FACULTY FOCUS A MONDAY MONTHLY SUPPLEMENT FACULTY OF SCIENCE
Frontiers of science Page 6&7
Homegrown knowledge Page 4&5
Big data Page 10&11
Citizen science Page 8&9
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A WORD FROM BLINDED THE DEAN BY SCIENCE? Professor Anton le Roex Curated by Yusuf Omar Dean of Science UCT facilities that let you take a closer look at the world around The Faculty of Science has a long and distinguished history. Formally you – whether you’re peering into the depths of space and time, or established in 1918 by UCT’s founding act, today it’s a sizeable faculty studying the behaviour of subatomic particles in very cold conditions. of 12 departments and multiple research units, whose teaching and research is internationally acknowledged for excellence.
Colleagues of days gone by include To maintain this high standard, building on our established research and learning that is going on in the two Nobel Prize winners (Aaron and to increase our international strengths and critical mass. They faculty at any one point in time, Klug and Allan Cormack, both visibility and impact, the faculty also lend themselves to cross- and I hope it inspires you – whether from the Department of Physics), agreed earlier this year to focus multi-disciplinary engagement – the you’re involved in the sciences or while today, some 40% of our its research energies on six broad watchwords of academic research not – to make connections with academic staff are rated by the impact areas that straddle the and teaching today. You can read and in the faculty; whether by NRF as either international leaders disciplines represented by the about each of them in the graphic engaging with students, teachers, (A-rated), having strong international existing 12 departments. These below. and colleagues, or simply by reputations (B-rated), or being impact areas are: African Climate This strategic focus also informs considering new perspectives. outstanding young researchers and Development; Biodiversity the overarching theme for this with the potential to become and the Cape Floristic Region; Monday Monthly supplement focused on the sciences: the importance of world leaders (P-rated). With over Chemistry and Biology for Health Further information about the faculty, Image supplied
understanding the world we live in, Michael Hammond by Photo BV Cryogenics of Leiden Image courtesy 800 research master’s and PhD in Africa; Marine Biology and its departments, research units and students, the faculty also contributes the Southern Oceans; Southern so that we can leave it an improved world for future generations. centres can be obtained from the 25% of the publication output of Skies and the Evolving Universe; website: www.science.uct.ac.za Electron microprobe Optical telescope Dilution fridge the university and over a third of the Human Evolution and the African While the stories you’ll read in university’s annual PhD graduates. Quaternary. These areas leverage this supplement represent only a With an electron microprobe, you can study the chemical It’s not immediately visible to passers-by, but neither UCT’s Physics Department will be home to the coldest composition of tiny volumes of solids (from boron through are the things it sees. The Department of Astronomy’s place on the African continent when the department takes There is much to be proud of. our geographic advantage, while fraction of the research, teaching to uranium), at the micron scale. [A single hair is 40 to 50 new optical telescope is tucked away in the dome of the delivery of a dry dilution fridge in early 2015. This state-of- microns wide]. This device effectively shoots electrons at RW James building. Offi cially named the Tony Fairall Teaching the-art instrument has a base temperature of 7mK, which your sample, causing elements contained in it to emit X-rays Observatory in December 2013, the facility comes equipped is seven thousandths of a degree above absolute zero. At that the microprobe diffracts through different crystals, and with a new Celestron 14-inch telescope, as well as a charge- -273.15 degrees Celsius, absolute zero represents the lowest then measures. coupled device, which captures light more effi ciently than temperature possible – nothing can be colder, and an object SETTING THE At UCT it’s often used to analyse kimberlite (a form of photographic plates, and a spectrograph cap (a device that at absolute zero retains no heat energy. igneous rock in which diamonds are found), for elemental allows you to see and record the lines in a spectrum of light). The cryogenic system uses a mixture of the isotopes mapping (showing the distribution of elements in a sample), The Celestron’s large 14-inch aperture gives stargazers helium-4 and helium-3 in combination with high-powered or for cathodoluminescence imaging of zircon grains (if you a sharp view of the solar system under clear conditions, MagLev (magnetic levitation) turbo pumps to achieve its SCIENCE AGENDA shoot electrons at luminescent materials, it can cause the including all the features on the moon, detail in Jupiter’s ultra-low temperatures and high cooling power. What kind of emission of visible wavelengths. Zircon (seen in this image clouds and belts, and even a faint glimpse of Pluto. Weather research can it be used for? Quantum cryptography (encoding Science’s new research focus has six areas of strategic impact – through an electron microprobe) is not only luminescent, but permitting, astronomers can also feast their eyes on deep- messages using physics, not mathematics), transporting single also incredibly durable, meaning it is contained in some of sky objects such as nebulae and galaxies. The Department electrons at a time, and the characterisation of nanocomposites making the most of the faculty’s research strengths and critical the oldest rocks on Earth. of Astronomy is compiling a 2015 calendar featuring images (man-made materials built using nanoparticles), for example. mass, in conjunction with our geographic advantage. UCT’s JEOL Superprobe JXA-8100 Electron Probe taken through the telescope. This facility will provide valuable training opportunities for Microanalyser facility is operated by Chief Scientifi c Offi cer The telescope is already being used to teach astronomical students at all levels and allow UCT to become a player in Christel Tinguely and supervised by Dr Johann Diener. techniques to second-year students and optical photometry to a very active and exciting international fi eld, says Professor third-year stellar astrophysics students. Mark Blumenthal, the physicist who will oversee the use of African Climate Biodiversity & the Chemistry & Biology The observatory runs under the direction of Professor Claude the dry fridge. & Development Cape Floristic Region for Health in Africa Carignan and Associate Professor Patrick Woudt.
Africa occupies a critical global position for the study The Greater Cape Floristic Region includes two Mediterranean biomes; The major global medical need of the 21st century of large-scale climate and environmental processes. fynbos (which includes renosterveld) and the succulent karoo. The will be in Africa, given the high disease burden Straddling the tropical, subtropical and temperate succulent karoo biome is the world’s greatest arid hotspot and the and scale of the populations. The clinical expertise climate systems, as well as the Indian, Atlantic and fynbos biome diversity competes with that of the Amazon forest. at UCT, coupled with the wide ethnic diversity Southern Oceans, the continent is infl uenced by a wide Besides encompassing an enormous amount of plant biodiversity, of patients, makes the Western Cape a good variety of atmospheric and oceanic circulation systems, the region includes high levels of animal biodiversity, archaeological environment to conduct translational science and including the dominant Agulhas and Benguela currents. diversity and important perspectives on landscape development, medicinal research relevant to Africa, and the These systems affect much on the African continent; its climate change and earth history. Faculty of Science is well placed to play a major changing climate, its biota and human development. As a role in this regard. The Western Cape is arguably developing continent, our location also provides us with the biotech hub of Africa – enjoying strong support a clear advantage in terms of science and technology from the Department of Science and Technology applications to social development in Africa. and strong links with the pharmaceutical industry. Bolus Herbarium curator Terry Trinder-Smith. Photo by Je’nine May
