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Is the future of science under threat in a post-truth world? the future of science under threat in a post-truth world?Faadiel Essop<p>​We need “inoculations" against fake news to help safeguard the future of science in a post-truth world, writes Prof Faadiel Essop (Department of Physiological Sciences / Centre for Cardio-metabolic Research in Africa) in an opinion piece for <em>Daily Maverick </em>(5 May).</p><ul><li>Read the article below or click <a href=""><strong class="ms-rteThemeForeColor-5-0" style="">here</strong></a><strong class="ms-rteThemeForeColor-5-0" style=""> </strong>for the piece as published.</li></ul><p><strong>​Faadiel Essop*</strong><br></p><p><em>Facts do not cease to exist because they are ignored</em> - Aldous Huxley.<br></p><p>The forwarded WhatsApp message on my phone boldly proclaimed that a post-mortem in Russia revealed that a radiation-exposed bacterium (and not the SARS-CoV-2 virus) is responsible for the Covid-19 pandemic and “causes human death by coagulation in the blood". The message triggered a tinge of despair as I realised that the plethora of similar, fake social media postings together with the widely reported (very rare) blood clotting side-effects of the Johnson & Johnson Covid-19 vaccine will only further fuel the burgeoning <a href=""><strong class="ms-rteThemeForeColor-5-0" style="">anti-vaxxer lobby</strong></a>.</p><p style="text-align:justify;">Of concern, the <a href=""><strong class="ms-rteThemeForeColor-5-0" style="">Centre for Countering Digital Hate</strong></a> reported that there are currently close to <a href=""><strong class="ms-rteThemeForeColor-5-0" style="">58 million people</strong></a> following anti-vaccine groups on various social media platforms with continued growth expected over the next years. Moreover, a recent <a href=""><strong class="ms-rteThemeForeColor-5-0" style="">Ipsos survey</strong></a> reported a lukewarm response to vaccination in several countries. For example, the findings indicated that only 40% and 53% of the French and South African populations respectively, intend to get vaccinated. Such alarming pseudoscience and fake news trends, and associated damaging outcomes raise a crucial question: will the scientific process survive this onslaught or will anti-vaxxers and other conspiracy theorists eventually hold sway in the public domain in a post-truth world?  </p><p style="text-align:justify;"><a href=""><em class="ms-rteThemeForeColor-5-0" style=""><strong style="">Post-truth</strong> </em></a>was the Oxford English dictionary's word of the year in 2016 due to a 2, 000% spike in its usage compared to the previous year. When viewed in a global context, it describes a world where public opinion and actions are now shaped by emotions, feelings and personal beliefs compared to objective facts. To put it bluntly, as facts are increasingly ignored and dismissed it holds serious consequences for the scientific process, evidence-based medicine and their broader impact. In the post-truth world, it is therefore essential to consider the definition of a <em>fact</em> that is listed by the Oxford English Dictionary as “a thing that is known to be true, especially when it can be proved". </p><p style="text-align:justify;">The basis of contemporary Science draws strongly on ideas of the philosopher Karl Popper who <a href=""><strong class="ms-rteThemeForeColor-5-0" style="">put forward</strong></a> the notion that scientists should do everything in their power to <em>disprove</em> a particular theory. Popper indicated that if, after repeated attempts, a particular theory <em>cannot</em> be disproven then it must be true. For example, if we aim to prove the theory that <a href=""><strong class="ms-rteThemeForeColor-5-0" style="">Santa Claus</strong></a> is real then the Popperian approach dictates that we should try everything in our power to <em>disprove </em>or falsify his existence. Thus, one may devise several observations to disprove the  “Santa is real" theory, for example, to watch the chimney during the entire Christmas evening to verify that he <em>actually </em>arrived with reindeers to deliver the lovely presents typically found the next morning, and so on.  Hence if the sender of the WhatsApp message regarding the Russian post-mortem applied this particular principle, it could be quite easily disproved as fake news and subsequently limited its proliferation on social media platforms. </p><p style="text-align:justify;">Thus, the scientific process is built on this premise. Here the best minds employ the most robust observational tools and equipment available at the time to meticulously amass sound and overwhelming evidence to eventually establish a  “scientific fact'' or  “truth", for example, that the earth is round or that an apple falls to the ground in accordance with the laws of gravity. The scientific process of gathering facts by meticulous observations and experimentation is pursued by many researchers often working independently in different laboratories across the globe. Findings generated are thereafter subjected to a rigorous peer-reviewed process of in-depth critique by various experts in the field in order to determine its veracity. <br></p><p style="text-align:justify;">After a sufficient body of peer-reviewed evidence has been gathered regarding a particular theory or concept, experts in this specialised field usually meet to review all such facts in order to reach a consensus.  This process will be repeated numerous times to refine the “facts" and to eventually establish scientific truths. Thus, the scientific process is a slow and self-correcting one, but that over time can result in major technological and health benefits for the broader society. For example, this process ensured that the global average life expectancy nearly doubled over the last 100 years, or that in-hospital mortality for heart attacks decreased from around 30% in the early 1960s to below 10% at present. <br></p><p style="text-align:justify;">However, with a cataclysmic event such as the Covid-19 pandemic the spotlight is shining brightly on those involved in this self-correcting process of fact generation with all its vulnerabilities and weaknesses. This created the perfect gap for <a href=""><strong class="ms-rteThemeForeColor-5-0" style="">conspiracy theorists</strong></a> to thrive by especially using social media platforms to spread false information for a variety of reasons. Moreover, fake news generated by internet “bots" and also political maneuverings, add additional layers of complexity in this regard. For example, it is becoming evident that Russian intelligence organisations are aiming <a href=""><strong class="ms-rteThemeForeColor-5-0" style="">to discredit vaccines developed by Western countries</strong></a> in order to promote their own Sputnik V version. In this instance, the Russians are prioritising their efforts in Africa where there is often a deep-seated resentment of former colonial powers. </p><p style="text-align:justify;">At a fundamental level, such schemes lie on the opposite spectrum of the slower, multi-step scientific process with its unique system of in-built checks and balances. In contrast, there is a very rapid spread of fake news often by so-called “experts" without any of the necessary checks and balances in place to attest to its veracity and truth. It is important to distinguish “disinformation" (completely false information spread by persons/organisations with evil intentions) from “misinformation" where someone spreads a false message without realising that it is actually not true.  <br></p><p style="text-align:justify;">Confirmation bias is rampant in such instances, where these individuals and organisations will only source, access or interpret information that will eventually confirm their deep-rooted, pre-existing beliefs.  In this case let us consider someone with a pre-existing bias that Santa may be real, who decides to prove his existence by collecting the required “facts" in an “objective" manner. Such “evidence" may include, for example, the fact that Santa was spotted at a nearby mall, or that he appeared on several television programmes and social media platforms, or that the cookies and milk left for him and his “team" on Christmas evening were gone the next morning.  Any information that does not fit this paradigm will be dismissed as part of a bigger ploy, or simply be ignored.    <br></p><p style="text-align:justify;">The current clash between these two vantage points is crucial when one considers major global challenges facing humanity, such as the current pandemic and future ones, the threat of climate change or food insecurity.  Despite the continued rise of the anti-vaxxer lobby, <a href=""><strong class="ms-rteThemeForeColor-5-0" style="">surveys</strong></a><strong class="ms-rteThemeForeColor-5-0" style=""> </strong>show that the broader public still display significant trust in scientists and the medical profession. However, such public goodwill may be eroded unless certain changes are implemented by those involved in the scientific research process and its eventual implementation.</p><p style="text-align:justify;">In the first instance, universities should strengthen science and medical curricula to better equip graduates to deal with the issues raised in this opinion article. At present, the focus is strongly on the subject discipline with limited focus on philosophical and societal contexts. This is a process we have now begun at Stellenbosch University.  Secondly, researchers also have a responsibility to better communicate with society as their endeavours are largely undertaken with public funds. Such interactions should not be done merely as dissemination of information (to an “ignorant" public), but instead as part of a constructive dialogue. For example, this may include sharing information regarding the nature of the scientific process with the public and to be honest that it is a self-correcting process with certain limitations versus it simply being a magic bullet. Thirdly, the media also needs to take responsibility in terms of reporting and to not sensationalise research findings. In this instance, the media often fails to accurately report the complexity and potential limitations of findings as typically indicated by researchers at press conferences. <br></p><p style="text-align:justify;">Finally, during such public engagements scientists should not try to debunk every myth as it is a near-impossible mission with the daily barrage of fake news encountered. They should instead focus only on the facts when dealing with the public, as well as explanations regarding the nature of the scientific process. In this way, a process of public “inoculation" against fake news will be established. Starting with this process at school level would be an excellent way to get the ball rolling. If these steps are implemented then I am confident that the scientific process should endure, as it has done previously, and thereby ensure that informed decision making and evidence-based medicine will prevail.  <br></p><p><strong><em>*Prof Faadiel Essop is Director of the Centre for Cardio-metabolic Research in Africa (CARMA) at Stellenbosch University</em></strong><br></p><p>​​<br></p>
Volunteers develop first machine translation benchmarks for 30 African languages develop first machine translation benchmarks for 30 African languagesWiida Fourie-Basson<p>​From Khoekhoegowab to Igbo and Sepedi – these are only three of the low-resource languages in Africa that a group of over 400 volunteers from more than 20 African countries are targeting to address the lack of diversity in the field of <a href="">natural language processing</a>.</p><p>Natural language processing (NLP) is a branch of artificial intelligence that helps computers understand, interpret and manipulate human language. But while Africa has more than 2000 living languages, most of these have very little data, making it difficult to develop speech and language technologies relevant to the African context. Hence the term low-resource languages.</p><p><a href="">The Masakhane project</a> is a grassroots initiative involving a virtual community of content creators, translators, curators, language technologists and evaluators – all with the mission of addressing the lack of geographic diversity in the field. It was established in 2019 by <a href="">machine learning engineer Jade Abbott</a> during the <a href="">Deep Learning Indaba</a> held in Kenya.</p><p>Now one of the project's research papers, on a participatory research model for low-resourced machine translation, is one of two papers to have won the inaugural <a href="">Wikimedia Foundation Research Award for 2020</a>.</p><p>Stellenbosch University's Dr Herman Kamper, a senior lecturer in the Department of Electric and Electronic Engineering, and Elan van Biljon, an MSc student in Computer Science, were among the 45 co-authors on the paper “<a href="">Participatory research for low-resourced machine translation: a case study in African languages</a>", published in the <em>Findings of the Association for Computational Linguistics: EMNLP</em> at the end of 2020.</p><p>Dr Kamper says they specifically contributed to a machine translation system for translating English to Afrikaans, while Elan also worked on English to Sepedi and Setswana translations: “For us, it was amazing to play a small part in such a big effort, working with people from across Africa as well as established researchers such as <a href="">Julia Kreutzer</a> from Google Research, who developed some of the core code".</p><p>In NLP terms, most African languages are classified as “The Left Behinds", “Scraping By" or “Hopeful". Only a few, such as Afrikaans, Kiswahili and Yoruba, find themselves in the “Rising Stars" category. There is also a lack of NLP researchers in Africa. In 2018, only five out of the 2 695 affiliations of participants in the five major NLP conferences were from African institutions. </p><p>In the paper, they describe how a participatory approach has enabled them to set machine translation benchmarks for 30 African languages. This means that, for the first time, machine translation systems have been developed to translate from English into these different languages (the way Google Translate would translate sentences from English to German), setting a benchmark and making it possible for researchers to make further improvements.