tag:theconversation.com,2011:/africa/topics/laboratory-18854/articlesLaboratory – The Conversation2023-05-08T12:18:30Ztag:theconversation.com,2011:article/2020842023-05-08T12:18:30Z2023-05-08T12:18:30ZGain-of-function research is more than just tweaking risky viruses – it’s a routine and essential tool in all biology research<figure><img src="https://images.theconversation.com/files/523909/original/file-20230502-4095-u8oni1.jpg?ixlib=rb-1.1.0&rect=0%2C94%2C1500%2C1221&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Gain-of-function experiments in the lab can help researchers get ahead of viruses naturally gaining the ability to infect people in the wild.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/illustration/molecule-illustration-royalty-free-illustration/1423893041">KTSDesign/Science Photo Library via Getty Images</a></span></figcaption></figure><p>The term “gain of function” is often taken to refer to research with viruses that puts society at risk of an infectious disease outbreak for questionable gain. Some research on emerging viruses can result in variants that gain the ability to infect people but this does not necessarily mean the research is dangerous or that it is not fruitful. Concerns have focused on lab research on the <a href="https://www.theguardian.com/world/2012/mar/28/bird-flu-mutant-strains">virus that causes bird flu</a> in 2012 and on the <a href="https://theconversation.com/why-gain-of-function-research-matters-162493">virus that causes COVID-19</a> since 2020. The National Institutes of Health had previously implemented a <a href="https://www.science.org/content/article/nih-lifts-3-year-ban-funding-risky-virus-studies">three-year moratorium</a> on gain-of-function research on certain viruses, and some U.S. legislatures have <a href="https://www.washingtonexaminer.com/news/senate/texas-state-ban-gain-function-research-covid-pandemic">proposed bills prohibiting</a> gain-of-function research on “potentially pandemic pathogens.”</p>
<p>The possibility that a genetically modified virus could escape the lab needs to be taken seriously. But it does not mean that gain-of-function experiments are inherently risky or the purview of mad scientists. In fact, gain-of-function approaches are a fundamental tool in biology used to study much more than just viruses, contributing to many, if not most, modern discoveries in the field, including <a href="https://doi.org/10.3201%2Feid2305.161556">penicillin</a>, <a href="https://theconversation.com/anti-cancer-car-t-therapy-reengineers-t-cells-to-kill-tumors-and-researchers-are-expanding-the-limited-types-of-cancer-it-can-target-196471">cancer immunotherapies</a> and <a href="https://www.sciencedaily.com/releases/2015/02/150204134119.htm">drought-resistant crops</a>.</p>
<p>As <a href="https://scholar.google.com/citations?user=IXDoiY4AAAAJ&hl=en">scientists who</a> <a href="https://scholar.google.com/citations?user=GBQiazwAAAAJ&hl=en">study viruses</a>, we believe that misunderstanding the term “gain of function” as something nefarious comes at the cost of progress in human health, ecological sustainability and technological advancement. Clarifying what gain-of-function research really is can help clarify why it is an essential scientific tool.</p>
<h2>What is gain of function?</h2>
<p>To study how a living thing operates, scientists can change a specific part of it and then observe the effects. These changes sometimes result in the organism’s gaining a function it didn’t have before or losing a function it once had. </p>
<p>For example, if the goal is to enhance the tumor-killing ability of immune cells, researchers can take a sample of a person’s immune cells and modify them to express a protein that specifically targets cancer cells. This mutated immune cell, called a <a href="https://theconversation.com/anti-cancer-car-t-therapy-reengineers-t-cells-to-kill-tumors-and-researchers-are-expanding-the-limited-types-of-cancer-it-can-target-196471">CAR-T cell</a> thereby “gains the function” of being able to bind to cancerous cells and kill them. The advance of similar immunotherapies that help the immune system attack cancer cells is based on the exploratory research of scientists who synthesized such “<a href="https://doi.org/10.1007/BF00820662">Frankenstein” proteins</a> in the 1980s. At that time, there was no way to know how useful these chimeric proteins would be to cancer treatment today, some 40 years later. </p>
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<iframe width="440" height="260" src="https://www.youtube.com/embed/mXADrg_ckhI?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">CAR-T cell therapy involves giving a patient’s immune cells an increased ability to target cancer cells.</span></figcaption>
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<p>Similarly, by adding specific genes into rice, corn or wheat plants that increase their production in diverse climates, scientists have been able to produce plants that are able to grow and thrive in geographical regions they previously could not. This is a critical advance to maintain food supplies in the face of climate change. Well-known examples of food sources that have their origins in gain-of-function research <a href="https://www.sciencenews.org/article/rice-agriculture-feeds-world-climate-change-drought-flood-risk">include rice plants</a> that can grow in high flood plains or in drought conditions or that contain vitamin A to reduce malnutrition.</p>
<h2>Medical advances from gain-of-function research</h2>
<p>Gain-of-function experiments are ingrained in the scientific process. In many instances, the benefits that stem from gain-of-function experiments are not immediately clear. Only decades later does the research bring a new treatment to the clinic or a new technology within reach. </p>
<p>The development of most antibiotics have relied on the <a href="https://doi.org/10.3389/fcimb.2021.684515">manipulation of bacteria or mold</a> in gain-of-function experiments. Alexander Fleming’s initial discovery that the mold <em>Penicillium rubens</em> could produce a compound toxic to bacteria was a profound medical advance. But it wasn’t until scientists experimented with <a href="https://www.sciencemuseum.org.uk/objects-and-stories/how-was-penicillin-developed">growth conditions and mold strains</a> that therapeutic use of penicillin became feasible. Using a specific growth medium allowed the mold to gain the function of increased penicillin production, which was essential for its mass production and widespread use as a drug. </p>
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<a href="https://images.theconversation.com/files/523678/original/file-20230501-1518-hmu9o0.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Worker monitoring penicillin capsules coming down production line" src="https://images.theconversation.com/files/523678/original/file-20230501-1518-hmu9o0.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/523678/original/file-20230501-1518-hmu9o0.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=759&fit=crop&dpr=1 600w, https://images.theconversation.com/files/523678/original/file-20230501-1518-hmu9o0.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=759&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/523678/original/file-20230501-1518-hmu9o0.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=759&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/523678/original/file-20230501-1518-hmu9o0.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=954&fit=crop&dpr=1 754w, https://images.theconversation.com/files/523678/original/file-20230501-1518-hmu9o0.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=954&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/523678/original/file-20230501-1518-hmu9o0.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=954&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
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<span class="caption">Gain-of-function research played a key role in the development and mass production of penicillin.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/penicillin-capsules-being-checked-as-they-come-off-the-news-photo/2667016">Wesley/Stringer/Hulton Archive via Getty Images</a></span>
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<p>Research on <a href="https://doi.org/10.1128%2FAAC.02381-18">antibiotic resistance</a> also relies heavily on gain-of-function approaches. Studying how bacteria <a href="https://theconversation.com/looming-behind-antibiotic-resistance-is-another-bacterial-threat-antibiotic-tolerance-200226">gain resistance</a> against drugs is essential to developing new treatments microbes are unable to evade quickly.</p>