Prof Anusuya Chinsamy-Turan inside the Michael Hammond by Photo FACULTY OF SCIENCE Bolus Herbarium Palaebiology Laboratory. Photo by Je’nine May Human Evolution & Mantle Room the African Quaternary UCT’s Bolus Herbarium houses more than 350 000 specimens of dried plants, and is particularly noted for its broad representation Palaeobiology Laboratory Thought to be the largest collection of its kind, the Mantle of Cape fl ora. The third-largest herbarium in South Africa The western and southern seaboards have archaeological Bones might be all that’s left of them, but that’s just enough Room in the Department of Geological Sciences houses a Southern Skies & Marine Biology & the and the third-largest university herbarium in the southern and palaeontological sites of world importance, which for UCT’s Palaeobiology Laboratory to uncover some of the collection of over 10 000 upper mantle-derived materials hemisphere, the Bolus Herbarium is ideal for teaching students shed light on human evolution and the behaviour of the Evolving Universe Southern Oceans mysteries of vertebrates past. (mantle xenoliths and xenocrysts, kimberlites and related early modern humans. Our geographic position, and about the diversity of Southern African fl ora, and for researching rocks, megacrysts, and deep-crustal xenoliths). These are our ‘living laboratories’ of local resources, provide The astronomical landscape in South Africa has changed dramatically The marine environments around South Africa are individual specimens. Bones refl ect a variety of events that affected an individual’s used for research purposes, and collected mainly from South the Faculty of Science with special opportunities, life, including phylogeny (a species’ historical evolution) and over the last decade. This is due to the construction of the largest among the most diverse anywhere in the world, and Housed in the Department of Biological Sciences, the herbarium African diamond mines, including Jagersfontein, Finsch, particularly in the earth and life sciences, to make optical telescope in the southern hemisphere (SALT), the Karoo Array result from the meeting of the major Benguela and ontogeny (an individual’s development from embryo to adult). Jwaneng and Kimberley. important contributions to questions of global scientifi c Telescope (KAT-7), and MeerKAT (to be completed in 2016), and with Agulhas currents associated with the South Atlantic facilitates research in various disciplines, such as taxonomy By studying the microscopic structure of fossilised bones, importance and establish ourselves as international the successful SKA bid for southern Africa (due for completion in and Indian Oceans, respectively, bounded to the south (scientifi c classifi cation), systematics (the diversifi cation of scientists can gain insights into the biology of extinct animals. A one-of-a-kind collection in terms of both the variety of leaders in the fi eld. Moreover, our location provides 2022). Given our geographic advantage (with access to the southern by the southern ocean. Furthermore, the interplay living forms), biogeography (the distribution of species across specimens and range in locality, the Mantle Room includes But it’s not just long-dead species that the lab studies. faculty researchers with ready access to southern- skies); close proximity to the South African Astronomical Observatory; between these major currents and the southern ocean geographic space and time), endemism (specimens unique to a samples from Russia to Brazil, assembled over the past 50 Reptiles, turtles, and a range of bird species are studied to hemisphere climatic and environmental records over the the SKA South Africa project offi ce and MeerKAT remote operations are central to African climate variability in the region, defi ned geographic region) and pollination biology. years, and is available to researchers from around the world. timespan of the Quaternary. These records are urgently headquarters; in addition to our strengths in observational astronomy, and diverse biology. The Faculty of Science has a long- provide a deeper understanding of factors that infl uence bone needed for integration into conceptual and computer- multi-wavelength radio astronomy, high-energy particle physics, gravity standing international reputation for marine research, It is also home to more than 14 500 type specimens (specimens growth. These enrich the lab’s core aim of shedding light based models of hemispheric and global climate change, and cosmology, the Faculty of Science has an unparalleled opportunity to both biological and oceanographic, and is thus used to describe a species for the fi rst time) with representatives on the lives and make-up of extinct animals, from fl ightless and will contribute to an improved understanding of become an international leader in the study of the southern skies and perfectly placed to be an international leader in this of the Cape fl ora forming the bulk – making it the most type-rich dinosaurs, to therapsids (mammals and mammal-like reptiles), earth system dynamics. the early universe. impact area. herbarium in South Africa. Each of the hundreds of thousands parareptiles (a contested sub-class of ancient reptiles) and of specimens is kept safe in steel cabinets. extinct elephants. 4 MONDAY MONTHLY SUPPLEMENT SCIENCE 5
Star trails over Sutherland emerged, and understanding more words: “Diseases like HPV, HIV and coastal fi shing communities and some about this progression can tell us about the rotavirus, which causes diarrhoea in of my work is about understandingGROWING The diversityour own physiology of our andoceans psychology.” babies, affect people disproportionally different ways of knowing about the in developing countries. I do think we Every year more than 500 different same ecological context, and how we have a responsibility to try and fi nd can co-produce useful knowledge in species of fi sh and seafood are solutions, especially at an institution YOUNG harvested from our waters – enough partnership with local communities. I such as UCT, which is capable of such think it is very important that we open to provide adequate food for our sophisticated science.” local population, in Professor Colin Local problems, local ourselves up to understanding the Atwood’s opinion. Atwood, who solutions different values and cosmology thatSCIENTISTS local communities may have, especially focuses on wild fi shing (as opposed South Africa remains the country to marine aquaculture), explains that in a country such as ours, with such aCompiled by Yusuf Omar with the highest incidence of those pluralistic legal environment, where up in some cases we have overfi shed living with HIV in the world, and the certain species; but that others, such to 50% of people follow customary enormous cost of the disease, both law. Ideally we should be collaborating as hake, show increasing population human and economic, is felt most UCT’s top scientists are numbers. “The real problem comes together with these communities to set keenly here. In cases such as this, local Proudlythe research African agenda.” science with governance. How can we ensure science can have an important role to recognised globally for their the proper regulation of our fi shing play in creating homegrown solutions. Do local scientists have a responsibility work, but Associate Professor industry in a way that protects our “Such problems also encourage to help raise the profi le of science natural environment while supporting a multidisciplinary approach, and I on the continent? Professor Bruce David Gammon recognises that the livelihoods of smaller fi shers?” believe this is something which has Hewitson believes so. As a climatologist Two major currents so close to each emerged naturally throughout the he believes it is essential that African grooming the next generation is other, the cold Benguela Current faculty,” says Le Roex. scientists educate the international just as important to keeping the along the west coast of South Africa Professor Janet Hapgood, from the community about our knowledge and the warm Agulhas Current off Department of Molecular and Cellular needs. “We must reverse the process Faculty of Science in shape. the east coast, together with the vast Biology, researches what form of as it has so often happened before, by Southern Ocean further south, mean contraceptives best suit women at risk making sure that African science leads For the second year running, the assistant dean has spent that South Africa occupies a unique of contracting HIV. She cautions that the Africa agenda, rather than simply a week in July sharing the wealth of UCT’s scientifi c oceanographic position. Professor while great strides have been made, responding to the priorities set from research with fi rst-year students, equipping and inspiring Chris Reason explains that “studying many challenges to collaboration elsewhere in the world.” them for the semester ahead. the Agulhas Current and the Southern still exist. “I believe that we must To raise the profi le of African HOMEGROWN SCIENCE Ocean is extremely important because Some 50 students discussed the physics of optical create better incentives and forums to science is also to invest in students of the key role they play in global phenomena such as sun halos – often seen around Cape facilitate interdisciplinary partnerships, themselves, both to encourage students Town – with mathematician Dr Jonathan Stock, and climate and change.” particularly between faculties and from diverse demographics to enter Story by Ambre Nicolson explored whether science could save lives with Dr Wendy different institutions.” the fi eld and also by giving them the Burger, with reference to her own work on HIV and TB. Dr Miguel Lacerda uses statistical opportunity to learn here and then Our problems This was among a range of other lectures and Why is it important for us to understand our local environment – models to identify regions in the HIV import that knowledge back into their Some of the problems we face as a genome that are important for vaccine own local contexts. “Something that is excursions, including a visit to the West Coast Fossil our southern skies, southern oceans and all the fl ora and fauna in country, and as a continent, are specifi c design. His work, he says, would not be very exciting about the current interest Park at Langebaan to see the active Stone Age dig and to the developing world, and many possible without collaboration between in our work, “ says Kraan-Korteweg, fossil evidence of bears and short-necked giraffes near between? And what role should scientifi c study play in advancing other global concerns still have specifi c very different kinds of scientists. “is the fact that many students from Cape Town. The students’ interest in oceanography was piqued by spending a morning on board Agulhas II, this understanding? consequences when viewed in the “The virologists I work with have across the continent now have the context of our status as a developing experimental methods for identifying opportunity to be at the forefront of South Africa’s research ship, with UCT oceanographer the world’s largest radio telescope, these regions, but they are expensive astronomy here at UCT, and then Dr Isabelle Ansorge and her colleagues. rather the ways that knowledge of nation and region. One such example is S -33.955533, E 18.460527. These with a collecting area of a million how organisms change over deep among these creatures over the climate change. and time-consuming. Working together, to take that knowledge back to their Between