</p><p>From Nigeria, volunteers are translating their own writings, including personal religious stories and undergraduate theses, into Yoruba and Igbo. This is in an effort to ensure that accessible and representative data of their culture are used to train models.</p><p>In Namibia, Jade Abbot is hosting collaborative sessions with Damara speakers, to collect and translate phrases in Khoekhoegowab that reflect Damara culture around traditional clothing, songs and prayers.</p><p>Another unique feature of the participatory approach is the human evaluation of the machine translation system developed for these languages. For example, in 2020 eleven participants volunteered to evaluate translations in their mother tongue, often involving family or friends to determine the most correct translations. Within only ten days, they gathered a total of 707 evaluated translations covering Igo, Nigerian Pidgin, Shona, Luo, Hausa, Kiswahili, Yoruba, Fon and Dendi. This was the first time that human evaluation of an MT system has been performed.</p><p>In their announcement, The Wikimedia Foundation says the paper and the Maskhane community have fundamentally changed the approach to the challenge of 'low-resourced languages' in Africa: “The research describes a novel approach for participatory research around machine translation for African languages. The authors show how this approach can overcome the challenges these languages face to join the Web and some of the technologies other languages benefit from today."</p><p>The Wikimedia Foundation Research team established the Wikimedia Foundation Research Award of the Year in 2021 to recognize recent research that has the potential to have significant impact on the Wikimedia projects or research in this space.</p><p><strong>Media enquiries</strong></p><p>Masakhane project</p><p>E-mail: <a href=""></a></p><p>Dr Herman Kamper</p><p>E-mail: <a href=""></a></p><p>Department of Electric and Electronic Engineering, Faculty of Engineering</p><p>Stellenbosch University<br></p><p>​<br></p>
The Table Mountain fire: what we can learn from the main drivers of wildfires Table Mountain fire: what we can learn from the main drivers of wildfiresProf Brian van Wilgen and Dr Nicola van Wilgen-Bredenkamp<p><br>The fires that started on 18 April 2021 on the slopes of Table Mountain in South Africa destroyed several buildings on the campus of the <a href="">University of Cape Town</a>. These included the Jagger Library, as well as the restaurant at Rhodes Memorial, the historic Mostert's Mill, and several residential houses.<br></p><p>This was a tragic event that will affect many people for a long time.</p><p>Many questions have been raised as to why this happened, and whether anyone should carry the blame.</p><p>Based on our research into fynbos fire ecology and management over the past four decades, we believe that rather than attempting to apportion blame, South Africans should be examining the causes of destructive wildfires, and what can be done about them.<br></p><p>Wildfires are the inevitable consequence of three factors coming together at the same time: weather that is conducive to the establishment and spread of a fire; enough fuel of the right type and arrangement to carry the fire; and a source of ignition to start it.</p><p>Simple as this may seem, there are many misconceptions and poor understanding around each of these elements.</p><p>The weather</p><p>The Cape summer and autumn historically have <a href="">suitable weather for fires to occur</a>, so a fire at this time of the year isn’t unusual. However, global climate change is exacerbating the situation.</p><p>Data from the South African Weather Service Cape Point monitoring station show clearly that average temperatures have been rising steadily over the past six decades. As a result of this, the percentage of days with above average temperatures in April <a href="">has doubled since 1960</a>.</p><p>The steady increase in hot, dry weather will dry out the vegetation, making it more likely to catch fire, and for fire to spread. This phenomenon is not restricted to the Cape, and has been <a href="">widely reported</a> in other parts of the world.</p><p><img alt="A graph showing rising temperatures at Cape Point between 1960 and 2019." src="" style="margin:5px;padding:0px;border-width:0px;border-style:initial;outline:0px;vertical-align:baseline;display:block;max-width:100%;width:754px;" /> </p><figcaption>Average maximum temperatures between 1960 and 2019 at Cape Point showing which years had temperatures above (red) and below (blue) the long-term average. Provided by lead author.</figcaption><p></p><p>The fuel</p><p>The natural fynbos vegetation that historically clothed the slopes of Table Mountain is highly inflammable.</p><p>That situation has also been exacerbated by the introduction of alien trees, which increase the fuel available to burn, and that burn with a much higher intensity than the natural fynbos.<br></p><p>For example, <a href="/english/Lists/news/DispForm.aspx?ID=5908">our work after the destructive fires in the South African coastal town of Knysna in 2017</a> showed that plantations of alien trees, and natural fynbos that had become invaded by these trees, burnt with much higher severity than uninvaded fynbos.</p><p>Alien trees don’t only increase the risk of uncontrollable fires, they also eliminate the natural biodiversity and reduce water runoff. This is particularly true if they become invasive, that is if they spread across the landscape without assistance, where they can form dense stands that crowd out the native fynbos and use more water than the vegetation that they replace.</p><p>In response to this, and in line with national legislation, South African National Parks has been clearing plantations of invasive pine trees from the Table Mountain National Park since <a href="">the establishment</a> of the park in 1998.</p><p>These operations have been conducted in the face of <a href="">substantial opposition</a> from the citizens of Cape Town, because the invasive trees are aesthetically pleasing and provide shade. Many people also <a href="">believe (incorrectly) that they bring rain</a> and provide the best cover to protect the soil.</p><p>Not all alien trees are invasive. It’s mainly invasive alien trees – those that are able to spread unaided across the landscape – that are targeted for control. The pine trees that have been removed from the Table Mountain National Park are invasive. The situation is further complicated because the trees in the line of most recent fires – mainly alien Mediterranean stone pines – are not invasive, so don’t have to be controlled in terms of South African law.