<p>Gain-of-function research in virology has also been critical to the advancement of science and health. <a href="https://www.cancer.gov/news-events/cancer-currents-blog/2018/oncolytic-viruses-to-treat-cancer">Oncolytic viruses</a> are genetically modified in the laboratory to infect and kill cancerous cells like melanoma. Similarly, the <a href="https://www.cdc.gov/coronavirus/2019-ncov/vaccines/different-vaccines/overview-COVID-19-vaccines.html">Johnson & Johnson COVID-19 vaccine</a> contains an adenovirus altered to produce the spike protein that helps the COVID-19 virus infect cells. Scientists developed <a href="https://onlinelibrary.wiley.com/doi/10.1002/(SICI)1099-1654(199910/12)9:4%3C237::AID-RMV252%3E3.0.CO;2-G">live attenuated flu vaccines</a> by adapting them to grow at low temperatures and thereby lose the ability to grow at human lung temperatures. </p>
<p>By giving viruses new functions, scientists were able to develop new tools to treat and prevent disease.</p>
<h2>Nature’s gain-of-function experiments</h2>
<p>Gain-of-function approaches are needed to advance understanding of viruses in part because these processes already occur in nature.</p>
<p>Many viruses that infect such nonhuman animals as bats, pigs, birds and mice have the potential to <a href="https://theconversation.com/what-is-spillover-bird-flu-outbreak-underscores-need-for-early-detection-to-prevent-the-next-big-pandemic-200494">spill over into people</a>. Every time a virus copies its genome, it makes mistakes. Most of these mutations are detrimental – they reduce a virus’s ability to replicate – but some may allow a virus to replicate faster or better in human cells. Variant viruses with these rare, beneficial mutations will spread better than other variants and therefore come to dominate the viral population – that is <a href="https://www.amnh.org/exhibitions/darwin/evolution-today/natural-selection-vista">how natural selection works</a>.</p>
<p>If these viruses can replicate even a little bit within people, they have the potential to adapt and thereby thrive in their new human hosts. That is nature’s gain-of-function experiment, and <a href="https://doi.org/10.1093/ve/veaa016">it is</a> <a href="https://doi.org/10.1016/j.chom.2020.08.011">happening constantly</a>.</p>
<p>Gain-of-function experiments in the lab can help scientists <a href="https://doi.org/10.1126%2Fscience.1222526">anticipate the changes</a> viruses may undergo in nature by understanding what specific features allow them to transmit between people and infect them. In contrast to nature’s experiments, these are conducted in <a href="https://www.cdc.gov/labs/BMBL.html">highly controlled lab conditions</a> designed to limit infection risk to laboratory personnel and others, including air flow control, personal protective equipment and waste sterilization.</p>
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<a href="https://images.theconversation.com/files/523674/original/file-20230501-20-lxf4la.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="People in protective clothing collecting dead pelicans on a beach" src="https://images.theconversation.com/files/523674/original/file-20230501-20-lxf4la.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/523674/original/file-20230501-20-lxf4la.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/523674/original/file-20230501-20-lxf4la.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/523674/original/file-20230501-20-lxf4la.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/523674/original/file-20230501-20-lxf4la.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/523674/original/file-20230501-20-lxf4la.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/523674/original/file-20230501-20-lxf4la.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
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<span class="caption">Researchers and public health officials are concerned that the bird flu virus is evolving to more readily infect people.</span>
<span class="attribution"><a class="source" href="https://newsroom.ap.org/detail/BirdFluMutations/6895d38a33de468c93c14da427b4dfff">Guadalupe Pardo/AP Photo</a></span>
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<p>It is important that researchers carefully observe lab safety to minimize the theoretical risk of infecting the general population. It is equally important that virologists continue to apply the tools of modern science to gauge the risk of natural viral spillovers before they become outbreaks. </p>
<p>A <a href="https://theconversation.com/as-bird-flu-continues-to-spread-in-the-us-and-worldwide-whats-the-risk-that-it-could-start-a-human-pandemic-4-questions-answered-200204">bird flu outbreak</a> is currently raging across multiple continents. While the H5N1 virus is primarily infecting birds, some people have gotten sick too. More spillover events can change the virus in ways that would allow it to <a href="https://doi.org/10.1126/science.adi1013">transmit more efficiently among people</a>, potentially leading to a pandemic. </p>
<p>Scientists have a better appreciation of the tangible risk of bird flu spillover because of <a href="https://doi.org/10.1126/science.1213362">gain-of-function experiments</a> <a href="https://doi.org/10.1038/nature10831">published a decade ago</a>. Those lab studies showed that bird flu viruses could be transmitted through the air between ferrets within a few feet of one another. They also revealed multiple features of the evolutionary path the H5N1 virus would need to take before it becomes transmissible in mammals, informing what signatures researchers need to look out for during surveillance of the current outbreak.</p>
<h2>Oversight on gain of function</h2>
<p>Perhaps this sounds like a semantic argument, and in many respects it is. <a href="https://www.statnews.com/2021/12/23/gain-of-function-research-advances-knowledge-and-saves-lives/">Many researchers</a> would likely agree that gain of function as a general tool is an important way to study biology that should not be restricted, while also arguing that it should be curtailed for research on specific dangerous pathogens. The problem with this argument is that pathogen research needs to include gain-of-function approaches in order to be effective – just as in any area of biology.</p>
<p><a href="https://doi.org/10.1128/jvi.00089-23">Oversight of gain-of-function research</a> on potential pandemic pathogens already exists. Multiple layers of safety measures at the institutional and national levels minimize the risks of virus research.</p>
<p>While updates to current oversight are not unreasonable, we believe that <a href="https://www.nih.gov/about-nih/who-we-are/nih-director/statements/statement-report-national-science-advisory-board-biosecurity">blanket bans or additional restrictions</a> on gain-of-function research do not make society safer. They may instead slow research in areas ranging from cancer therapies to agriculture. Clarifying which specific research areas are of concern regarding gain-of-function approaches can help identify how the current oversight framework can be improved.</p><img src="https://counter.theconversation.com/content/202084/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Seema Lakdawala receives funding from National Institutes of Health and the Flu Lab. </span></em></p><p class="fine-print"><em><span>Anice Lowen receives research funding from the National Institutes of Health and Flu Lab. </span></em></p>From cancer immunotherapy and antibiotics to GMO crops and pandemic surveillance, gain of function is a cornerstone of basic research.Seema Lakdawala, Associate Professor of Microbiology and Immunology at Emory University and Adjunct Professor Microbiology and Molecular Genetics, University of PittsburghAnice Lowen, Associate Professor of Microbiology and Immunology, Emory UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1968742023-02-14T13:27:07Z2023-02-14T13:27:07ZHow do blood tests work? Medical laboratory scientists explain the pathway from blood draw to diagnosis and treatment<figure><img src="https://images.theconversation.com/files/509538/original/file-20230210-16-9ds3x9.jpg?ixlib=rb-1.1.0&rect=15%2C0%2C2101%2C1412&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Pathology analyzes bodily fluids and tissues using a variety of methods.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/doctor-manipulating-blood-plasma-tubes-green-royalty-free-image/1404395240">Alvaro Lavin/Moment via Getty Images</a></span></figcaption></figure><p>Medical laboratory testing is the heartbeat of medicine. It provides critical data for physicians to diagnose and treat disease, <a href="https://doi.org/10.1093/labmed/lmaa098">dating back thousands of years</a>. Unfortunately, laboratory medicine as a field is poorly understood by both the public and health care communities. </p>