all this, students were given a head start on geographical co-ordinates pinpointour local context can help advance square metres) is the fact that we time, across millions of years”. course of 120 million years through Dr Gina Ziervogel, who studies we can develop and validate predictive home country.” scientifi c concepts that they would encounter in the fi rst a very specifi c location: the PDglobal human understanding. By boast some of the clearest skies in She is also the fi rst head of one of fossils. Everyone knows about social and environmental adaptation to models that will save time and money.” two weeks of the new semester, and also took part in Hahn Building, administrative homeusing our geographic location as the world. the faculty’s youngest departments: our human fossil record in South Encouraging interdisciplinary an advantage we can ensure that we climate change, claims that while the a session on ‘thinking about thinking’, and how to re- to some of the 12 departments According to Professor Renée biological sciences, created last year Africa, but here in Africa we also steps required to mitigate or adapt to approaches at UCT is Professor Robert For the sake of future are the leading experts in specifi c evaluate their approach to their own studies. that make up the UCT Faculty of Kraan-Korteweg, head of the by combining the Departments of have an incredible history of life on climate change are often seen as being Morrell’s job. He has been tasked with, generations Science. As precise degrees fiof elds. This in turn encourages the Department of Astronomy, the Botany and Zoology. “A central our planet.” among other things, promoting African Gammon says that the winter school targets some incompatible with development, this The principle of intergenerational longitude and latitude they describeperception of Africa as a place of development of the SKA project theme that binds our research is is not the case. “Take for example the collaboration through the Programme interconnected challenges that are common to the fi rst- a place balanced on the tip ofworld-class a science, and enables will have many positive side effects our unique geographical location, Our record of human for the Enhancement of Research equity is the idea that we have an year experience in the faculty. These include the fact that case of policymakers in Durban who obligation to preserve our natural continent and poised betweenus to remain competitive as an beyond attempting to answer which we think of as a gateway evolution did not support taking steps to adapt Capacity. “When we acknowledge that students often have limited knowledge or experience of two major ocean currents. Whateducational institution.” questions about the cosmos. “SKA to terrestrial biodiversity, as well there are different ways of knowing, we environment and resources for future the range of options open to them, and have encountered It is this record of human habitation to the consequences of climate change generations. To do so, we must rely at they can’t tell you is that this is aSo what makes our geographic is not just exciting because of what as to the Southern and Antarctic in the future. When unseasonal storms have the opportunity of using a variety relatively few role-models of working scientists; and place surrounded by abundant andlocation distinct in the eyes it might achieve for pure science, Oceans,” Chinsamy-Turan explains. and migration that interests of approaches and methodologies. least in part on scientifi c knowledge to that they consequently struggle to fi nd inspiration and archaeologist Professor Judith Sealy. disrupted the roll-out of low-cost understand, conserve and protect our diverse animal and plant life andof science? but also for what it might mean for “Our department’s vision is to be housing and services to urban areas, This broadens horizons and allows motivation in their studies – which adds to the challenges “I do chemical analyses of materials biodiversity for the future. Science, that it has been the site of scientifi c everyday life. As a fl agship project, it recognised as a leading biodiversity they began to see climate change not for new questions, the possibility of they already face in coping with demanding subjects, says study for almost two centuries. In found at archaeological sites in order as Chinsamy-Turan points out, can requires the highest level of research research and teaching department, only as an environmental issue but also different answers, and better remedies Gammon. the past, as in the present, much Our clear skies to fi nd out what ancient humans give us a sense of perspective: “What infrastructure and computing with strong inter-disciplinary as a social one. As scientists we have for sickness. The challenge is to fi nd of the work that has occurred is a year or a decade in the scale of “So the idea was to put together an interesting and If you have ever been in the Karoopower – this will certainly be an research linkages that understand and animals were eating. This can a responsibility to ensure that these ways of promoting dialogue between here has been in the pursuit of a geological time? Looking at the past inspiring programme, drawing on the wealth of expertise on a cloudless night and looked up,economic and technological driver biodiversity resources in the face tell us about the environment at issues get on the agenda.” different approaches, and of melding better understanding of this local can tell us about the present; but it can in the Faculty of Science and the range of scientifi cally you’ll agree that South Africa hasand a means to create jobs. Just as of climate change, both locally and the time they were alive, and their local knowledge with scientifi c method. environment. Human health is another area also highlight the fragility of life on our interesting projects and initiatives both at UCT and in the some of the clearest skies in theimportant, it promotes South Africa globally.” behaviour where our geographic location makes The old idea that science presents fi xed, immutable facts is changing; and planet, because even small changes, greater Cape Town region,” Gammon says. world. The altitude, climate and lackas a scientifi c leader, encourages In terms of her research, South Africa has a much longer particular diseases relevant. Professor as it does, the realm of possibility is over time, can lead to catastrophic One student said of the winter school: “I sense a shift Our place in the world of light pollution lead to conditionsstudents to enter the fi eld, and will Chinsamy-Turan also points out history of human habitation than Ed Rybicki from the Biopharming becoming greater.” events.” in my confi dence; and more importantly, an increasing that are not just good for amateurcontinue to attract top scientifi c that South Africa has the best elsewhere in the world, with many Research Unit in the Department of In a world beset by global challenges, record of the evolution and spread sites on both our coastlines showing Associate Professor Merle Sowman The question of how we can best go passion for science.” stargazing, but also for the kindminds to our shores.” Molecular and Cellular Biology works about being responsible stewards, so however, is it myopic to be focusing of mammal-like reptiles, as well as the emergence of modern humans from the Department of Environmental Another reported that the winter school “has made that requires a radio telescope and on developing new ways of making and Geographical Sciences believes that that our children’s children will still be on our own backyard? seeks answers to how our universe of the early ancestors of dinosaurs, 200 000 years ago. “People often me feel less helpless and alone by showing me that other “Science is universal,” says Dean vaccines for some of our region’s in order to achieve authentic homegrown born into an environment teeming with began. In fact, one of the reasons mammals and modern reptiles. assume that this human habitation people just like me are experiencing the same confl icts I of the Faculty of Science Professor most pressing diseases, such as HIV solutions, the role of local knowledge diversity and abundance, is one that that South Africa has been chosen Our biodiversity “We have a unique fossil record in was quite static, but it was actually and HPV [the human papillomavirus, am. It has sharpened my resolve to improve this semester, Anton le Roex. “So it’s not about the South Africa, and we can track the must also be recognised. “I work with science is well placed to answer. to host the Square Kilometre Array very dynamic. The study of these which causes cervical cancer]. In his and to actually get gritty and work hard”. value of African-centred scientifi c Professor Anusuya Chinsamy-Turanevolutionary changes that happened societies shows how our species knowledge for its own sake, but (SKA) Project (which aims to create is a paleobiologist who “looks at
Aspirant scientists at UCT Open Day. Photos by Michael Hammond and Raymond Botha. 6 MONDAY MONTHLY SUPPLEMENT SCIENCE 7
