle. The charging infrastructure and energy usage of these vehicles, which make use of large lithium-ion batteries, are being studied by the team. Also being evaluated are electric game-viewing and rough-terrain vehicles (RTVs), which are being used by a local game reserve in their antirhino poaching initiatives. ‘We will look at the performance of the batteries in these in-use vehicles and their use of off-grid charging stations.’

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Books

Identifying through behaviour Behaviour briefs: Quick guide to southern and East African mammal behaviour. By Chris and Mathilde Stuart. (Cape Town. Struik Nature. 2014) This is another in the ‘briefs’ series and is literally pocket sized – perfect if you are hiking and want to carry as little as possible. Although the book concentrates on behaviour, the photographs and descriptions allow this to double as a quick identification guide. The book discusses that mammal species and the behaviours that you are most likely to encounter in the game parks of southern and East Africa. The authors hope that using this book will whet the appetite for not just identifying, but understanding what you see and interpreting the ‘signposts’ that mammals leave. There is a brief description of the evolutionary reasons for particular behaviours, such as territoriality, mating and breeding behaviour, competition, social interaction, feeding and personal hygiene. The book deals with individual species or groups of related species, so if you know what you are watching you can use the contents list and check the images on the correct pages to see if you can recognise the animal’s behaviour. You could also read through the whole text, so that the next time you encountered a specific animal you would already have an idea of its behaviour.

Ecological management

Meteorites: A southern African perspective. By Ronnie McKenzie. (Cape Town. Struik Nature. 2014)

Fynbos: Ecology and Management. Editors: Karen J Esler, Shirley M Price and Charl de Villiers. (Pretoria. Briza. 2014)

Meteorites are the remnants of meteors from space that have survived the journey through Earth’s atmosphere without being burnt up. These relatively rare remnants have fascinated people for centuries and carry important information about the formation of our universe. This book provides a handy basic guide for anyone who is new to the topic and for anyone who would like to collect meteorites. The introduction explains what meteorites are, how they are derived from meteors, where meteorites come from and what they are made of. There are many famous structures associated with meteors in southern

The Fynbos Biome is possibly one of the best known of our unique floral kingdoms and parts have attained World Heritage Site status. The word fynbos probably derives from the Dutch fijnbosch – describing the timber of the region, which was too slender or fine for harvesting for use by the settlers of the mid 1600s – probably just as well. Another possible reason for the

Rocks from space

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Africa, such as the Vredefort impact structure in South Africa and the Roter Kramm crater in Namibia, and these are covered in some detail. Obviously identifying meteorites is important and this is covered in detail, with excellent explanations of technical terms such as fusion crust, flow lines etc., as well as information on the age of meteorites and their classification. Did you know that in South Africa, Namibia and Botswana all new meteorites belong to the government of the country in which they were found and are protected by law? And that you can invest in meteorites – if you know what you are doing? This book provides a wealth of information for curious minds.

10 |3 2014


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name is the small or fine-leaved shrubs that dominate the fynbos. There are three shrubland types that are broadly categorised as belonging to the fynbos region – true fynbos, renosterveld and strandveld. The book includes all three when ‘fynbos’ is referred to. Perhaps fortunately, fynbos grows in nutrient-poor sandy soils that are unsuited to conventional agriculture and it covers a large area of the Western Cape region. This book covers just about everything you could possibly want to know about the fynbos. The biome is discussed in detail. Fire management is all important and there is a section on how to burn your own land when you are lucky enough to own a tract of fynbos that requires seasonal burning. Alien management is discussed, as is the management of natural vegetation fragments in agricultural and urban environments. Essentially the nine chapters in the book provide all you require to understand the ecology and management of this wonderful vegetation. The guide has been compiled to allow land users to manage the veld sensibly, but is also a wonderful compilation of information for anyone interested in this type of vegetation.