</p><p>In addition, mature stone pines, including those at Rhodes Memorial, are protected by heritage legalisation and cannot be damaged or removed. These trees were planted over 200 years ago, and are valued icons of the city’s history. Whether or not, or to what degree, the stone pines contributed to the intensity and spread of the recent fires is not yet known.</p><p>What is known is that many buildings and historic infrastructure caught alight some distance from the fire front due to embers that were carried a long distance – <a href="">an occurrence termed “spotting” by fire fighters</a>.</p><p>Some (as yet unknown) plants, <a href="">which include alien pines and palms</a>, would have provided the fuel for those embers. Under these circumstances, even carefully maintained firebreaks would not have stopped this spotting.</p><p>Source of ignition</p><p><a href="">Research in other parts of the world</a> has clearly demonstrated a strong link between human population density in an area, and the number of fires that occur.</p><p>Cape Town is now home to <a href="">almost 5 million people</a>, <a href="">many of them poor and homeless</a>. That fires will be started, either accidentally or deliberately, is therefore almost a given and very difficult to effectively prevent.</p><p>Urban densification, crime, and homelessness are broad social issues about which organisations like South African National Parks can do very little.<br></p><p>Going forward<br></p><p>Very little can be done locally about climate change – it is a global issue that must be addressed at a global scale.</p><p>The risks of human ignitions will remain a constant factor. That leaves two things that could be improved.</p><p>First, buildings should be fire-proofed as far as possible by using fire-resistant building materials and clearing gutters and other points where plant material accumulates. Secondly and most importantly, vegetation needs to be managed, especially tall alien trees that can significantly increase the risks of damaging fires.</p><p>Burning the fire-adapted and fire-dependent fynbos vegetation under milder weather conditions, and at appropriate intervals, to reduce fuel loads could also reduce the risk of runaway fires. This is currently impeded by very risk-averse wildfire legislation that needs to be carefully <a href="">re-examined</a>.</p><p><em>Dr Chad Cheney, a park planner at Table Mountain National Park, also contributed to this article.</em></p><p><em>This article was first published in The Conversation Africa -</em></p><p><em>Image: <span style="font-size:12pt;font-family:"times new roman", serif;">Ashraf Hendricks/GroundUp</span></em></p><p>​<br></p>
SU’s Guy Midgley one of Reuters’ most influential climate scientists’s Guy Midgley one of Reuters’ most influential climate scientistsMedia & Communication, Faculty of Science<p>​​<br>Stellenbosch University's <a href="">Prof Guy Midgley</a> is one of four South African scientists listed on the <a href="">Reuters Hot List</a> of the top 1000 most influential climate change scientists in the world.<br></p><p>Prof Midgley is number 180 on the list, together with Prof Mark New (151) and Prof Chris Reason (722) from the University of Cape Town, and Prof Mark Jury (828) from the University of Zululand. Prof Midgley heads the <a href="">global change biology research group</a> in SU's <a href="/english/faculty/science/botany-zoology/Pages/default.aspx">Department of Botany and Zoology</a>.</p><p>To identify these scientists, Reuters combined three rankings based on the number of climate change-related research papers published, how often these papers were cited by other scientists in similar fields of study, and how often those papers were referenced in the lay media, social media, policy papers and other outlets. According to the Reuters website, the Hot List does not claim to be a rank of the “best" or “most important" climate scientists in the world, but rather a measure of their influence.</p><p>In this effort, at least 350 000 papers were examined, 99% of which were published after 1988. According to Reuters: “In 1988, US scientist James Hansen went before Congress and testified about his research into the warming of the planet. More than 30 years later, Hansen's prediction that the average global temperature could rise by about one degree Celsius by 2019 has come to pass. His warning, and appeals for action from Hansen and others, went largely ignored by policymakers, despite an avalanche of confirmatory research from ensuing generations of climate scientists".</p><p>Prof Midgley says reports about James Hansen's testimony in 1988 encouraged him to consider climate change as a topic for his PhD-thesis: “I worked on how plants respond to rising CO<sub>2</sub>, a process now suspected to be behind the role of terrestrial ecosystems soaking up about one third of CO<sub>2</sub> emissions annually".</p><p>More significantly, though, he does not believe that climate scientists are largely ignored – the so-called Cassandra-effect (in Greek mythology King Priam's daughter, Cassandra, is endowed with the gift of prophecy but fated never to be believed): “You surely cannot expect to change such a fundamental dependence as ours on fossil fuel in a short time. The science has most certainly shifted the debate significantly towards solutions, and there is still time to ensure a better future if more beneficial decisions can be made.</p><p>“My research group has just published <a href="">a new assessment</a> in collaboration with international colleagues of climate change risks to endemic, indigenous and invasive species. The message remains: We have time to avoid the worst," he says.</p><p>At present, his research group is working on the functioning of important species in diverse southern African ecosystems, such as savannas, arid shrublands, fynbos and estuaries, and linking this to the resilience of these systems to climatic drivers.<br></p><p>​<br></p>
Trout ‘voracious predators’ of indigenous Redfins ‘voracious predators’ of indigenous RedfinsBrian van Wilgen, Centre for Invasion Biology<p></p><p><a href="">Prof Brian van Wilgen</a>, emeritus professor in invasion biology, recently replied to an article published on 3 April in <em>Daily Maverick</em>'s <em>168</em> weekly newspaper by Ed Stoddard, entitled “Trout wars: In a developing country with so many challenges, the fuss looks fishy" (Online at <a href=""></a><br></p><p>His reply, titled “Contrary to Ed Stoddard's contention, trout are voracious predators and legislation has been proposed to regulate the fish, not to declare it illegal" was published in <em>DM168</em> on 6 April 2021. Read the reply below:</p><p><em>By Brian van Wilgen, emeritus professor, <a href="">DSI/NRF Centre for Invasion Biology</a>, Stellenbosch University</em></p><p>The article by Ed Stoddard (“Spawning debate: the fuss over trout looks fishy"; Daily Maverick, 3 April 2021) is unfortunately flawed, and arguably heavily partisan because of his own admitted status as a “passionate fly-fisher". The issue of regulating trout has recently become particularly contentious. Debates like these prevail where alien species are introduced to provide some form of benefit, but then go on to become invasive, causing harm to the environment. It is important in these cases to present a balanced view, so I will address some of the points made in Mr Stoddard's article.