“Within our context at the tip matter, and force in the context of on quantum mechanics. Without a exploitation of genome information. a theoretical model to produce what of Africa, the big unknown is what is called quantum fi eld theory. clear understanding about the way This involves the exploitation of are considered unshakable results how the great Agulhas Current, “In many ways it was the missing in which the laws of physics work, known biological targets in one pulsing from the printer next to sweeping hundreds of tonnes of piece that completed the puzzle. we cannot use the laws of physics disease for the development of drugs the machine. warm water down the east coast Unfortunately, the fi nished puzzle to build technology that helps our in other diseases with homologous “We must acknowledge that of South Africa towards Port still does not give us a complete everyday life.” targets. This has sometimes been the bias lies in the model sitting Elizabeth and beyond, will change understanding of the universe – referred to as ‘target repurposing’.” between the detector and the under changing wind conditions in New uses for old drugs scientist. In chemistry, for example, the Indian Ocean. there are other puzzles out there! In my opinion, the largest question Organic chemist Computer-aided design it is ironic that the very essence “About 80% of this huge in physics (post-Higgs boson Professor Kelly Chibale Computational chemist of this science relies on a model current does a U-turn on itself Professor Kevin Naidoo interpretation of things we cannot discovery) is the unifi cation of “One of the exciting areas in drug and re-circulates back into the see, such as electrons and bonds gravity with quantum fi eld theory. discovery is the exploitation of “The computational revolution Indian Ocean, but the important between atoms. remaining part travels into the “Is there one thing that underpins genome information within the has changed the way we do science. Atlantic Ocean, supplying both and connects our understanding of context of drug repurposing and In every scientifi c discipline, the “Reproducibility and prediction heat and salt to the northern all three? Answering the quantum repositioning – the investigation frontier lies in the progression are the enviable achievements of the Atlantic Ocean, and thus helping to gravity question may lead to the of existing drugs as potential of computation, from an adjunct scientifi c method. Computational complete the circuit of the Great nature of dark matter, dark energy therapies for other diseases. to an essential part of our scientists increasingly provide predictable computational models Ocean Conveyor, or Meridional and black holes. “Whereas these two terms have understanding nature. The cusp of of electrons, atoms and molecules Overturning Circulation (MOC). been used interchangeably by some, progressive knowledge acquisition “This will not change the way we that can be used to design materials drug repurposing specifi cally refers is in the reformulation of the “How this southern surface think about rain, or ice cream, or and pharmaceuticals, and interpret to cases in which an existing drug, scientifi c method. This relies on part of the MOC may change in emails, but if it were not for CERN the interwoven chemistry of cells approved by a regulatory agency in the production of computer response to changing wind forcing researchers we might be thinking to connect to the chemical events one disease area, is found to have models that are verifi able and is being studied through the about emails in a very different that have long passed in galaxies deployment of a deep-reaching activity against another disease. able to predict the outcomes of way. Do you every wonder why an experiments, and so provide a view light years away. array of moored ocean buoys from SMS costs 50 cents, but an email is “Drug repositioning describes into nature that’s not accessible “Computer models and data Cape Town to South America, as free? Part of the answer is thanks a situation in which a drug active from microscopes, telescopes analytics provide a rational approach well as by satellite remote sensing to particle physics researchers in one disease is ‘derivatised’, or spectrometers. to discovery that is in contrast to by different radar instruments. at CERN.” or used as a template for the “We tend to believe what we traditional trial-and-error searching. This photo, looking across the southwestern tip of South Africa, was taken from the International Space Station on 9 May 2013 by Canadian astronaut Chris Hadfi eld. “With the increasing availability [Hamilton points to a CERN link, synthesis of derivatives active in of large data sets from satellites, can see and touch. Yet in many This rational approach to chemistry Writing in Wired, Hadfi eld said: “While I was on the space station, I used Twitter to ask hundreds of thousands of people what they would like me to take a picture which describes the birth of the another disease. and vast quantities of suitable fi elds, such as chemistry, our and biology promises to address of. Resoundingly, the answer was ‘home’. After millennia of wandering and settling, we are still most curious about how we fi t in and how our community looks in the World Wide Web – developed in “The concept can also be numerical ocean model output, knowledge is deliberately biased burning problems such as the context of the rest of the world.” Image courtesy of NASA/JSC extended to new uses for drugs that it is envisaged that big data 1989 by Tim Berners-Lee, initially to by what we indirectly measure with development of biomarkers for meet the demand for information- have failed for one indication, either physical instruments. early detection of cancer, drug and its visualisation, analysis pre- or post-approval, or have been sharing between physicists at “I say ‘indirectly’ because resistance, and making bottomless and presentation will eventually abandoned in development, in be required.” universities and institutes around experimentalists often forget barrels of biofuels from cellulose the world. Twenty years ago CERN which case the term ‘drug rescue’ that the raw feed of light and sound (the most abundant molecules in NEW FRONTIERS, published a statement that made is used. wavelengths coming from their the biomass).” Physics: the game changer the World Wide Web technology “These approaches can signifi cantly detectors has been washed through Particle physicist Dr available on a royalty-free basis. shorten the drug discovery process, NEW ADVENTURES Andrew Hamilton And so the web fl ourished, and as in most cases the candidates will We tend to believe what we can see transformed the world and the way have been through several stages of “The discovery of the Higgs boson we communicate, innovate, work clinical development and will have and touch. Yet in many fi elds, such as “Discoveries in science ... will continue to create a thousand new in 2012 was very big news and and live.] well-known pharmacokinetic and chemistry, our knowledge is deliberately completed our understanding of the safety profi les. frontiers for those who would still adventure,” said former US “Today’s technology depends on biased by what we indirectly measure standard model of particle physics, fundamental physics: the GPS in “One of the many scientifi cally with physical instruments. president Herbert Clark Hoover. Helen Swingler asked a handful our current best understanding of your phone depends on general rational approaches to repurposing the fundamental nature of energy, relativity, your computer depends and/or repositioning is the Prof Kevin Naidoo of UCT researchers to speak about their adventures at the outer limits of science.
The debate is over “Second, and related, is the need quantum physics, even though we are advocating for disastrously low- existing samples are from depths Climate scientist for integration. Climate will impact understand a great deal of how level educational methods. Tackling shallower than 1 000m – in fact, Professor Mark New on society as a whole, so the classical it works. this area should be a high priority 83% are from less than 100m. The reductionist approach in science, “There are really great experiments for quality interdisciplinary research abyssal zone thus remains almost “The debate about whether while useful for building basic that takes a deeply human view as completely unexplored. greenhouse emissions cause climate taking place in this regard. This understanding of components of well as being fully aware of the latest WHAT’S system warming is over. Frontiers might have repercussions for many “Yes, there are vessels that can a system, does not address the questions in physics, cosmology, scientifi c understandings of brain take samples, and a handful of of knowledge in the physical and structure and function.” natural sciences now concern complexities of the real-world and even biology – where a key issue submersibles that can physically take how different aspects of the systems, whether these are cities, is what (if any) genuinely quantum researchers down to those depths, IN A NAME? climate system will respond to food systems, or ecosystems in effects infl uence biology in general, Under the sea but they cost tens of thousands of overall warming. At the most the larger social-ecological systems and the brain in particular. For Marine taxonomist dollars a day, and we have not been Compiled by Yusuf Omar fundamental level, there is still a lot we are part of; and in particular, me, that kind of issue – a deeper Professor Charles able to raise that type of funding.” to understand about feedbacks in the political-economic realities of understanding of the emergence Griffi ths of complexity from the underlying The scientifi c method might be stringent, the climate system – those internal responding to climate change. “Some frontiers are tantalisingly Currents of change physics and chemistry – is one of responses that can act to amplify “We need new paradigms of close; a mere 1 000m under the Oceanographer but the methods for naming can often be This frilled nudibranch, Leminda millecra, is named after Prof Charles Griffi ths’ daughter, or dampen the direct greenhouse the most exciting areas of all. thinking, drawing on – among ocean. We’re describing some 30 Professor Frank weird and wonderful. Melinda. Image by Georgina Jones. gas effect. others – complexity science and “We need to do both blue-sky new marine species a year in South Shillington “In the Southern African context, transdisciplinary methodologies. We research and research directed at Africa; and many of these are ‘on “Climate change has affected both Take quarks, for example. Rather than burrowed under the soils of the Western Mathiasite. This potassic iron-zirconium- these animals in a roadside stream! The we have a critical role to play in need to bring together expertise areas of critical need, such as the our doorstep’ in False Bay, as that’s the scope and the urgency of being given a name derived from ancient and Northern Cape many ice ages ago. magnesium chromian titanate is named