<p><a href="https://asm.org/Articles/2021/October/Using-Laboratory-Medicine-to-Support-Direct-Patien">Laboratory medicine</a>, also known as clinical pathology, is one of two main branches of pathology, or the study of the causes and effects of disease. Pathology covers many <a href="https://www.urmc.rochester.edu/encyclopedia/content.aspx?contenttypeid=85&contentid=P00955">laboratory areas</a>, such as blood banking and microbiology. Clinical pathology diagnoses a disease through laboratory analysis of body fluids such as blood, urine, feces and saliva. The other branch of pathology, <a href="https://www.hopkinsmedicine.org/health/treatment-tests-and-therapies/anatomical-pathology">anatomic pathology</a>, diagnoses a disease by examining body tissues.</p>
<p>We are <a href="https://scholar.google.com/citations?user=8XtvOZ8AAAAJ&hl=en">public health</a> and <a href="https://www.rushu.rush.edu/faculty/nicholas-moore-ms-mlsascpcm">medical laboratory</a> scientists who specialize in microbiology and infectious diseases. There are a lot of steps between when your doctor orders a blood test to establishing a diagnosis. From the bedside to the lab bench, here’s how laboratory testing works.</p>
<h2>It all starts with a specimen</h2>
<p>When you see a doctor, sometimes a physical exam and detailed medical history are enough for them to make a diagnosis, offer recommendations or prescribe medications for your condition. There are many instances, however, where your doctor may need additional information to make an accurate diagnosis. This information is often obtained from procedures like <a href="https://medlineplus.gov/ency/article/007451.htm">imaging scans</a> or <a href="https://doi.org/10.1309/LM4O4L0HHUTWWUDD">blood tests</a>.</p>
<p>The first step involves getting your blood drawn through a practice known as <a href="https://www.webmd.com/a-to-z-guides/what-is-phlebotomy">phlebotomy</a>. A health care professional, typically a phlebotomist or a nurse, inserts a needle into a vein to collect a blood specimen. </p>
<p>Multiple tubes of blood may be needed, as certain tests are only performed using certain types of blood specimens. For example, one test commonly used to <a href="https://www.nhlbi.nih.gov/health/anemia">diagnose anemia</a> requires blood to be collected in a chemical that prevents the blood from clotting. Patients being evaluated for a <a href="https://www.nhlbi.nih.gov/health/clotting-disorders">clotting disorder</a>, on the other hand, often have their blood collected in a tube containing another anticoagulant.</p>
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<span class="caption">Different tests require different types of blood specimens.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/rack-with-tubes-blood-samples-from-patients-for-royalty-free-image/1446655782">angelp/iStock via Getty Images Plus</a></span>
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<h2>Testing pathways</h2>
<p>Specimens then make their way to a clinical laboratory. Laboratories can be found within hospitals, reference labs or physician offices, or they can be located in a public health setting such as the Centers for Disease Control and Prevention or a state public health laboratory. In 2021, there were <a href="https://www.bls.gov/ooh/healthcare/clinical-laboratory-technologists-and-technicians.htm#tab-1">more than 329,000 laboratory professionals</a> working in the U.S. in <a href="https://www.cms.gov/regulations-and-guidance/legislation/clia#">more than 320,000 federally regulated laboratories</a>. An estimated <a href="https://www.cdc.gov/csels/dls/strengthening-clinical-labs.html">14 billion laboratory tests</a> are ordered annually in the U.S., on top of <a href="https://www.worldometers.info/coronavirus/#countries">over 1 billon COVID-19 tests</a> during the pandemic. With such a large volume of specimens to test and examine, various sections of a laboratory are automated. </p>
<p>Laboratory tests examine the biological, chemical and physical properties of the cells and molecules that make up a blood specimen. The first step is often to centrifuge a blood specimen into separate components. This divides the sample into one portion that contains solid components, such as cells, and another that contains liquid components and dissolved solutes, known as serum or plasma.</p>
<p>Analyzing the serum or plasma portion of a blood specimen measures the levels of different substances within the body. One of the most common is your blood sugar, or glucose concentration. For the doctors of <a href="https://www.cdc.gov/csels/dls/strengthening-clinical-labs.html">more than 37 million Americans with diabetes</a>, knowing how high their patient’s blood glucose is helps them establish a new diagnosis or ensure their condition is under control.</p>
<p>If your doctor suspects you have an infection, they will collect specimens to test for the presence of a pathogen. For example, they might collect a throat swab for strep throat or a urine sample for a urinary tract infection. Scientists incubate these samples to screen any organisms that grow and resemble pathogens of interest. They may perform additional testing to identify the microbe. Once an organism is identified, the <a href="https://deepdive.tips/index.php/2022/12/01/putting-a-face-on-clinical-laboratory-sciences-w-dr-rodney-rohde/">medical laboratory professional</a> can then test a variety of antimicrobial agents against it to inform your doctor what the best treatment would be against your infection.</p>
<h2>Evolution of medical laboratory testing</h2>
<p>The <a href="https://doi.org/10.1093/clinchem/43.1.174">first hospital clinical laboratory in the U.S.</a> was established in 1894. Some of the methods <a href="https://deepdive.tips/index.php/2022/12/01/putting-a-face-on-clinical-laboratory-sciences-w-dr-rodney-rohde/">laboratory professionals</a> use to analyze samples have been in use for over a century. </p>
<p>One such staple, the <a href="https://www.ncbi.nlm.nih.gov/books/NBK562156/">Gram stain</a>, was introduced in 1882. It uses two different dyes and exploits differences in the bacterial cell wall to discriminate between two different groups of bacteria. This helps lab scientists identify the correct antimicrobial therapy to use against an infection.</p>
<p>Another commonly used technology, the <a href="https://doi.org/10.1002/cyto.a.24505">Coulter Principle</a>, was developed in the 1940s to identify and sort individual cells based on physical size and resistance to an electrical current. Medical laboratory professionals routinely use this technique to conduct <a href="https://medlineplus.gov/lab-tests/complete-blood-count-cbc/">complete blood count</a> tests, which measure unusual increases or decreases in the number of different types of blood cells that could provide insights into a disease or condition, such as cancer or sickle cell anemia.</p>
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<a href="https://images.theconversation.com/files/510360/original/file-20230215-28-e6jp0p.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Medical laboratory professional holding blood tube" src="https://images.theconversation.com/files/510360/original/file-20230215-28-e6jp0p.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/510360/original/file-20230215-28-e6jp0p.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/510360/original/file-20230215-28-e6jp0p.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/510360/original/file-20230215-28-e6jp0p.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/510360/original/file-20230215-28-e6jp0p.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/510360/original/file-20230215-28-e6jp0p.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/510360/original/file-20230215-28-e6jp0p.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Medical laboratory professionals use different techniques to analyze samples.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/feamle-scientist-preparing-a-blood-sample-for-royalty-free-image/1023297260">Westend61/Getty Images</a></span>
</figcaption>
</figure>
<p>In 1986, scientists devised the <a href="https://www.nobelprize.org/prizes/chemistry/1993/mullis/facts/">Nobel Prize-winning</a> <a href="https://www.ncbi.nlm.nih.gov/probe/docs/techpcr/">polymerase chain reaction</a> method to amplify, or rapidly produce, multiple copies of the DNA of a pathogen present within a sample. PCR is widely used to diagnose infections, identify genetic disorders and monitor cancer progression.</p>