<br></p><p>In general, Mr Stoddard's article acknowledges that invasive species can cause harm, notably on islands, but also contends that in many cases this damage is negligible. It is true that islands are more vulnerable to invasive alien species, but these impacts are now increasingly being felt on the mainland, and they certainly are not negligible. The impacts of invading alien plants in South Africa have recently been conservatively estimated at over R13 billion per year, for water resources, rangeland productivity and biodiversity only – and they are growing alarmingly. </p><p>Mr Stoddard has uncritically repeated arguments by a group within the trout industry as to why trout should not be regulated, namely that trout do minimal harm to the environment; that they have been naturalized in the country for so long (over 100 years) that they should be regarded as indigenous (rather than as alien species); and, that regulation would cause the lucrative trout industry to go “belly-up" (to use Mr Stoddard's terminology). </p><p>The contention that trout have a “fairly minimal" impact, only posing a threat to the rare redfin minnow in the Krom River in the Western Cape, is incorrect. Trout are voracious predators, and their impact is far greater than posing a mere threat to one indigenous fish species. There is now a mounting body of evidence that trout have caused the local extinction of many indigenous freshwater fish species, as well as amphibians and large invertebrates, with knock-on effects for plant life in streams. More importantly, many of the threatened fish species are found nowhere else on Earth, and South Africa is obliged to protect such species both in terms of its own laws, and in terms of the international Convention on Biodiversity. </p><p>The notion that introduced (alien) species should be granted indigenous status if they have been here for a long time is also unsound. This notion is argued in Duncan Brown's book (<em>Are trout South African?</em>), cited in Mr Stoddard's article. Any informed South African alive today would have known trout as occupants of our streams all of their lives. However, our lives are short. Indigenous fish, frogs and dragonflies have evolved over hundreds of thousands of years in environments without voracious predators. They have no instinctive means to avoid predation, and will be driven to extinction long before they are able to learn how to respond to this relatively new and deadly threat.   No “new balance" has been reached, as is often contended.  </p><p>It is also dangerous to start regarding invasive alien species as indigenous. Consider, for example, the case of mice on Marion Island, where they have been for over 200 years. They have decimated the invertebrates found (mostly) only on the island, have impacted on the indigenous plants, and now are attacking the nesting sea-birds.  Projections are that they will cause the local extinction of 18 species of birds, if left alone.</p><p>The nub of the argument though is that regulating trout will impose an unreasonable burden on the industry, requiring a permit for “every step in the trout value chain". Such a requirement would make unpermitted hatcheries, trout-fishing farms, and restaurants serving trout illegal. Further, it is contended that the government does not have the capacity to administer this, and so the industry will simply have to go out of business. However, if one reads the proposed regulations, it immediately becomes clear that many trout “value chain" activities have been exempted from requiring permits, making it perfectly legal, for example, to process, transport, consume, sell or serve trout as long as they are not alive.</p><p>The government's approach to regulating trout is carefully nuanced. The intention is to grant long-term permits that will allow for the continuation of all existing operations in demarcated areas, allowing the industry to continue to operate and to generate benefit. They have even conceded that this can continue in proclaimed protected areas. The main issue here is to prevent the spread of trout to new areas where they do not yet occur. It is well known that freshwater anglers regularly introduce new fish species into catchment areas where they do not yet occur, for the purposes of recreational fishing, and for angling competitions. To prevent the consequent harm to these ecosystems, and to the unique indigenous species that occur there, regulation is necessary. This approach should be seen as a win-win compromise, rather than a cause for prolonged and expensive litigation, which is simply unnecessary and wasteful. As Mr Stoddard points out, there are bigger fish to fry.</p><p> <strong>On the photo:</strong> Redfin minnows are one of the indigenous fish species that form the prey of trout. Streams with trout in them are simply devoid of these charming fishes. <em>Photo supplied by Brian van Wilgen​</em></p><p>​<br></p>
World Health Day: Primary health care helps combat COVID-19, lifestyle diseases Health Day: Primary health care helps combat COVID-19, lifestyle diseasesBob Mash & Resia Pretorius<p>​<br><br></p><p>Wednesday (7 April) was World Health Day. In opinion pieces for the media, Profs Bob Mash (Division of Family Medicine and Primary Care) and Resia Pretorius (Department of Physiological Sciences) focus on health issues that should receive attention during and after the pandemic. Click on the links below to read the articles.</p><ul><li>​Prof Bob Mash (<a href=""><strong class="ms-rteThemeForeColor-5-0">Cape Times</strong></a>)<br></li><li>Prof Resia Pretorius (<a href=""><strong class="ms-rteThemeForeColor-5-0">Health24</strong></a>)​</li></ul><p>​<br></p>
SharkSafe BarrierTM withstands two years of testing at La Réunion Island BarrierTM withstands two years of testing at La Réunion IslandMedia & Communication, Faculty of Science<p style="text-align:justify;">​The SharkSafe Barrier, an eco-friendly alternative to the traditional shark-control programmes, have withstood two years of testing in Réunion's bay of St Paul. This is part of ongoing efforts by the island's shark security centre <em>Centre Sécurité Requin</em> (CSR) to find a workable and eco-friendly solution to the island's shark crisis. </p><p style="text-align:justify;">The SharkSafe Barrier<sup>TM</sup> technology, originally developed in South Africa, bio-mimicks a thick forest of kelp. Combined with shark-repellent magnets to further deter sharks, the technology has been undergoing rigorous testing in South Africa and The Bahamas since 2012, with the results of these tests published in various <a href="">peer reviewed scientific journals</a>.</p><p style="text-align:justify;">A test barrier of 200 pipes was constructed in February 2019 to form a 10m x 10m square in order to replicate, in La Réunion waters, previously published experiments. The aim was to test the efficacy of the SharkSafe Barrier<sup>TM</sup> to exclude local bull sharks from a food source.