shrimp, named Mathamelita, was described southern hemisphere climate change from both the natural and physical coming water crisis. The whole point where most of our sampling is done. particular aspects of the various Latin concepts, the subatomic particles It is closely related to the living Cape after the late, legendary UCT geologist by Griffi ths and a colleague in 1995. research. With regards to carbon sciences, with other disciplines of blue-sky research is that what If we could get deep-sea samples, the branches of oceanographic research. derive their names from James Joyce’s golden mole, Chrysochloris asiatica, which is Morna Mathias. The Griffi ths family was also involved cycling, the southern ocean is a key such as law, economics, humanities, will come out in genuine discovery majority of the species would be new, is often quite unexpected – for Finnegans Wake, which reads: common in the South-Western Cape and with the naming of a new family of sea player in ocean carbon cycling, and health, on an equal footing.” but we lack the capacity to collect Firstly, it’s impressed on us the need The mineral was described in a 1983 example the nature of quantum Northern Cape coastal plain. slugs – former UCT scientist Dr Roberta is very poorly understood. Also, we these samples. for longer and more comprehensive Three quarks for Muster Mark! paper by Steve Haggerty of the University do not have a good understanding theory, of the genetic code, of the observations of the ocean, particularly Sure he has not got much of a bark Bronner was a member of the research of Massachusetts, Amherst, and others, Griffi ths (wife of Charles) named the The emergence of “So, the frontier regarding of how carbon cycling in African way the brain is structured. This can around the southern tip of Africa. And sure any he has it’s beside his mark. team that was deriving a phylogeny in honour of Mathias’ seminal studies on colourful sea slug Lemindidae after their complexity biodiversity is certainly the deep sea, grasslands and forest biomes will then lead to major important new (evolutionary tree) from the then-poorly- alkaline rocks and her early contribution to daughter Melinda (herself a recent PhD Cosmologist and applications, such as the existence which is extremely poorly explored. “As researchers, one of the limits While Joyce’s “quark” rhymed with “mark”, graduate from UCT). respond to climate change. Distinguished Emeritus on our detailed knowledge of how studied Chrysochloris family, comprising 21 the mineralogy, petrology and geochemistry of transistors and lasers. I’d want to get my hands on samples physicist Murray Gell-Mann coined the golden mole species. of mantle-derived eclogites and peridotites. “There are also a number of Professor George Ellis the physical processes of the ocean term ‘quark’ – as in ‘cork’ – because “However, research into areas of from the 70% of South Africa’s Bat brothers critical research challenges and behave is not having a comprehensive protons and neutrons each contain three Mathiasite is found in the earth’s “Key questions for today’s cosmology critical need is essential; indeed, it is exclusive economic zone that lies questions around adaptation. First, and detailed observing system. As this of them. The names of the six types of Maroon orchids and minerals deep mantle, more than 100km below Associate Professor David Jacobs also are the nature of dark energy and the our duty to society to work on these deeper than 1 000m. the development of methods quarks might also raise an eyebrow: up, Southern Africa. decided to keep it in the family when nature of dark matter. The nature of areas too – for example, climate has steadily improved, along with the When it burrows up towards the surface, and techniques that enable the “Continental South Africa has a down, charm, strange, top and bottom. he named a new bat species in 2009. dark energy, and particularly why it is change and energy issues on the coastline of some 3 650km, and capability to numerically model the the golden mole might bump the roots interpretation and development of coupled ocean-atmosphere system, of Disa linderiana, an orchid species Shrimps and sea slugs Jacobs and his students came upon the response strategies that embrace so small, is still a mystery. one hand, and poverty on the other. the EEZ is over one million square our knowledge will continue to Golden moles named after former UCT professor Peter yellow-bellied bat in the iSimangaliso uncertainty; and of course, training “There are also many other “A particular critical area is kilometres. Waters here are as deep Sticking to the depths but moving under Wetland Park in KwaZulu-Natal in 2003. increase. Linder. The maroon orchid was spotted by practitioners and policymakers to key areas where new theory and education. Our educational success or as 5 700m, with more than 65% Dr Gary Bronner is a more visible example water, a genus of freshwater shrimp It was startlingly similar to its sympatric be comfortable with planning for observations are needed to probe failure relates to how we understand deeper than 2 000m. Although the “The next big frontier will be to of a somewhat liberal scientifi c naming CapeNature fi eld ranger Jacques van Rooi endemic to the Knysna area has the unique sibling, Scotophilus dingani, a bat named a more climate-resilient society the nature of fundamental physics. learning processes in the brain. There coastal zone is quite well sampled, sample the ocean at what are called process. The UCT zoologist was “rather in 2004, in the Cederberg. honour of being named after Professor after the Zulu king Dingane. So Jacobs as part of an overall sustainable- One example is that we still don’t are some high-profi le neuroscientists most samples were collected ‘sub-meso’ scales, of between one bemused” to have had a fi ve-million-year- Ducking back below terra fi rma – but Charles Griffi ths’ son, Matthew, whose decided to name the new addition development agenda. understand the foundations of out there with reductionist views who before 1980. And over 99% of and 10 kilometres. old fossil mole named after him in 2010. much deeper than your average mole could request for a loo stop during a family Scotophilus mhlanganii, after Dingane’s Chrysochloris bronneri was a golden mole that hope to dig – one fi nds a mineral called holiday in the area led to his father noticing half-brother, Mhlangani. 8 MONDAY MONTHLY SUPPLEMENT SCIENCE 9
MSc students venture into a wasteland created by open-cast pit diamond mining along the Namaqualand coastline. They are part of the Namaqualand Restoration Seeds and Knowledge Initiative, a community-focused project to rehabilitate this fragile ecosystem. Image by Carina Bester. gives smallholder farmers, “Long-term public participation farmers – women in particular – have particularly women, or citizen science projects make more control over seed procurement more control over seed it possible for observations made and food production. procurement and food by many different people to be production, and harnesses “The fi rst priority of the community knowledge. pooled and analysed as a whole,” project is to help communities the authors explain in their and farmers revive traditional introduction. “They provide the seed and agricultural knowledge best opportunity for assessing systems,” says Wynberg. “Farmer population trends in species such exchanges have fostered horizontal as the secretary bird.” learning and knowledge exchanges The relationship of reciprocity is between communities, and across refl ected in the fact that the team the region’s borders. Learning chose to publish their paper in PLOS exchanges are also taking place ONE, an open-access journal: “Since between researchers involved in the data we used was contributed formal seed systems such as gene freely by citizen scientists, and banks and custodians of farmer- freely available to them as well, it led systems.” made sense to publish in a way that Ongoing research, documentation, allows anyone access to the article,” and experiential learning are vital to says Hofmeyr. shifting the paradigms governing policymaking in science, she says. Seed knowledge SCIENCE ON THE GROUND Environmental scientist “Traditional knowledge and seed Associate Professor and agricultural systems are part Rachel Wynberg of a complex socio-ecological Story by Helen Swingler system in farming communities In environmental and geographical throughout Southern Africa. We The interface between community and science is a complex science, National Research Foundation want to bridge the gap between Bioeconomy Research Chair Associate community realities and policies, into a common conservation entity, Sea change in support for a well-managed interaction best described as a relationship of reciprocity. From Professor Rachel Wynberg is thinking and to support this process with to that of a park or wilderness with community education penguin colony, even though this about seeds. research that has a social impact.” its consequent separation between Marine ecologist will increase vehicle and tourist humans and nature. smallholders and artisanal fi shers to bundu-bashing citizen The Seeds and Knowledge Professor Astrid Jarre traffi c. The planned interpretative centre has huge potential to evolve scientists, communities are making their mark on science – and Initiative works with farmers, NGOs, Peace parks “What was supposed to be For the Marine Research Institute’s researchers and policymakers to Human geographer a progressive multi-land-use (MA-RE) Professor Astrid as a true collaboration among the both are benefi ting. revive and enhance traditional seed Associate Professor transfrontier conservation area is Jarre, natural and human social residents, and with the managing and knowledge systems, while also Maano Ramutsindela becoming an exclusive transnational systems are at the heart of a authority.” Upside down and Initiative (NRI), launched in 2005 Carrick, who won an NSTF- that have been degraded by centuries Animal Demography Unit’s (ADU) deepening scientists’ understanding