<p>An explosion of modern laboratory tools to research and diagnose disease followed PCR. To name a few of these cutting-edge tools, <a href="https://doi.org/10.1038/labinvest.2014.156">matrix-assisted laser desorption ionization, or MALDI</a>, is one of the most commonly used techniques to identify microbes that are difficult or impossible to culture. Genome editing and <a href="https://medlineplus.gov/genetics/understanding/genomicresearch/genomeediting/">CRISPR-Cas9</a> give scientists the ability to change an organism’s DNA, aiding in <a href="https://doi.org/10.1016/j.biopha.2021.111487">identifying pathogens and detecting dysfunctional genes</a> by adding, removing or altering genes of interest. <a href="https://theconversation.com/genomic-sequencing-heres-how-researchers-identify-omicron-and-other-covid-19-variants-172935">Next-generation sequencing</a> has become a powerful modern tool to determine the sequence of the genetic material in biological samples and has been extensively used to <a href="https://doi.org/10.3390%2Fijms12117861">identify variants</a> and wastewater surveillance of pathogens like the virus that causes COVID-19.</p>
<h2>Challenges and solutions</h2>
<p>One of the most critical challenges in laboratory medicine is <a href="https://doi.org/10.1309/LM4O4L0HHUTWWUDD">understanding and interpreting test results</a>, because errors can occur throughout the testing process. Specimens must be properly collected and transported to the lab for accurate results. Likewise, at-home tests need to be properly stored. Clinicians and patients need to take into account the chances of false positive or negative results by considering the <a href="https://theconversation.com/coronavirus-tests-are-pretty-accurate-but-far-from-perfect-136671">limitations of the test</a> alongside the patient’s individual case.</p>
<p>Collaboration between clinicians and medical laboratory professionals could help <a href="https://www.elsevier.com/connect/preventing-diagnostic-errors-by-uniting-the-clinical-laboratory-with-direct-patient-care">reduce errors</a> in diagnosis and treatment. Laboratory data can and often is extremely useful to patient care, but a holistic approach that takes into account a patient’s medical history, genetics and health habits, among other factors, is necessary for an accurate diagnosis and treatment. While powerful, a laboratory result should not be used in isolation. Clear and accurate communication on laboratory testing is critical for effective patient care.</p>
<p><em>A photo was replaced to more accurately reflect medical laboratory work</em></p><img src="https://counter.theconversation.com/content/196874/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Rodney E. Rohde has received funding from the American Society of Clinical Pathologists, American Society for Clinical Laboratory Science, U.S. Department of Labor (OSHA), and other public and private entities/foundations. Rohde is affiliated with ASCP, ASCLS, ASM, and serves on several scientific advisory boards. See <a href="https://rodneyerohde.wp.txstate.edu/service/">https://rodneyerohde.wp.txstate.edu/service/</a>.</span></em></p><p class="fine-print"><em><span>Nicholas Moore previously received funding from Abbott Molecular, bioMerieux, and Cepheid for contracted research work related to the development of laboratory assays. Funds were paid directly to Rush University. Nicholas Moore is a volunteer with the American Society for Clinical Laboratory Science, the American Society for Clinical Pathology, the American Society for Microbiology, and the Clinical and Laboratory Standards Institute. He is a member of the editorial board of Clinical Microbiology Reviews and BMC Infectious Diseases.</span></em></p>Lab testing provides doctors with essential information to help them diagnose and treat disease. Here’s what happens behind the scenes after you roll up your sleeve for a blood draw.Rodney E. Rohde, Regents' Professor of Clinical Laboratory Science, Texas State UniversityNicholas Moore, Associate Professor of Medical Laboratory Science, Rush UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1824862022-05-09T16:46:08Z2022-05-09T16:46:08ZUnlocking the secrets of maple syrup, one molecule at a time<figure><img src="https://images.theconversation.com/files/461824/original/file-20220506-18-5xkyt0.jpg?ixlib=rb-1.1.0&rect=42%2C67%2C5565%2C3665&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Maple syrup contains bioactive molecules whose benefits go far beyond the simple pleasure of a sweet treat.</span> <span class="attribution"><span class="source">(Shutterstock)</span></span></figcaption></figure><p>Nature conceals a phenomenal number of molecules as varied as they are imperceptible. The plant kingdom is particularly chemically complex. </p>
<p>Plant evolution has taken place over hundreds of millions of years, giving plants the ability to respond to various environmental stresses and threats. Several species have developed an arsenal of molecules allowing them to adapt and to protect themselves against competitors and predators. Some of these molecules also have health benefits for the animals that consume them.</p>
<p>Advances in food science over recent decades show that many plants provide a wealth of benefits that, until recently, were largely unknown. Taken together, these discoveries support more than ever the fact that a varied and balanced diet offers benefits that go beyond simple energy intake. As a result, consumer demand for plant-based foods with higher nutritional value is currently at record highs. This trend has yet to run out of steam. At the same time, sugary foods are increasingly marginalized and categorized as unhealthy. </p>
<p>But in the realm of sweets, maple syrup is finally claiming its rightful place! Maple syrup is no longer only the jewel of Canada’s culinary heritage, its nutritional reputation is also improving. Because of its unique natural source and manufacturing process, maple syrup contains bioactive molecules whose benefits go far beyond the simple pleasure of a sweet treat.</p>
<h2>Benefits that go beyond energy intake</h2>
<p>In eastern Canada, March and April herald maple sugaring time. Higher temperatures cause <a href="https://doi.org/10.1139/b03-079">maple trees to convert their energy reserves (stored as complex carbohydrates) into soluble sugars</a> that mix with the water in the tree. Producers collect the flavoured sap by drilling holes in the trees.</p>
<figure class="align-center ">
<img alt="Maple syrop in a bottle on a wooden table." src="https://images.theconversation.com/files/459344/original/file-20220422-18-zenfms.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/459344/original/file-20220422-18-zenfms.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=461&fit=crop&dpr=1 600w, https://images.theconversation.com/files/459344/original/file-20220422-18-zenfms.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=461&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/459344/original/file-20220422-18-zenfms.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=461&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/459344/original/file-20220422-18-zenfms.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=580&fit=crop&dpr=1 754w, https://images.theconversation.com/files/459344/original/file-20220422-18-zenfms.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=580&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/459344/original/file-20220422-18-zenfms.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=580&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Maple syrup, Canada’s liquid gold, contains bioactive molecules whose benefits go far beyond the simple pleasure of sweet treats.</span>
<span class="attribution"><span class="source">(Shutterstock)</span></span>
</figcaption>
</figure>
<p>The sap is approximately 98 per cent water, and it takes about 40 litres of this maple water to generate one litre of syrup. During this concentration process, the levels of sugars and nutrients increase substantially. The high temperature that comes from boiling the sap causes a series of chemical reactions as the excess water evaporates.</p>
<p>The main components of maple syrup are sucrose and water. Glucose and fructose also contribute to the sweet taste of the syrup, but to a lesser extent. While these three simple carbohydrates are sources of energy, maple syrup is also an excellent source of manganese and riboflavin (vitamin B2), as well as a significant source of other <a href="http://www.internationalmaplesyrupinstitute.com/uploads/7/0/9/2/7092109/__nutrition_and_health_benefits_of_pure_maple_syrup.pdf">vitamins and minerals (zinc, potassium, calcium and magnesium)</a>.</p>