Your body BodyWorks. By Anna Claybourne. (Cape Town. Struik Lifestyle. 2014) How do you hear, see and smell? How do muscles make you move? Why is blood red? Are you ready to discover how your body works? This book is described as ‘bursting with revolting facts and cool activities – the perfect book for budding biologists’. I would add health professionals to that. This is not a collection of facts, but a romp through the incredible world of the human body – a complex organism, but easy to understand if approached in this way. Each organ or system is described and then explained using activities that are easy to set up and do not require lots of equipment – useful at school and at home – and for kids of all ages. Anyone who wants to learn about their body would enjoy this book.

Ancient beasts Famous Dinosaurs of Africa. By Anusuya Chinsamy-Turan. Illustrated by Luis V Rey. (Cape Town. Struik Nature. 2014) Although this book is written for children it will appeal to anyone who loves dinosaurs and I know plenty of adults who do. The word dinosaur means ‘terrible lizards’ but as the introduction to the book explains, dinosaurs were not lizards. They were specialised reptiles that descended from a prehistoric group of reptiles called archosaurs, which means ‘ruling reptiles’. The archosaurs also gave rise to flying reptiles called pterosaurs and to the crocodilians from which crocodiles and birds descended – the only living relatives of this group. There is a dinosaur family tree that explains all these relationships. The earliest dinosaurs evolved during the Triassic Period and the group was present on Earth until towards the end of the Cretaceous Period. Between the Triassic and the Cretaceous there was massive continental movement of the Earth’s crust and so the group spread across the globe. The process of fossilisation and how fossils are excavated is explained in a simple way, leading into early dinosaur discoveries in Africa – from Madagascar, to South Africa to Tanzania. Dinosaurs were a diverse group and the book is split into sections dealing with fish-eating dinosaurs, meat-eating dinosaurs, the armoured sauropods and all the other groupings including cannibals and sociable dinosaurs – not forgetting the famous flying dinosaurs. Suggested projects are making a cast of a ‘fossil’, making a model dinosaur, examining tracks made in sand (to work out what sort of animal made the track) and a quiz about dinosaurs to be answered after reading the book. One of the most interesting of the projects is testing the effectiveness of the stomach stones or gastroliths that are found in dinosaur stomachs (fossils of course) in breaking down vegetation and generally aiding digestion. This is their function in the modern animals in which gastroliths are found, such as ostriches, crocodiles and seals. A really fun book! 10 |3 2014

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❚❚❚❙❙❙❘❘❘ News

Not all songbirds sing about love A divorce rate of over 60% after the first year, extramarital affairs, illegitimate offspring and deceit. This is the world of the Crimson-breasted Shrike, a nimble and restless South African bird best known for its striking red colour and penetrating whistles. By Wiida Fourie-Basson.

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he Crimson-breasted Shrike (Laniarius atrococcineus) belongs to the family of songbirds called oscines. This group of more than 4 600 species worldwide are known for their beautiful singing and include orioles, warblers and thrushes. The Crimsonbreasted Shrike, however, is one of the few species (less than 5% of all bird species) that engage in duets.

What is so special about duets? What do shrikes sing about? And what is so special about duets? Based on three years of observation and genetic analysis, researchers from Stellenbosch University and the University of Oldenburg in Germany can now say with relative certainty that they have a very good idea what shrikes sing about. The results of the research were published in September 2014 in the journal Behavioral Ecology and Sociobiology entitled ‘Crimson-breasted Shrike females with extra-pair offspring contributed more to duets’. Prof. Michael Cherry, a behavioural ecologist in the Department of Botany and Zoology at Stellenbosch University and one of the authors, says that while social monogamy is relatively rare in the animal kingdom, over 90% of avian species are socially monogamous, compared with only 3-5% of mammalian species. However, social monogamy does not imply sexual monogamy. Since the advent of paternity testing in the 1980s, scientists now know that, on average, about 11% of the baby birds in any nest are sired by someone other than the resident male: ‘Both males and females can actively seek out extra-pair matings,’ he explains. Duetting birds, however, were thought to be an exception: ‘One hypothesis is that duetting functions to reinforce the bond between the couple, thereby reducing extra-pair mating in both sexes. The male will sing “I am here” and then the female answers “I am also here” and so on. Other hypotheses are that duets serve in territorial defence, mate guarding, mutual recognition and maintaining contact in dense vegetation.’ Doctoral student Irene van den Heuvel, supervised jointly by Prof. Cherry and Prof. Georg Klump of the University of Oldenburg,