park that allows free movement of transdisciplinary project on coping The Southern Cape Interdisciplinary turned around as part of the Succulent Karoo BHP Billiton award in 2012 for of ploughing and constant grazing. Postdoctoral Research Fellow Dr ‘Community’ is a watchword for wildlife and tourists, while ensuring of their functioning in the context of human geographer Associate with global change in the Benguela Fisheries Research (SCIFR) project Ecologist Dr Peter Ecosystem Programme. this work, has since established Research is being done into Sally Hofmeyr. agricultural, cultural and ecological that the movement of ordinary Current large marine ecosystem, is another example of research Carrick Nurture Restore Innovate, an Professor Maano Ramutsindela, local residents is restricted,” says This initiative tapped into restoration systems for these Hofmeyr has been studying practices. whose work on peace parks examines which extends along South Africa’s involving citizens: “Fishers, learners Namaqualanders’ deep knowledge initiative that provides long-term Ramutsindela. Along the 400km coast of rangelands that can be rolled out secretary birds (Sagittarius serpentarius), “We want to build a community of the movement of human and animal west coast and south coast, and academic researchers are now of the land to equip teams from ecological advice, support and as part of government’s Expanded large, terrestrial birds of prey What’s happening to the land – approximately to East London. involved, through SCIFR, on a Namaqualand, diamond mines mentoring to projects that affect practice around seeds and knowledge communities. local communities to rebuild the Public Works Programme, or endemic to Africa and usually found in the region,” says Wynberg, who is and other resources – that residents Researchers are hoping to create collaborative process to improve our have turned the fragile ecosystem ecosystem. The NRI did a ‘sweep’ landscapes on a larger scale. Peace parks – such as the Kgalagadi upside down. Literally. Designated what could be called ‘Working for in the open grasslands and savannah one of the organisation’s partners, living near these conservation knowledge that will help coastal understanding of long-term change of local and scientifi c knowledge “This extends the work of Transfrontier Park, which straddles as one of the world’s 43 biodiversity Ecology’ or ‘Working on Rangelands’ of the sub-Saharan region. Using itself a long-term collaboration with areas relied on? communities tackle many of the on the Agulhas Bank, south of from farmers, mine operators, the Namaqualand Restoration the border between South Africa and problems they’re facing. hotspots, this zone is the most programmes, says Carrick. data from her fi rst postdoctoral Biowatch South Africa and the Mupo “The answer is ‘green grabbing’; the Cape Agulhas.” agricultural scientists, and local Initiative, both geographically and Botswana – link conservation areas species-rich arid environment in “This all works to alleviate poverty study in 2012/2013, she published Foundation. and ecological and cultural footprints. appropriation of land and resources The South African Research Tangible results have resulted naturalists and herders (often with by creating systems to implement Chair in Marine Ecology and the world. Many species are few resources but great insight), to in the short term by creating pro- a paper in PLOS ONE (a scientifi c Local agricultural systems have They’re meant to promote local for environmental conservation and from collaborations; one is a the restoration at scale.” Fisheries, Jarre says that collaboration habitat specialists. synthesise their working knowledge poor work opportunities, and in the journal put out by the Public Library been eroded for decades by community development, biodiversity the greening of the planet. In the seawater sampler, co-designed The new NRI has recently context of peace parks, this process between researchers from various It’s ironic that jewels other of restoration techniques. long term by restoring productivity of Science), co-authored with the policies and laws that promote the conservation and regional integration. with local fi shers, that is deployed completed the fi rst phase of research ADU’s director, Emeritus Professor interests of commercial farmers and enlarges the conservation areas home disciplines (from the natural and from commercial ski boats: “The than endemic bulbs and Local teams operate as formal to dry, degraded rangelands, so that “They’re founded on the philosophy with mining operators on the arid people can earn more productive Les Underhill, and Wits University’s multinational seed and agro-chemical through colonial-era removals, the social sciences) and including citizens, incoming data on temperature at mesembryanthemaceae are also businesses and contract to mining edge of the Kalahari in Namibia. This of co-existence among humans and sustainable livelihoods from Dr Craig Symes. companies. Traditional seed varieties creation of wildlife management is generating transdisciplinary the sea surface and at fi shing depth found here – in rich seams just operators, gaining access to the creates comprehensive restoration and between humans and nature,” approaches that are distinctive in the land.” It pointed to an alarming trend. have all but disappeared in many areas, co-management of land, are quality-assured by researchers, 50 metres or less under ground. formal economy and negotiating their systems for the land degraded by Ramutsindela explains. “Regionally and outright purchase of land in research progress and outcome. areas, along with the associated they’re an avenue for integration; and further processed by learners Open-cast mining has overturned terms; and with them, increasingly, mining in this area, principally “This interesting and iconic species private hands.” thousands of hectares in their future. The service they offer Citizen power knowledge and culture. for example, Southern African One such project is a citizen-in- in coastal schools in the Hessequa turning massive overburden and appears to be declining in the science approach to the colony of municipality in the Eden District,” discontinuous patches, leaving holes has been scientifi cally developed and in numbers country – most severely, apparently, “Industrial agriculture produces states united by a common vision Research, Ramutsindela says, waste rock dumps into hills that is vital to assess and monitor the endangered African penguins at says Jarre. and dumps of overburden that have is a tried-and-tested system involving Biologist in the Kruger National Park, usually only 30% of the world’s food,” and managing their shared natural look and function like those found environmental and social outcomes Stony Point, Betty’s Bay. all but destroyed locals’ livelihoods. ‘restoration packs’, wind-erosion naturally in that landscape. Dr Sally Hofmeyr thought to be a haven for large notes Wynberg, “but it’s a leading resources together.” “We envisage that communication barriers and transplants to restore contributor to climate change and of these processes in the parks. “As human contact needs to be on climate-related questions, Legislation now requires mining raptors,” says Hofmeyr. Peace parks have increased former mining sites. The NRI is also This work has been done in Citizen scientists in the veld, plains, environmental degradation through The irony, he notes, is that local carefully managed, citizen scientists which will involve all three groups, companies to clean up, restoring the habitat for species such as able to provide assurance to mining partnership with MSc students and bush and mountains play a small The researchers were able to destructive farming practices, use communities, whose land rights are can’t be involved in direct contact- will enhance scientifi c research, the landscape during and after researchers from the University identify this trend using data elephants and have brought some operators that the system has been but invaluable role in the scientifi c of fossil fuels and reliance on areas with critical biodiversity often precarious, are not involved based penguin research,” says Jarre. and community understanding of mining operations. of Namibia. citizen scientists had contributed implemented correctly. endeavour. These are ordinary chemical inputs.” under protection. But they have also in the planning of these parks. “But drawing on sociological and the scientifi c process – as well as That’s where the Plant Conservation An offshoot of NRI, NM In Namaqualand the new NRI people who enjoy documenting to the Southern African Bird Atlas The long-term vision is to collaborate metamorphosed, from the initial idea “Issues of human rights should anthropological techniques, our long-term change.” Unit’s Dr Peter Carrick comes in, Restoration, is now a business has now broadened its restoration the natural world, their collective Project and the Co-ordinated with communities, and national and of bringing together a mosaic of be central to the planning and research has shown that Betty’s with the Namaqualand Restoration owned and run by Namaqualanders. research to the koppies and uplands data guiding researchers like the Avifaunal Roadcounts. regional partners, so that smallholder land under various forms of tenure establishment of peace parks.” Bay residents show overwhelming SCIENCE IN THE ARCHIVES Curated by Renate Meyer Compiled by Helen Swingler Photos by Michael Hammond