<p>The composition of phenolic compounds of maple syrup is even more impressive. Since the beginning of the 20th century, <a href="https://doi.org/10.1016/j.foodchem.2021.131817">researchers have discovered more than 100 of these molecules in plants</a>. Many of them are antioxidants, and contribute to the taste, aroma, colour of maple syrup. They are primarily responsible for its recent superfood status. </p>
<p>One of the most promising phenolic components (in terms of biological activities) is a molecule found nowhere other than in Canada’s most famous product.</p>
<h2>A molecule worthy of national pride</h2>
<p>Quebecol – named after the province where <a href="https://www.worldatlas.com/articles/the-world-s-top-producers-of-maple-syrup.html">the majority of the world’s maple syrup production originates</a> – is a polyphenolic compound (carrying several phenol groups), <a href="https://doi.org/10.1016/j.jff.2011.02.004">first isolated in 2011 by a team led by Navindra Seeram at the University of Rhode Island</a>. This compound is so exclusive to maple syrup that it is not even present in raw maple sap! Rather, current knowledge suggests that it is the product of chemical reactions that occur during the transformation of sap into syrup.</p>
<figure class="align-center ">
<img alt="Molecular structure of quebecol" src="https://images.theconversation.com/files/461819/original/file-20220506-22-8urv2e.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/461819/original/file-20220506-22-8urv2e.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=434&fit=crop&dpr=1 600w, https://images.theconversation.com/files/461819/original/file-20220506-22-8urv2e.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=434&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/461819/original/file-20220506-22-8urv2e.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=434&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/461819/original/file-20220506-22-8urv2e.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=546&fit=crop&dpr=1 754w, https://images.theconversation.com/files/461819/original/file-20220506-22-8urv2e.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=546&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/461819/original/file-20220506-22-8urv2e.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=546&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Structure of quebecol [2,2,3-tris(4-hydroxy-2-methoxyphenyl)propan-1-ol], a molecule exclusively found in maple syrup whose secrets are just beginning to be revealed.</span>
<span class="attribution"><span class="source">(Sébastien Cardinal)</span>, <span class="license">Author provided</span></span>
</figcaption>
</figure>
<p>Early laboratory studies, <a href="https://patents.google.com/patent/WO2012167364A1/en">quebecol inhibited cell proliferation of breast cancer and colon cancer cells</a>. But only a small quantity of polyphenol could be isolated, and these tests didn’t go beyond the preliminary stage. More than 20 litres of maple syrup is needed to isolate less than a milligram of quebecol.</p>
<p>Judging that this syrup would be of better use in kitchens than in laboratories, Normand Voyer, a chemistry professor at Laval University, and I (Sébastien) decided to tackle this supply problem. When I was a PhD candidate in 2013, <a href="https://doi.org/10.1016/j.tetlet.2013.07.048">we published a chemical synthesis pathway to build this natural molecule much more efficiently in the laboratory from simple precursors</a>. As this work made quebecol much more accessible, the investigation of its properties continued and deepened.</p>
<p>In particular, Normand Voyer, Daniel Grenier and their teams, in the faculty of dentistry of Laval University, published two studies <a href="https://doi.org/10.1016/j.bmc.2017.01.050">demonstrating the molecule’s anti-inflammatory properties</a>. This research also made it possible to <a href="https://doi.org/10.1016/j.bmcl.2015.11.096">determine the active portion of the molecular structure</a>.</p>
<h2>A compound still relevant today</h2>
<p>Our 2021 study showed that quebecol’s <a href="https://doi.org/10.1021/acsomega.1c03312">anti-inflammatory properties may benefit periodontal disease</a>, a severe infection of the gums. We expect additional studies to be published this year, including one showing that quebecol might help with the treatment of a skin condition.</p>
<p>Although the evidence of biological activity of quebecol has been limited to in vitro experiments, these results certainly encourage further study in more complex systems. It is also important to note that the results came from using the isolated pure molecule. </p>
<p>These studies do not propose using pure maple syrup as a medicinal agent against different conditions. Given the quantity of maple syrup one would have to eat to get the necessary dose of quebecol, the harms from a massive ingestion of sugar would obscure any benefit. It’s also difficult to establish the distribution of the molecule in the human body when it’s taken orally.</p>
<p>In any case, these discoveries once again highlight the uniqueness of maple syrup and help to strengthen its status as a singular food. Perhaps it contains other equally promising molecules just waiting to be discovered. Let’s bet that this local treasure has not yet revealed all its secrets!</p><img src="https://counter.theconversation.com/content/182486/count.gif" alt="La Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Les auteurs ne travaillent pas, ne conseillent pas, ne possèdent pas de parts, ne reçoivent pas de fonds d'une organisation qui pourrait tirer profit de cet article, et n'ont déclaré aucune autre affiliation que leur organisme de recherche.</span></em></p>Apart from being a jewel of Canada’s culinary heritage, maple syrup has a complex chemical constitution.Sébastien Cardinal, Professeur en chimie organique, Université du Québec à Rimouski (UQAR)Amy McMackin, Candidate MSc Chimie, Université du Québec à Rimouski (UQAR)Licensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1685522021-10-12T12:07:43Z2021-10-12T12:07:43ZReporting all biosafety errors could improve labs worldwide – and increase public trust in biological research<figure><img src="https://images.theconversation.com/files/424277/original/file-20211001-23-1442y9w.jpg?ixlib=rb-1.1.0&rect=0%2C10%2C7252%2C5004&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Some institutions publish information about their mishaps, while others do not.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/february-2021-bavaria-munich-soldiers-of-the-german-armed-news-photo/1231180728">Peter Kneffel/picture alliance via Getty Images</a></span></figcaption></figure><p>The <a href="https://doi.org/10.1016/S0140-6736(21)02019-5">origin of SARS-CoV-2</a> remains a mystery. One theory is that the coronavirus that causes COVID-19 was transmitted from animals to humans – <a href="https://www.cdc.gov/onehealth/basics/zoonotic-diseases.html">a fairly common occurrence</a>. Another is that it came from a laboratory accident – a <a href="https://my.absa.org/LAI">more infrequent circumstance</a>. </p>
<p>Around the world, scientists conduct many kinds of biological research experiments – from basic studies exploring how living systems operate to synthesizing novel organisms. Applications range from developing medical treatments to protecting the food supply to modifying bacteria to cleaning up oil spills and much more. A subset of experiments may also involve <a href="https://theconversation.com/why-gain-of-function-research-matters-162493">gain-of-function research</a>, which involves modifying an organism to gain a new property or ability.</p>
<p>The idea that a pathogen could escape from a laboratory and infect the entire world is the stuff of horror movies. Working with biological materials does have inherent risks, and <a href="https://www.liebertpub.com/doi/pdf/10.1177/153567601502000103">laboratory incidents will happen</a> – the goal is to minimize risks to laboratory personnel, the community and the environment. </p>
<p>We are <a href="https://scholar.google.com/citations?hl=en&user=CcisQ1kAAAAJ">biosafety</a> <a href="https://scholar.google.com/citations?hl=en&user=sNOHbC4AAAAJ">and</a> <a href="https://scholar.google.com/citations?user=YkYvOhoAAAAJ">biosecurity</a> professionals with expertise in mitigating risks associated with biological research. Without a standardized, international framework for reporting laboratory incidents and responses, the task of mitigating such risks is quite difficult. If laboratories were more open about when things go wrong, others could learn from their mistakes and lessen the chances of a future accident.</p>