The Crimson-breasted Shrike. Image: Irene van den Heuvel

Doctoral student, Irene, with her study species. Image: Irene van den Heuvel

set out to test two of these hypotheses. First, that duetting is used for paternity guarding and, second, that participation in a duet is a signal of commitment to genetic monogamy. They combined an analysis of the acoustics of duetting with a genetic analysis using microsatellite DNA markers to investigate the mating patterns of the Crimson-breasted Shrike at the Kuruman River Reserve in the southern Kalahari Desert. During three consecutive breeding seasons, they studied 19 pairs and 83 nestlings from 44 broods.

What they found The results were completely the opposite of what they had expected. Twenty per cent of all young born to the 19 females tested were sired by extra-pair males. The results offered no support for the idea that duets function in paternity guarding. Most remarkably, females with illegitimate offspring were significantly more likely to answer their mates’ song than females without. Prof. Cherry says they found no evidence for duets functioning as a signal of commitment: ‘Female vocal behaviour was in fact the reverse of that predicted. Levels of infidelity among social females were positively related to female answer rate of their mates’ song. ‘These results suggest that females may use increased answer rates as a form of manipulation, to prevent divorce and to make sure that the male helps with building nests and feeding the young,’ he says.

One of the pairs of Crimson-breasted Shrikes that were part of the study. Image: Irene van den Heuvel

An earlier paper by the same authors recorded that divorce in Crimson-breasted Shrike pairs is uncommon after the pair has been together for more than one breeding season. Newly formed pairs, by contrast, have a 60% chance of divorce. But as extra-pair paternity is not confined to females in newly formed pair bonds, it is unlikely that males of this species are able to assess their chances of being cuckolded, the researchers conclude. Q Wiida Fourie-Basson is media-officer for the Faculty of Science at Stellenbosch University. She is a former journalism lecturer and holds an MA-degree in Communication from UNISA. Irene M van den Heuvel, Michael I Cherry, Georg M Klump. Crimson-breasted Shrike females with extra pair offspring contributed more to duets. Behavioral Ecology and Sociobiology. 2014;68:1245-1252.

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Back page science

Supernova seen in two lights The destructive results of a mighty supernova explosion reveal themselves in a delicate blend of infrared and X-ray light, as seen in this image from NASA’s Spitzer Space Telescope and Chandra X-Ray Observatory, and the European Space Agency’s XMM-Newton. The bubbly cloud is an irregular shock wave, generated by a supernova that would have been witnessed on Earth 3 700 years ago. The remnant itself, called Puppis A, is around 7 000 lightyears away, and the shock wave is about 10 light-years across. The pastel hues in this image reveal that the infrared and X-ray structures trace each other closely. Warm dust particles are responsible for most of the infrared light wavelengths, assigned red and green colours in this view. Material heated by the supernova’s shock wave emits X-rays, which are coloured blue. Regions where the infrared and X-ray emissions blend together take on brighter, more pastel tones. The shock wave appears to light up as it slams into surrounding clouds of dust and gas that fill the interstellar space in this region.

during warm phases and became extinct during cold ones. Today, crocodiles are so-called coldblooded animals living mainly in fresh waters, though two species are exceptions that venture occasionally into the sea – Crocodylus porosus and Crocodylus acutus. Because crocodiles live in tropical climates, their fossils are often used as markers of warm conditions. While only 23 crocodile species live today, there were hundreds in the past, according to scientists. And four times in the past 200 million years, major lineages entered the seas, then died out.

Image: Torresol Energy, Spain ©SENER

Source: Fraunhofer-Gesellschaft

Delivery by drone

Artist’s illustration of a type of marine crocodilian called dyrosaurid, near the end of the Cretaceous period. Image: Guillaume Suan

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

From continent to continent: Electricity transmission between Africa and Europe

The supernova. Image: NASA/ESA/JPL-Caltech/GSFC/IAFE)

Past global warmings were good times for sea crocs Courtesy of the University of Bristol and World Science staff

Past episodes of naturally caused global warming were golden opportunities for sea crocodiles to spread, according to a new study. The work found that ancestors of today’s crocodiles colonised the seas

In the ‘Super Grid’ project, Fraunhofer ISE is working on the optimisation and integration of thermal storage systems in order to increase the flexibility and efficiency of solar thermal power plants.