Among the university’s special collections are numerous scientifi c archives: papers, notebooks, A reproduction of Prof JLB Smith’s famous A hand-coloured print of Disa spathulata A spore pressing of a scaly psalliota, a This photograph by Edmund Schelpe Astronomer Dr Andrew David Thackeray’s One of four large mounted drawings of coelacanth leafl et (offering a reward for belonging to UCT’s Bolus Herbarium. mushroom found at Brakkloof on the Cape – the former curator of the Bolus detailed plottings of the variances of the Royal Observatory in Cape Town photographs and plates that document – mostly specimens of the prehistoric fi sh), republished Peninsula, and a notebook listing the Herbarium and professor of plant star clusters. (now the South African Astronomical in his 1956 book, Old Fourlegs: The story of peninsula’s poisonous, edible, eatable, taxonomy in the Department of Botany Observatory) from the papers of Jacob by hand – scientifi c endeavour and discovery in the coelacanth. non-edible and unknown fungi, made by – is of entomologist John Riley next to a and Eric Halm. an earlier age, before computers, cameras and botanist Edith Stephens. giant lobelia, taken during an expedition to Mount Kenya in 1949. colour printing. 10 MONDAY MONTHLY SUPPLEMENT SCIENCE 11
read out every single event, they Complex climate models UCT’s climate research also has of SKA Phase 1 when that Africa – on the map in terms of would need around 40 terabytes unique cross-disciplinary skills, instrument is constructed, stands data capacity. “Global research per second, which is way beyond The challenge to provide trained and this gives the university a 19.5 metres tall and weighs 42 leadership requires that we have the confi nes of current technology. people connects all big data projects, competitive advantage globally. tons. The complete MeerKAT the capacity to extract information Using high-speed fi ltering called whatever their divergent hardware “We have a chance to take a research array will have 64 receptors – from big data,” he says, and there ‘triggers’, researchers can get this requirements. For instance, acquiring lead on these global research antennas with receivers, digitisers is likely to be a limited window of down to hundreds of megabytes and retaining skilled researchers is the challenges,” says Hewitson, “and and other electronics. Connected opportunity to establish national THE BIG DATA per second. greatest strategic challenge in climate to contribute to major policy by 170 kilometres of underground leadership in data-intensive research research, according to Professor While this may already sound like development in Africa.” fi bre optic cable, the 64 receptors and a global presence in this Bruce Hewitson, director of the will operate as a single, highly emerging fi eld. a tall order, it is only part of the big Climate System Analysis Group. In order to take this lead, we will REVOLUTION data challenge faced by the LHC. have to fi nd ways to face up to the sensitive astronomical instrument, While big data is by its very In order to defi ne expectations This is partly because of the big data challenges. Part of the controlled and monitored remotely nature a massive challenge to the Story by Tracy Gilpin, Carolyn Newton and (so that researchers know what complexity of the big data research answer might lie in the stars. from the MeerKAT control university, it is also a driver of the Jane Notten they expect to see), the entire challenge in the fi eld, particularly room in Cape Town. When fully transformation of science, and around climate modelling. “There detector is digitally simulated in Big data from the sky operational, the MeerKAT will by extension, a driver of global are about 40 mainstream global generate enough data from the Big data – large and complex data sets that excruciatingly fi ne detail, and a change; and UCT is already part of computer algorithm is written to climate models,” says Hewitson. The research fi eld that is wrestling antennas to fi ll about four-and-a- the revolution. “All produce comparable resolution with the biggest data of all is half million standard 4.7-gigabyte are diffi cult to process using traditional simulate the billions of events that “We are not trying to break into results, but no model is perfect. astronomy, and Africa’s biggest DVDs in a day. might produce a rare particle like a fi eld where we are absent – we Some uncertainty arises from model science project, the MeerKAT computational hardware and software – is the Higgs boson. All of this data An eminent role player in this are already there,” says Visser. error – how it’s coded up. Some is Large Surveys, has put UCT at then needs to be stored. fi eld has been attracted from “If we grasp the opportunity to a popular term that has gained ground from the inherent variability in the the coalface of this challenge. The Factor into this the collaborations Canada: Professor Russ Taylor, take leadership in this area, we climate system. So even in one MeerKAT radio telescope is a involved (just one of the LHC’s one of the founding international can really make a difference in the in the last decade, not only in everyday category of modelling, we don’t precursor to the square kilometre seven experiments has 1 000 SKA project scientists, who joined country and to science around the have a clear analytical approach.” array (SKA) telescope. Led by life, but also in research. UCT is taking the members belonging to 116 the university early in 2014 as joint world: solving Africa’s issues, but four UCT astronomers, MeerKAT institutions, based in 33 countries), Add in regional models and UCT/University of the Western also making Africa part of the lead in creating the framework to allow is expected to gather up to one and the scale of the challenge other impact models, and you Cape SKA Research Chair, will global solutions.” petabyte (1 000 terabytes) of data African researchers to get to grips with the is evident. have a major challenge in distilling coordinate a big data vision for information so that it can be per year, so advanced tools will radio astronomy in South Africa: increasing volume, velocity and variety of The LHC has created a solution analysed and produce defensible have to be developed to process, “The global SKA big science data to this very big data problem – regional information. It is the analyse and store the data. world is coming to South Africa Construction of the MeerKAT antenna. Image courtesy of SKA South Africa the Worldwide LHC Computing data, and turn it into actionable knowledge. single leading challenge in climate There is nothing small about the this decade,” says Taylor, adding Grid (WLCG), a form of cloud modelling, according to Hewitson, SKA – it is the biggest science that it is probably one of the two computing that stores and The modern world is experiencing The more data available, the bigger specialist support and analysts are In line with moves at other leading The 27-kilometre LHC is the and there has been no substantive project ever carried out on African projects in the world driving a big processes information. It currently a data deluge: “The data fl ow is the potential for more accurate in constant demand. international research institutions, world’s largest particle accelerator, advance on it in the last decade. soil. When completed, it will be data revolution in astronomy. has 150 centres in 40 countries and so fast that the total accumulation analyses. And with more accurate “Without the right support, UCT the centre will provide integrated and it is one of the most important the world’s largest radio telescope, operates through a tiered structure Researchers acquire skills in this of the past two years – a zelabyte information available, decisions can be researchers risk diverting time and support to help researchers do work tools available to high-energy located in Africa and Australia, but that varies in the funding model, fi eld only by working in an applied A research revolution – dwarfs the prior record of made with increasing confi dence, while resources into the development and that is high-impact, locally relevant and physicists in their bid to investigate shared by astronomers around the human civilisation,” wrote Harvard better decision-making leads to the storage space and the number environment – learning on the maintenance of potentially sub- internationally competitive. One of its the fundamental particles that globe. Each MeerKAT antenna, In addition to his own research Magazine in March 2014. No-one is greater effi ciencies, cost reductions of cores required. job. However, the academic job standard or ineffi cient solutions, important roles will be in managing make up the universe. The UCT- which will be incorporated into with SKA, Taylor will also be immune – least of all researchers, and reduced risks across societies. large data sets. CERN Research Centre is part of market for graduates is minimal, or just generally taking much Creating the infrastructure and this is compounded by the the mid-frequency component working to put South Africa – and who now work with large data sets But this will only happen if more time to do meaningful The university could go further, two experiments running at the required to play in this big data that are increasing exponentially LHC: the ATLAS experiment, likelihood of losing highly skilled the capacity exists to interpret analysis,” says Professor Danie however, building on the eResearch league sounds expensive; however, people to the private sector or in size, complexity and velocity. Visser, deputy vice-chancellor with which explores the fundamental that data correctly. Getting Centre to take the intellectual money is not the greatest challenge research institutions overseas, where While data-intensive research cuts from data to knowledge is not a responsibility for research. “There lead in establishing expertise and particles of the standard model for UCT, according to Dr Hamilton. across the disciplines – including is increased potential for valuable of particle physics, and ALICE, there is more opportunity and WHAT’S IN A BYTE? simple equation, and the need to driving innovation in data science. “We need the people trained in high- higher pay. engineering, computer science, support data-intensive research data or intellectual property to There are a number of global and which is aimed at understanding performance computing to operate 1 bit = a binary digit (0 or 1) archival science, humanities, be lost, stolen or corrupted, and the quark-gluon plasma. “We also have too many single at universities is therefore acute. national developments that the and administer these facilities,” he 8 bits = 