<h2>Science and technology mishaps</h2>
<p>In 1984, <a href="https://www.theatlantic.com/photo/2014/12/bhopal-the-worlds-worst-industrial-disaster-30-years-later/100864/">30 tons of a highly toxic gas</a> were released in Bhopal, India. Considered one of the <a href="https://www.theguardian.com/cities/2019/dec/08/bhopals-tragedy-has-not-stopped-the-urban-disaster-still-claiming-lives-35-years-on">world’s worst industrial accidents</a>, the explosion killed several thousand people. </p>
<p>When one of Chernobyl’s radioactive nuclear cores had a meltdown in 1986, the Soviet government hid details and <a href="https://www.reuters.com/world/unsealed-soviet-archives-reveal-cover-ups-chernobyl-plant-before-disaster-2021-04-26/">spread misinformation</a> about the event, even though the heat from the reactor could be <a href="https://www.epa.gov/radnet/chernobyl-epas-radiological-monitoring">seen from space</a>.</p>
<p>By contrast, when an accident occurs with a biological material, it is not a spectacular event like an explosion or meltdown. A disease caused by a biological organism takes time to appear. It may take days or weeks for symptoms to present after infection. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/425344/original/file-20211007-15-wff7l1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A woman stands in front of an area cordoned off with caution tape and a sign saying 'Keep Out.'" src="https://images.theconversation.com/files/425344/original/file-20211007-15-wff7l1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/425344/original/file-20211007-15-wff7l1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/425344/original/file-20211007-15-wff7l1.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/425344/original/file-20211007-15-wff7l1.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/425344/original/file-20211007-15-wff7l1.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/425344/original/file-20211007-15-wff7l1.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/425344/original/file-20211007-15-wff7l1.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Investigators found laboratory security breaches at the heart of a foot-and-mouth outbreak in Britain, 2007.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/government-official-stands-near-signs-warning-of-an-news-photo/76685039">Peter Macdiarmid/Getty Images News via Getty Images</a></span>
</figcaption>
</figure>
<p>The <a href="https://doi.org/10.1126/science.7973702">1979 Sverdlovsk Anthrax Outbreak in the Soviet Union</a> and the <a href="https://www.newscientist.com/article/dn12615-faulty-pipe-blamed-for-uk-foot-and-mouth-outbreak/">2007 Pirbright Institute’s foot-and-mouth incident in the U.K.</a> are examples where biological materials unintentionally escaped the laboratory. People got sick and farm animals died. </p>
<p>Laboratory-related infections are frequently tied to the breakdown of a particular laboratory safety procedure, equipment or organizational process. </p>
<p>Here in the U.S., several well-documented laboratory errors have resulted in potential exposures, including the <a href="https://www.cdc.gov/labs/pdf/Final_Anthrax_Report.pdf">2014 unintentional release of potentially viable anthrax bacteria</a>, the <a href="https://www.cdc.gov/labs/pdf/Investigation-into-Dec-22-2014-CDC-Ebola-event.pdf">2014 potential exposure of a laboratory technician to Ebola virus</a> and the <a href="https://www.usatoday.com/story/news/2016/09/21/gao-inactivation-failures-high-containment-labs/90776218/">2015 discovery of improperly inactivated anthrax bacteria</a> that was shipped around the globe. <a href="https://www.cdc.gov/media/releases/2014/p0711-lab-safety.html">In</a> <a href="https://www.cdc.gov/media/releases/2015/s0204-ebola-lab.html">each</a> <a href="https://www.cdc.gov/media/releases/2014/s0619-anthrax.html">case</a>, medical care was provided and no one became ill. </p>
<h2>Biological incident reporting</h2>
<p>In the U.S., a <a href="https://www.aappublications.org/news/2019/03/08/mmwr030819">standardized system to report</a> all biological incidents and potential exposures does not exist. </p>
<p>The U.S. <a href="https://osp.od.nih.gov/biotechnology/nih-guidelines/">National Institutes of Health</a> has requirements for reporting any <a href="https://osp.od.nih.gov/biotechnology/faqs-on-incident-reporting/">significant problems, accidents and illnesses</a> involving experiments with altered genetic material. If a research institution receives U.S. government funding, failure to comply with NIH rules can result in a loss of this funding, no matter where in the world the lab is located. </p>
<p>But private, corporate or <a href="https://www.brookings.edu/blog/techtank/2017/10/09/do-it-yourself-biology-shows-safety-risks-of-an-open-innovation-movement/">DIY biology laboratories</a> operate with even less government oversight and fewer reporting requirements – though many have adopted their own <a href="https://www.genspace.org/community-biology-biosafety-handbook">biosafety practices</a> and follow local requirements and best management practices. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/424281/original/file-20211001-23-18xjcsn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A woman in full body PPE reaches for a beaker containing a murky liquid." src="https://images.theconversation.com/files/424281/original/file-20211001-23-18xjcsn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/424281/original/file-20211001-23-18xjcsn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=422&fit=crop&dpr=1 600w, https://images.theconversation.com/files/424281/original/file-20211001-23-18xjcsn.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=422&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/424281/original/file-20211001-23-18xjcsn.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=422&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/424281/original/file-20211001-23-18xjcsn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=530&fit=crop&dpr=1 754w, https://images.theconversation.com/files/424281/original/file-20211001-23-18xjcsn.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=530&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/424281/original/file-20211001-23-18xjcsn.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=530&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Numerous biolabs operate around the world.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/laboratory-technician-works-in-the-production-plant-of-the-news-photo/1231378210">Yamil Lage/AFP via Getty Images</a></span>
</figcaption>
</figure>
<p>Outside the U.S., the <a href="http://doi.org/10.1177/1535676016661772">robustness of biosafety and biosecurity oversight</a> varies significantly from country to country. </p>
<p>[<em>Over 110,000 readers rely on The Conversation’s newsletter to understand the world.</em> <a href="https://theconversation.com/us/newsletters/the-daily-3?utm_source=TCUS&utm_medium=inline-link&utm_campaign=newsletter-text&utm_content=100Ksignup">Sign up today</a>.]</p>
<h2>Sharing information</h2>
<p>Although reporting to the U.S. government is required in certain circumstances, the information contained in the reports may never reach the public. </p>
<p>Some institutions openly publish information about their incidents, while others keep that data private. Reasons may include concerns about reputation, protection of personal health information or even sensationalism in the media. Some fear reprisal from a disgruntled employee, a competitor or even a nation-state. Others are concerned about the spread of misinformation by <a href="https://www.bostonmagazine.com/2006/05/15/fear-in-the-air/">individuals who fear biological labs</a> or those who seek to <a href="https://time.com/5550654/crispr-gene-editing-human-embryos-ban/">end human genetic engineering research</a> or <a href="https://www.cbsnews.com/news/peta-complaint-lab-animals-pitt-research-lab-university-of-pittsburgh/">ban animal experiments</a>. </p>
<p>Even with these concerns, we believe a more transparent and comprehensive system of reporting biological incidents to a neutral third party would help reduce the number of laboratory incidents – and could improve public trust in the scientific enterprise. If this type of system had been in place prior to COVID-19, more data would presumably have been available to help evaluate the Wuhan laboratory leak hypothesis and cut down on speculation.</p>