The largest solar power plant in North Africa is presently being built in Ouarzazate, Morocco. In 2016 the plant should produce cheaper, emissions-free electricity for half a million people. In future, projects like the one in Ouarzazate could also generate electricity for the European continent. Electricity transmission between continents requires a reliable network, even at the production sites. The Fraunhofer Institute for Solar Energy Systems ISE, together with other Fraunhofer institutes, is investigating different aspects of a so-called ‘Super Grid’. Their research involves modelling a suitable energy system, developing technological solutions for storage as well as the generation and distribution of DC power.

A new algorithm lets drones monitor their own health during long package-delivery missions. In the near future, the package that you ordered online may be deposited at your doorstep by a drone. Last December, online retailer Amazon announced plans to explore drone-based delivery, suggesting that fleets of flying robots might serve as autonomous messengers that shuttle packages to customers within 30 minutes of an order. To ensure safe, timely, and accurate delivery, drones would need to deal with a degree of uncertainty in responding to factors such as high winds, sensor measurement errors, or drops in fuel.

An experimental delivery drone. Image: myventure.in

Source: MIT

MIND-BOGGLING MATHS PUZZLE FOR Quest READERS Q uest Maths Puzzle no. 30

There are 6 astronauts in a rocket with enough food for 40 days. 2 new astronauts joined them after being rescued. If the new crew did not have any food with them, how many days would the food last with all 8 on board?

Answer to Maths Puzzle no. 29: Place 1 white marble in one bowl, and place the rest of the marbles in the other bowl (49 whites, and 50 blacks). 
This way you begin with a 50/50 chance of choosing the bowl with just one white marble, therefore life! BUT even if you choose the other bowl, you still have ALMOST a 50/50 chance at picking one of the 49 white marbles.

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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, 31 October 2014. 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. 30’ 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.


STUDY PHYSICS AT THE FACULTY OF SCIENCE AT THE UNIVERSITY OF JOHANNESBURG

Study Chemistr Innovatively Creatingy at the New Knowledge Faculty ofand Science, Leading Scientists University of Johannesburg OUR MAJOR RESEARCH FOCUS IS ON: • CATALYSIS WITH EMPHASIS ON SELECTED INDUSTRIAL APPLICATIONS AS WELL AS • ORGANIC AND INORGANIC MEDICINAL COMPOUNDS • DETERMINATION OF MOLECULAR STRUCTURES • NANOMATERIALS • ATOMIC SPECTROSCOPY AND HYPHENATED TECHNIQUES WE ALSO OFFER • An undergraduate academy where promising chemistry students get the opportunity to do research alongside postgraduate students • 100% bursary plus R5000 for top learners in science • The highest quality of education at all levels • A comprehensive range of degrees and diplomas • Internationally accredited qualifications • World-class research facilities • Top notch academics with high quality research output • Opportunities for conducting groundbreaking research

OUR RESEARCH FOCUS IS ON Astrophysics | Condensed Matter Physics | High-Energy Physics | Nuclear Physics | Theoretical Physics | Solar irradiation | Physics VISIT OUREducation WEBSITE AT

WWW.UJ.AC.ZA/SCIENCE Some research projects in UJ Physics are tailored to use MeerKAT and the SKA OR in the long term Academic staff at UJ Physics are taking a leading role(011) in broadening CONTACT US AT 559-2374 the training of students in astronomy, astrophysics, space science and cosmology across South Africa, as part of the National Astrophysics and Space Science Programme WE ALSO OFFER 100% bursary plus R5000 for top learners in science | The highest quality of education at all levels | A comprehensive range of degrees and diplomas | Internationally accredited qualifications | World-class research facilities | Top notch academics with high quality research output OPPORTUNITIES FOR CONDUCTING GROUNDBREAKING RESEARCH. Visit our website at www.uj.ac.za/science or contact us at 011 559 3826


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