</p><p style="text-align:justify;">According to <em>Centre Sécurité Requin</em> (CSR) Director of Operations Michael Hoarau, the barrier's efficiency to exclude bull and tiger sharks species in this instance could not be established, as the underwater cameras and the sonar did not record any bull and tiger sharks approaching the barrier during the tests. However, the developers are encouraged by the fact that the structure, which consists of vertical pipes anchored to the sea bottom, survived two seasons' winter swell, with minimum maintenance.</p><p style="text-align:justify;">“This means that the maintenance of this technology during the last two years was three times cheaper than it would have been to deploy shark exclusion nets," explain Dr Sara Andreotti, COO of SharkSafe Barrier Pty.</p><p style="text-align:justify;"><strong>Ongoing research and product development</strong></p><p style="text-align:justify;">In parallel with the St Paul experiment, differently designed units were tested in Etang-Salé, to form part of an ongoing research and development effort in the high energy zone (perpendicular to the shoreline). This research aimed to adapt the current design to enable more versatile installations across the globe. The designs were installed at different water depths and across different substrates, testing cost-effective options to provide robust solutions. The Etang-Salé experiment was sponsored entirely by the SharkSafe Barrier Pty start-up, and was conducted between January 2019 and June 2020. Three rounds of increasingly expensive and robust designs have been installed during the trials, but none proved robust enough for the Etang-Salé conditions.</p><p style="text-align:justify;">The costs associated with the experimentation in Etang Salé prompted the decision to suspend the research and development efforts in Réunion, and to continue the product development tests in South Africa. The different designs tests are being continued in Glencairn in South Africa and these are showing promising results.</p><p style="text-align:justify;"><strong>Global solution to replace current shark-control programs</strong></p><p style="text-align:justify;">According to Dr Sara Andreotti, one of the co-inventors of the SharkSafe Barrier<sup>TM</sup> technology, there is an urgent need to find an alternative to traditional shark-control programs worldwide: “The SharkSafe Barrier is currently the only available eco-friendly and shark-specific technology to reduce shark-human conflict."</p><p style="text-align:justify;">“In the case of Réunion, for example, a non-invasive shark barrier will have a positive impact on the local ecology by protecting top-predators and their key role in the marine ecosystem. It will also positively impact on the local economy, by protecting beach-goers and thereby promote potential tourism revenue. Lastly, it can help the community to better cope with the historical trauma associated with a number of shark accidents since 2011.</p><p style="text-align:justify;">“Irresponsible and unsustainable fishery practices are still undoubtedly the biggest global threat to sharks. The socio economic and ecological impact of a solution such as the SharkSafe Barrier<sup>TM</sup>, is a step in the right direction. For Blue Economy inspired countries such as France, it could prove key to ensuring long term and peaceful coexistence between humans and sharks, while promoting ocean sustainability and coastal eco-tourism," she concludes.</p><p style="text-align:justify;"><strong>For the editors</strong></p><ul><li>Developed in South Africa the <a href="">SharkSafe Barrier<sup>TM</sup></a> is the only eco-friendly shark management method in the world combining biomimicry and magnetism to reduce shark-human conflict, by keeping sharks and surfers physically separated from each other. Distributed by SharkSafe Barrier Pty Ltd, a start-up spin-off company of Stellenbosch University, the <a href="">SharkSafe Barrier<sup>TM</sup></a> is designed to be a visual shark-deterrent by mimicking a thick forest of kelp composing of vertical recycled plastic pipes, coupled to a strong magnetic field, also tested and proven to affect the swimming behaviour of large sharks.</li><li>Réunion's <em>Centre Sécurité Requin</em> (CSR) and SharkSafe Barrier Pty Ltd respectively contributed 66% and 34% towards the construction and installation of the test barrier at St Paul. The pipes were constructed in South Africa, and shipped to Réunion at the end of 2018. The construction of 40 meters of barrier at St Paul took nine days, and was performed in collaboration with local subcontractors TSMOI, as well as a crane boat and four divers.</li><li>To collect data on the bull sharks' behaviour the CSR operators deployed underwater cameras and sonar, with a canister of fish positioned in the middle of the exclusion square. This activity was performed sixty three times over the two year period. Unfortunately, no bull and tiger sharks were recorded during the data collection, despite adjacent acoustic tags indicating the sporadic presence of bull sharks in the bay. This resulted in the experiment being inconclusive.</li><li>The CSR's research permit conditions require that the installation in St Paul must now be removed from the bay.</li><li>The SharkSafe Barrier<sup>TM</sup> was also labelled as a Solar Impulse Efficient Solution in 2020, completed the <a href="">Oceanhub Africa business accelerator program</a>, was the recipient of the prestigious NSTF-Lewis Foundation Green Economy Award at the <a href="/english/Lists/news/DispForm.aspx?ID=7542">National Science and Technology Forum</a> and was one of the finalists in the Smart-Eco-responsible Tourism category of the France <a href="">Tech4Island Award</a>. More recently the company was recognised by the <a href="">World Economic Forum</a>'s digital platform UpLink as one of its top ocean innovators.</li></ul><p style="text-align:justify;"><strong>ENDS</strong></p><p style="text-align:justify;"><strong><em>Contact details</em></strong></p><p style="text-align:justify;">Dr Sara Andreotti</p><p style="text-align:justify;">E-mail:</p><p style="text-align:justify;">Mobile: 072 3219198</p><p style="text-align:justify;"><strong><em>Website and Social Media links:</em></strong></p><ul><li>OIO LinkedIn:</li><li>OIO Facebook:</li><li>OIO Instagram: (@oceanimpactorg)</li><li>OIO Twitter: (@oceanimpactorg)</li><li>SSB Website: <a href=""></a></li><li>SSB Facebook: <a href=""></a></li><li>SSB LinkedIN: <a href=""></a></li><li>SSB Instagram: <a href=""></a></li><li>SSB Twitter: <a href=""></a><br></li></ul><p>​<br></p>