<p>In the U.S., a possible way to do this is to expand the American Biological Safety Association’s <a href="https://my.absa.org/LAI">Laboratory Acquired Infection database</a>. Currently, it contains incident data only from published research papers. But it could be broadened to include all kinds of incident data. In our opinion, an international version of such a reporting system would also help reduce the number and severity of laboratory incidents, both locally and worldwide. The more information available about the root cause of incidents, the more it could be used to help improve training, procedures and controls – and prevent future problems. It would also suggest how safety systems break down and what systems might be at risk. </p>
<p>Biosafety and biosecurity professionals have been discussing this topic for a <a href="https://www.nature.com/articles/nm0811-919">long time</a>, including at a <a href="https://www.phe.gov/Preparedness/legal/boards/biosafetytaskforce/meetings/Documents/agenda-081208.pdf">U.S. Trans-Federal Task Force on Optimizing Biosafety and Biocontainment</a> and by a <a href="https://www.phe.gov/s3/Documents/fesap.pdf">Federal Experts Security Advisory Panel</a>. But to make a centralized reporting system a reality, key players will need to commit and act. They include governments, international agencies, industry partners and the scientific community.</p><img src="https://counter.theconversation.com/content/168552/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>David Gillum is the past president of the American Biological Safety Association (ABSA) International. He is a past-judge and member of the safety and security committee for the International Genetically Engineered Machine Competition.</span></em></p><p class="fine-print"><em><span>Kathleen Vogel receives funding from the U.S. National Science Foundation, Carnegie Corporation of New York, U.S. Department of Defense, U.S. Department of State, Ploughshares Fund. </span></em></p><p class="fine-print"><em><span>Rebecca Moritz is the 2021 President-Elect of the American Biological Safety Association</span></em></p>A centralized reporting system for laboratory incidents involving dangerous pathogens in biological research does not exist in the US or internationally.David Gillum, Executive Director of Environmental Health and Safety and Chief Safety Officer, Arizona State UniversityKathleen Vogel, Interim Director and Professor of the School for the Future of Innovation in Society, Arizona State UniversityRebecca Moritz, Biosafety Director and Responsible Official, Colorado State UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1631972021-07-14T12:24:12Z2021-07-14T12:24:12ZWe work with dangerous pathogens in a downtown Boston biocontainment lab – here’s why you can feel safe about our research<figure><img src="https://images.theconversation.com/files/410851/original/file-20210712-70807-1iay608.JPG?ixlib=rb-1.1.0&rect=600%2C0%2C4959%2C3275&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Security precautions, thoughtful facilities design, careful training and safe lab practices help keep pathogens isolated.</span> <span class="attribution"><span class="source">Boston University Photography</span></span></figcaption></figure><p><em><a href="http://www.bumc.bu.edu/microbiology/people/faculty/ronald-b-corley-phd/">Microbiologist Ronald Corley</a> has gone to work every day throughout the pandemic as director of the <a href="https://www.bu.edu/neidl/">National Emerging Infectious Diseases Laboratories</a>. Within this secure lab facility in Boston, scientists study pathogens as diverse as tuberculosis, Ebola virus, yellow fever virus and Zika virus. Many investigators there quickly turned their attention in 2020 to SARS-CoV-2, the virus that causes COVID-19.</em></p>
<p><em>Here Corley answers some of the most frequently asked questions about this kind of biosecure lab and the work researchers do inside it.</em></p>
<h2>What is the purpose of a biocontainment facility?</h2>
<p><a href="https://doi.org/10.1016/j.cell.2020.08.021">A newly emerging or reemerging human pathogen</a> is detected somewhere around the globe <a href="http://infectiousdiseases.edc.org/">every 12 to 18 months</a>.</p>
<p>Infectious diseases don’t respect borders. Because of the global economy and unprecedented mobility, everyone on the planet is vulnerable to potentially devastating infectious diseases that may have originated halfway across the world. In this age of high-speed travel, we are as little as 36 hours away from any outbreak.</p>
<p>As with SARS-CoV-2, scientists may know little about emerging pathogens or the diseases they cause. Studying these germs – whether bacteria, viruses or other microorganisms – in the safe environment of a biocontainment laboratory is the best protection humankind has against these diseases. In the lab, researchers can safely test new diagnostics, therapeutics and vaccines. The more scientists learn about these new diseases, the better prepared we are for the ones that will come after.</p>
<p>This is where labs like the NEIDL, and our stringent safety measures, are important. I feel safer from infection working in the NEIDL than I do in my apartment building. We know what we’re working with in the lab and how to keep ourselves and others safe. But outside, I don’t know who I might pass who could have a transmissible pathogen, including the coronavirus.</p>
<p>This is not to say that there is no risk working within the laboratory – there is. But we minimize it through a series of safety measures – including building systems, laboratory design, personal protective equipment, training and safety protocols – that have been tried and tested in laboratories across the world.</p>
<h2>How do you try to minimize risk?</h2>
<p><a href="http://www.bu.edu/researchsupport/compliance/ibc/#biosafety-manual-tab">Our biosafety manual</a> sets the standards for all work with biological material in the NEIDL. Requirements increase in complexity from Biosafety Level 2 (BSL-2) on to BSL-3 and BSL-4.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=329&fit=crop&dpr=1 600w, https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=329&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=329&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=413&fit=crop&dpr=1 754w, https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=413&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=413&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Biosafety levels are defined by how much risk is involved in working with particular pathogens.</span>
<span class="attribution"><span class="source">The Conversation</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>In the U.S., the Centers for Disease Control and Prevention determines each pathogen’s biocontainment level, based on what’s known about how it infects its host, the severity of the disease it causes, how easily transmissible the pathogen may be and the nature of the work itself – does it potentially create aerosols, for example.</p>
<p>The biosafety levels require <a href="https://www.cdc.gov/cpr/infographics/biosafety.htm">different types of engineering controls</a> – such as the building materials the space uses, directional air flow to ensure pathogens can’t get out, HEPA filtration so that only sterile air is discharged from the lab space and so on.</p>
<p>The administrative controls required vary by biosafety level, as well – safety protocols, requirements for personnel training, limiting access and so forth.</p>
<p>Each level requires different types of personal protective equipment: gloves and lab coats in a BSL-2 laboratory, protective lab wear and N95 or PAPR respirators in BSL-3 or a fully encapsulating suit in a BSL-4 laboratory.</p>
<p>“Safety First” is not just a bumper-sticker phrase at the NEIDL. Everyone from public safety officers to support staff to researchers has fully bought into the culture of safety. It informs the way we’re trained and drilled, the way pathogens are transported to the facility, and policies that govern our employees. We know the risks of the work, train on protective measures, and ensure every member of our staff follows our protocols.</p>
<h2>What does containment look like with these safety strategies in place?</h2>
<p>Everyone undergoes annual background checks, medical clearances and training. Only cleared staff can enter the building alone. </p>
<p>There are limited ways into the space, one for pedestrians, and one for vehicles, like delivery trucks. Entry requires access via biometric or card access or both, and screening by security. Access controls limit staff members to entering spaces where they have permission to work, based on their training, clearances and biosafety protocols. A network of security systems and closed-circuit cameras monitors the facility.</p>