1 byte (the average sentence equals 100 bytes) economics and fi nance – the Increasingly, researchers are for signifi cant interruptions to university can harness. The nature of its work means says. Which is where the WLCG, points of failure,” says Hewitson. sciences frequently fi nd themselves battling to move data sets between research activity. A centralised that the LHC has been grappling “one of the largest research “We have world-class capacity, but 1 kilobyte = 1 000* bytes (1 kilobyte would be equal to a short paragraph) at the frontier of attempting to collaborator sites, test parameters effort is needed to provide a with the problem of big data sets computing networks in the world”, if one individual leaves, a whole 1 megabyte = 1 000 kilobytes (1 megabyte could hold a 200-page book) solve big data problems. mechanism for researchers to learn An accelerating thread of activity collapses.” to optimise analysis of large data challenge for 20 years. Many of the particles comes in. “If UCT wants to be a 1 gigabyte = 1 000 megabytes (a standard DVD holds 4.7 gigabytes) In 2001, Gartner Inc, a leading sets, and faciliate access to these from one another and develop it investigates (like the famous leader in big data research, we need However, it is in this world- 1 terabyte = 1 000 gigabytes (1 terabyte could hold 1 000 copies of the information and technology sets by international research institutional best practice.” One such opportunity lies with Higgs boson) need to be created to demonstrate that we can operate class capacity that Hewitson fi nds research and advisory company, communities. In the last 12 months, It is partly for this reason that UCT the European Organisation for by colliding protons at what is a big data centre that participates cause for optimism: “UCT climate Encyclopaedia Brittanica) defi ned big data as: “High-volume, UCT researchers have more than is establishing an eResearch Centre. Nuclear Research (CERN), home close to the speed of light. Because on the global scale. The WLCG research punches above its weight 1 petabyte = 1 000 terabytes (close to 250 000 standard DVDs) -velocity and -variety information doubled their use of central high- eResearch is focused on how of the Large Hadron Collider the particles are very rare, tens gives us the opportunity to both internationally. We have the largest assets that require cost-effective, performance computer (HPC) information and communications (LHC), says Dr Andrew Hamilton, of millions of collision ‘events’ contribute to one of the largest single concentration of capacity innovative forms of information facilities for data-intensive research. technologies help researchers to a lecturer in the Department of are produced per second, which research computing networks on on the continent, and are leading *This is the decimal interpretation most commonly used for disk storage; in a binary processing for enhanced insight Demand for research storage is collect, process, store, manage, Physics and researcher in high- need to be captured and read by the planet, and learn from their research from the perspective of a interpretation, used for processor or virtual storage, the value is 1 024 for each. and decision-making.” growing substantially each year, and fi nd, share and re-use information. energy particle physics at CERN. a detector. If researchers were to expertise at the same time.” developing nation.”
UCT’s many books on marine biology The Cape Mountain Club kept an extensive A photograph of Wilson Cave, a small An archival image of the Thomas B Davie, One of Afrikaans poet C Louis Leipoldt’s include a recent donation from the photographic collection, including glass Department of Biological Sciences: a plate slides (in picture) and minutes and but highly decorated cave near Hunt in a research ship named after the former very many day planners – tiny diaries fi lled Texas Hill County with over 800 feet of UCT principal and one of several research with the day-to-day matters that needed volume on nudibranchs dating to 1854, the correspondence from the past century, British monograph Nudibranchiate Mollusca passageway, taken in 1990. It belongs to the vessels the university has owned over Dr Francis Thackeray’s photograph of his attention. Leipoldt was encouraged at refl ecting the landscape and vegetation (Joshua Alder, Albany Hancock, Ray South African Speleological Association’s A cardboard model of a brain and head the years. It is part of the TB Davie Mare Tranquillitas (Sea of Tranquility), an early age to read widely, and was given over the years, including events such as Society). These volumes feature beautiful, comprehensive collection of photographs, measure belonging to the JG Davidson collection, which includes cruise reports, including the Apollo 11 landing site, a grounding in several languages and the snow on Table Mountain, and the existence hand-coloured illustrations, such as this Illustrations inside the 1930 publication minutes, correspondence, general records phrenological collection, which includes asset registers, charters of the vessel taken from the grounds of the Radcliffe natural sciences, particularly botany and of the historic fi sh market in Cape Town. Thecacera pennigera (winged thecacera), a Rock Paintings of South Africa, which and cave maps gathered between 1954 correspondence, minutes and reports and photographs. The 205-ton Thomas Observatory, Pretoria, in 1969, using geology. Whenever the family visited species of sea slug. includes a folding map showing the and 1999. of the British Phrenological Society. B Davie was commissioned after its a 12½-inch telescope, and signed by Cape Town, he was sent to his father’s specifi c location of works, and an Phrenology, the study of skulls to predecessor the John D Gilchrist’s sea American astronaut Neil Armstrong, the friends, such as Professor PD Hahn, for introduction and descriptive notes by determine an individual’s character and days ended in 1966. Launched in 1965, fi rst moonwalker. special instruction. Dorothea Bleek. This forms part of mental capacity, enjoyed some popularity the new vessel permitted longer cruises Special Collections’ UNESCO-recognised in Europe in the early 19th century, but is further off shore, notably two visits to the Bleek and Lloyd collection. now considered a pseudoscience. Vema Seamount in the Atlantic Ocean. 12 MONDAYSCIENCE MONTHLY SUPPLEMENT
THIS WILL MAKE YOU SMARTER Photos by Je’nine May
If you had to take away one life lesson from the sciences – one small fact that could expand your world – what would it be? We asked young scientists at UCT what they’ve learnt from their subject – and what others stand to learn.
Morema Moloisi Astrophysics
I would like people to know about the sun. The fi rst thing I’d like to tell them is that the sun is also a star, just like all the other stars which you see in the night sky. The only difference is that it’s the star in our solar system, and it’s closer to us than all the other stars, which are much, much further away. The second thing is that the sun is not really yellow, because it’s emitting white light. It’s actually a white star. It’s just that our atmosphere refracts the light from the sun and makes it look yellow.
Samantha Julius Chemistry
Everything that exists in this world is made from just a few different atoms. It is so intricately connected that a single atom missing or out of place determines the difference between a disease or a perfume. Everything that is, exists for a purpose.
Simone le Roux Biochemistry and human physiology
Studying the human body and how it works, you realise how amazing your body is and how much it does for you. It really is the least you can do to take care of your body. It’s much easier to stay healthy than it is to get healthy again. You shouldn’t wait until something goes wrong before you start looking after your body. I think it’s really important to educate yourself about what you Simeon Brown need to be healthy. There are so many Biochemistry and genetics products out there that make frankly ridiculous health claims, and people I think that people shouldn’t just swallow everything they see or hear from people waste money on them when there are or the media. Make your own opinions. Form your own conclusion. Think about it for way cheaper, way easier alternatives. yourself. By just swallowing everything whole, you’ll just get fat from the force-feeding Learn about what you need, read the of information. Think for yourself. The world is more interesting with your mind in it. labels on the products you buy, fi gure out for yourself if a product is really Candice Koopowitz going to help you. There is so much Archaeology information available now that there’s no excuse for being fooled by some fancy Archaeologists look to tell the packaging. story of how we came about and the different paths that were taken Dr Takalani Theka by our ancestors to get to where Chemistry we are today. It provides people with an understanding and sense of According to the World Health equality and belonging in that we’re Organisation, more than 70% all humans, evolved from the same of the world’s population uses ancestors, who overcame the same traditional medicine. So it’s not problems. surprising that scientists all over the world are involved in research on medicinal plants, trying to fi nd out which chemicals in the plants have healing properties. Scientists then ‘make’ or synthesise the chemicals in the laboratory … A famous example would be the bark of the willow tree, which patients were traditionally James Pelser advised to chew in order to cure Genetics and microbiology pain and fever. Scientists studied To the average person on the this medicinal plant and later street, science is daunting – often ‘made’ or synthesised aspirin. I seen as more diffi cult than it study the chemical compounds actually is. However, it is only with in the essential oils obtained from science that we have advanced medicinal plants that can be used this far, and only with it can we in pharmaceuticals, cosmetics, advance further. perfumery and food products.