Accurate quantification of cell dynamics possible with new software tool quantification of cell dynamics possible with new software toolWiida Fourie-Basson<p>​Engineers and scientists from Stellenbosch University have developed a visualisation tool that can automatically localise and quantify specific cellular processes such as mitochondrial fission and fusion – and that in three-dimensional space and time.<br></p><p>Mitochondria are organelles that generate most of the chemical energy needed to power the cell's biochemical reactions. Mitochondrial processes, such as fission and fusion, therefore play a central role in the balance, function and viability of cells. When things go wrong, it is often a sign of the onset of neurodegenerative diseases such as Parkinson's and Alzheimer's disease.</p><p>To date, however, the accurate quantification of these cell dynamics has been a challenge, with most of the work being done manually.</p><p>Prof Ben Loos, a physiologist in the Department of Physiological Sciences, says they are very excited about this work: “We believe it moves the field forward on many fronts, from life sciences dealing with mitochondria and microscopy, to the fields of image analysis and object recognition, computation and machine learning, data handling and analysis, and 3D visualisation.</p><p>Since 2015, he has been working with Prof Thomas Niesler from the Department of Electronic and Electrical Engineering on improving 3D visualisation tools associated with microscopy. The current tool, called the Mitochondrial Event Localiser (MEL), was developed by Dr Rensu Theart as part of his PhD research into the virtual reality visualisation and analysis of microscopy data. </p><p>Prof Loos says image analysis of biological data is often so time consuming that only few research groups embrace such a task: “With MEL, we are able to quantify the structures and the interaction (fission and fusion) between the structures in the cell, as well as pin-pointing where these are occurring.</p><p>“This is incredibly exciting, to locate where in the cell fission, fusion and depolarisation occurs, and to quantitatively describe their magnitude of occurrence".</p><p>Why is this so important? </p><p>He says researchers struggle to interpret the morphology of the mitochondrial network: “Some say that a highly networked mitochondrial structure indicates improved cellular health, other evidence suggests that it is the beginning of a stress response. The same for a fragmented mitochondrial picture, some scientists advocate that fragmentation equals stress and detriment, while other evidence indicates it as adaptive mechanism to enable mitochondrial quality control.</p><p>“This really bothered us. Especially since this plays such an important role in neurodegenerative disease, we wished to come up with a tool that could describe the mitochondrial network dynamically, meaning to work with real-time data sets. In doing so, a completely new data set is generated, which allows to showcase the state of equilibrium of mitochondria between a fission and a fusion state." </p><p>They believe this software tool will be of major benefit to the research community dealing with mitochondrial dysfunction. Especially those laboratories focussing on Alzheimer's disease and Parkinson's disease.</p><p>“It could also become part of a diagnostic tool, if integrated into so called high throughput imaging platforms. And because mitochondrial depolarisation is a critical part in the beginning of cell death, there may be an even wider application base," he concludes. </p><p><strong>Information box: How does MEL work?</strong></p><ol><li>First, a time-lapse sequence of a cell, labelled for mitochondria, is acquired in 3D with confocal microscopy.</li></ol><ol start="2" style="list-style-type:decimal;"><li>This time-lapse sequence is then pre-processed to ensure the best image quality and consistency between the frames in the sequence.</li><li>Two consecutive frames are then chosen, and binarized. From this the separate mitochondrial structures can be extracted.</li><li>Through various mathematical steps, including a new algorithm called “back-and-forth structure matching", the presence and location of the mitochondrial events can be determined.</li><li>These locations are then overlaid as different colours on the original mitochondrial image.</li><li>This process is then repeated for all consecutive image pairs in the time-lapse sequence, thereby allowing a quantitative evaluation of how the mitochondrial events vary over time. </li></ol><ul><li>Compiled by <em>Dr Rensu Theart</em></li></ul><p>The article “Mitochondrial event localiser (MEL) to quantitatively described fission, fusion and depolarisation in the three dimensional space" was published in the journal <em>Plos One</em> recently and is available online at <a href=""></a></p><p>The code that implements MEL is available for download at <a href=""></a></p><p><strong><img src="/english/PublishingImages/Lists/dualnews/My%20Items%20View/MEL%20event_Image%20credit%20Renso%20Theart_small.png" alt="MEL event_Image credit Renso Theart_small.png" style="margin:5px;" /></strong> </p><p>This is the result produced by the Mitochondrial Event Localiser (MEL) when applied to an image showing only the mitochondrial network of a cell acquired by confocal microscopy. The different colours indicate the location of where the mitochondrial fission, fusion, and depolarisation events were detected. <em>Image: Rensu Theart</em></p><p><strong>Contact details</strong></p><table cellspacing="0" width="100%" class="ms-rteTable-default"><tbody><tr><td class="ms-rteTable-default" style="width:33.3333%;"><p>Prof Ben Loos</p><p>E-mail:</p><p> </p></td><td class="ms-rteTable-default" style="width:33.3333%;"><p>Dr Rensu Theart</p><p>E-mail:</p><p> </p></td><td class="ms-rteTable-default" style="width:33.3333%;"><p>Prof Thomas Niesler</p><p>E-mail:​ </p></td></tr></tbody></table><p><em><br></em></p><p>​<br></p>
Early detection of increased risk for colorectal cancer detection of increased risk for colorectal cancer Wiida Fourie-Basson<p><br><br></p><p>A PhD student from Stellenbosch University has established that the early detection of colorectal cancer risk would be greatly enhanced by a holistic approach that takes into account the complex interplay between chronic inflammation, abnormal blood clotting and the involvement of a bacterial presence. </p><p>Colorectal cancer, also known as colon cancer, is currently the third most diagnosed cancer in the world. When diagnosed early, about 90% of the patients will have a five-year life expectancy. It reduces to 13% with a late or delayed diagnosis.</p><p><a href="">Dr Greta de Waal</a>, who received her doctoral degree during the Faculty of Science's SU's graduation ceremony on 1 April 2021, emphasises that colorectal cancer is a multifactorial and heterogeneous cancer, with various contributors and drivers involved in its pathogenesis: “Most cases of colorectal cancer encompass a variety of contributing risk factors, in addition to genetic features. Because of the heterogeneity of the disease, it is crucial to employ holistic approaches to determine how all the different factors involved in the carcinogenic process are linked to (and may fuel) each other," she explains.</p><p>In her research, she analysed and described both the systemic environment and local tumour environment of patients with colorectal cancer. She developed and optimised a novel fluorescence antibody-based technique to detect the bacterial inflammagen, lipopolysaccharide (LPS), in blood. She was then able to show that the circulating levels of this bacterial wall component are significantly elevated in patients with colorectal cancer, compared to healthy individuals. In addition, she also demonstrated an intratumour bacterial presence in these patients. She thus found that the presence of a bacterial component forms a key part of the overall profile of patients with colorectal cancer, with systemic inflammation and increased hypercoagulability also being central.</p><p>Dr De Waal says there is an intricate relationship between a dysfunctional gut microbiome and a pro-inflammatory profile in these patients: “Alterations in the composition of the gut microbiota can contribute to the development of a dysfunctional gut barrier, thereby facilitating the translocation of bacteria and their inflammagenic molecules. Such leaky gut conditions can promote systemic inflammation, of which a hallmark is abnormal blood clotting".</p><p>Chronic inflammation and hypercoagulation are both implicated in the formation of tumours. The researchers believe these conditions – elevated presence of certain circulating bacterial and other inflammatory markers, and the incidence of abnormal blood clotting – could be used as biomarkers in blood-based screening tools when screening patients for colorectal cancer risk.</p><p>“All of this information can be obtained by taking a simple blood sample, and then knowing what to look for," adds <a href="">Prof Resia Pretorius</a>, her supervisor and a physiologist in the <a href="">Department of Physiological Sciences</a> at SU.</p><p>Prof Pretorius says the work is the result of a fruitful collaboration between herself and clinicians from SU's Faculty of Medicine and Health Sciences at Tygerberg, with the SU rector Prof Wim de Villiers, who is a gastroenterologist himself, acting as co-supervisor.</p><p>“While we benefited from Prof De Villiers' expertise of the clinical side of colorectal cancer and its treatment, we could add our expertise of what is happening at the molecular level," she explains.</p><p><strong>Media enquiries</strong></p><p>Prof Resia Pretorius</p><p>Head: Department of Physiological Sciences, SU</p><p>E-mail: <a href=""></a></p><p>​Dr Greta de Waal<br></p><p>Postdoctoral Fellow, Department of Physiological Sciences, SU</p><p>E-mail:<br></p><p>On the photo, Dr Greta de Waal (middle), together with her study leaders Prof Resia Pretorius and Prof Wim de Villiers, after the 1 April 2021 graduation ceremony. <em>Photo: Stefan Els</em><br></p><p>​<br></p>
Why tree diversity in the tropic matters tree diversity in the tropic mattersWiida Fourie-Basson<p></p><p>What can the decomposed leaf litter from 40 streams on six continents tell us about the impact of biodiversity loss on global carbon fluxes?</p><p>According to a study published in <em>Science Advances </em>today (26 March 2021), there is reason to be concerned, especially at low latitudes where the rate of deforestation and conversion of forest to monoculture, plantations and agricultural land are already high. </p><p>The decomposition of plant litter in streams is a fundamental ecosystem service, as it mainly serves as a sink for carbon, thereby keeping the global carbon budget in balance. When the optimal functioning of that ecosystem service is disturbed, some of the world's rivers could become a source rather than a sink for carbon, creating potential feedbacks on climate.</p><p>Prof Cang Hui, a bio-mathematician from Stellenbosch University and a co-author of the article, says some broad-scale roles of biodiversity and the impacts of climate change only emerge and become detectable at the global scale. In this study, for example, the latitudinal gradient of instream decomposition only became clear over more than 100° of latitude, roughly around 10 000 km.</p><p>To conduct this global experiment, scientists from 67 institutions across six continents joined forces to coordinate the sampling of the rivers. From 2017 to 2019, they placed a total of 2 580 leave litter bags in 40 streams. Four rivers from Africa were sampled: the Lourens River near Somerset West in South Africa, the Njoro and the Ngetunyek rivers in Kenya and the Djigbè River in Guinea. </p><p>The bags were retrieved after 23 to 46 days, depending on the water temperature in each stream, put in individual ziplock bags and transported on ice to various laboratories. The aim of the study was to assess how the decomposition rates in streams vary from the lower to the higher latitudes, from which we can infer how biodiversity loss and climate change affect this ecosystem service.</p><p>The results demonstrated that plant diversity has a major impact on litter decomposition. The experiment was able to show that plant litter high in diversity (e.g., in toughness, nutrient content, presence of toxins) stimulates decomposition more at low latitudes than in cooler climates. This suggests that stream ecosystem functioning could be particularly vulnerable to forest practices that are detrimental to native tropical forests.</p><p>In other words, biodiversity loss in the lower latitudes will negatively affect tropical detritivores, as they require a diet high in diversity. If their ability to break down leaf litter is diminished, it will enhance the relative contribution of microbial decomposition in rivers to carbon fluxes.</p><p>Prof Hui, the only South African scientist to participate in the study, holds a <a href="">South African Research Chair on mathematical biosciences</a> in the Department of Mathematical Sciences at SU, and has been collaborating with the lead author of the study, Prof Luz Boyero from the University of the Basque Country in Spain, for the past ten years. She is also the coordinator of the <a href="">GLoBe network</a>, an international network of freshwater ecologists.</p><p>“For me, biodiversity is the most striking reality and puzzle of our biosphere. How biodiversity structures and functions across spatial and temporal scales is the focus of our research," he explains.</p><p>He believes we cannot enter an era of global change with the traditional view of a stable ecosystem: “Such novel ecosystems, constantly challenged by human activities and issues such as biological invasions and climate change, are in persistent transition. We are yet to develop a new set of theoretical frameworks to study such systems."</p><p>“Biomathematics, with its reaches into data science and informatics, provides a powerful set of tools from different areas of mathematics to (re)invent this theoretical framework for open adaptive systems. This era is not only an opportunity for global change biology, but also a chance for mathematics and physics to create new pathways," he concludes.</p><p>The article, “Latitude dictates plant diversity effects on instream decomposition" was published in <em>Science Advances</em> on 26 March 2021.</p><p><strong>Media enquiries</strong></p><p>Prof Cang Hui</p><p><a href="">South African Research Chair in Mathematical Biosciences</a>, Department of Mathematical Sciences, Stellenbosch University, South Africa</p><p>E-mail: <a href=""></a></p><p>Tel: +27 _21 808 3853<br></p><p>​<br></p>