<p>Entering laboratories requires that workers don the appropriate PPE for the area. Within the labs, we know what pathogen we are working with and how it is being used and are confident staff are following the safety measures required to keep them safe. This ensures the safety of others in the building as well as the surrounding community.</p>
<p>Importantly, the biosafety practices ensure that each pathogen we’re studying is restricted to the appropriate spaces. Researchers work at biosafety cabinets that sterile-filter the air before releasing it back into the lab.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/410845/original/file-20210712-27-1o9ypjl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Scientist in full PPE works under the hood of a biosafety cabinet" src="https://images.theconversation.com/files/410845/original/file-20210712-27-1o9ypjl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/410845/original/file-20210712-27-1o9ypjl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/410845/original/file-20210712-27-1o9ypjl.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/410845/original/file-20210712-27-1o9ypjl.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/410845/original/file-20210712-27-1o9ypjl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/410845/original/file-20210712-27-1o9ypjl.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/410845/original/file-20210712-27-1o9ypjl.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Working with pathogens only within a specially ventilated biosafety cabinet provides another layer of security.</span>
<span class="attribution"><span class="source">Boston University Photography</span></span>
</figcaption>
</figure>
<h2>What kinds of regulation and oversight are there?</h2>
<p>Biocontainment laboratories do not function in a vacuum. The building and laboratory designs, and the PPE and operating procedures that protect staff, meet the guidelines set by the CDC and by the 574-page book “<a href="https://www.cdc.gov/labs/pdf/SF__19_308133-A_BMBL6_00-BOOK-WEB-final-3.pdf">Biosafety in Microbiological and Biomedical Laboratories</a>” from the CDC and National Institutes of Health.</p>
<p>To carry out a project, the lead scientist begins with an application to the Institutional Biosafety Committee. Experts in biosafety and science review the application, as do laypersons who provide a community perspective. These deliberations are open and transparent thanks to public participation on the committee. Its <a href="https://www.bu.edu/researchsupport/compliance/ibc/about-the-ibc/ibc-meeting-minutes/">minutes are posted online</a>. Safety professionals also inspect the laboratory facilities before work gets underway. </p>
<p>In the city of Boston, projects that involve any BSL-3 or BSL-4 work require review and approval from the Boston Public Health Commission, one of the only local public health departments with this type of oversight. Work with certain types of pathogens called “<a href="https://www.selectagents.gov/sat/list.htm">select agents</a>” that pose a severe threat is further regulated by the <a href="https://www.cdc.gov/cpr/dsat/fsap.htm">Division of Select Agents and Toxins</a> within the CDC.</p>
<p>Here at the NEIDL, both city and federal officials inspect the laboratories, interviewing personnel and reviewing records, including maintenance records. They also inspect pathogen inventories. Inspections can be announced or unannounced. </p>
<h2>What would happen if something went wrong?</h2>
<p>An important aspect of safety is making sure everyone knows what to do in an emergency. Three trainings per year involve first responders from the city as well as from Boston University. These are done as either live drills or tabletop exercises with experts walking through what an emergency would look like. Afterward we review how we did and develop plans for improvement.</p>
<p>Community members are also part of the exercises, and this keeps our neighbors involved and hopefully provides assurance of our ability to handle accidents, keeping ourselves and the community safe.</p>
<p>At Boston University, we post all laboratory incidents, including those at the NEIDL, on a quarterly basis to ensure that we remain transparent in our activities. Depending on what went wrong, we may also report to the BPHC and the CDC. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/410846/original/file-20210712-27-14f8fjq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="exterior of a building" src="https://images.theconversation.com/files/410846/original/file-20210712-27-14f8fjq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/410846/original/file-20210712-27-14f8fjq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=399&fit=crop&dpr=1 600w, https://images.theconversation.com/files/410846/original/file-20210712-27-14f8fjq.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=399&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/410846/original/file-20210712-27-14f8fjq.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=399&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/410846/original/file-20210712-27-14f8fjq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=502&fit=crop&dpr=1 754w, https://images.theconversation.com/files/410846/original/file-20210712-27-14f8fjq.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=502&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/410846/original/file-20210712-27-14f8fjq.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=502&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">The safety of a facility like the NEIDL benefits from the expertise and resources available in a densely populated area.</span>
<span class="attribution"><span class="source">Boston University Photography</span></span>
</figcaption>
</figure>
<h2>Why place these high-security labs in urban environments with lots of neighbors instead of the middle of nowhere?</h2>
<p>Scientific research is a communal activity, and advances happen in places where diverse expertise is concentrated. It’s no different for research on emerging pathogens. Research on pathogens relies on faculty with expertise in not only the pathogens themselves but chemistry, engineering, stem cell biology, structural biology, immunology and more.</p>
<p>Biocontainment research also requires facilities engineers, safety professionals and security personnel. You can find personnel with diverse experience and expertise in metropolitan areas that are already home to biomedical research.</p>
<p>The original permitting process of the NEIDL mandated a <a href="https://www.bu.edu/neidl/files/2013/01/SFEIR-Volume-III.pdf">comprehensive risk assessment</a> to determine any potential danger for the community. After two years and independent review by two scientific panels, we ended up with the most extensive analysis of risk for any BSL-3 or BSL-4 facility in the U.S. It considered hundreds of possible scenarios that might result in exposure of a worker to a pathogen, or the release of a biological agent. The report concluded that it’s as safe, or even safer, to have such a facility in an urban environment than in a rural or suburban environment.</p>
<p>“Near misses” have occurred at these kinds of labs within the U.S. and Europe. A near miss might, for example, involve glove tears and a potential exposure to a pathogen during laboratory work, but these have never resulted in any community infections. At the NEIDL, we intend to maintain this track record.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/410849/original/file-20210712-25-gcc2ln.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="three men in full PPE gather around lab equipment" src="https://images.theconversation.com/files/410849/original/file-20210712-25-gcc2ln.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/410849/original/file-20210712-25-gcc2ln.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/410849/original/file-20210712-25-gcc2ln.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/410849/original/file-20210712-25-gcc2ln.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/410849/original/file-20210712-25-gcc2ln.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/410849/original/file-20210712-25-gcc2ln.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/410849/original/file-20210712-25-gcc2ln.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Scientists put their intellectual curiosity to work on problems that challenge public health.</span>
<span class="attribution"><span class="source">Boston University Photography</span></span>
</figcaption>
</figure>
<h2>What are the risks of not doing this research?</h2>
<p>Science builds on what’s been learned before, accelerating our ability to respond to new outbreaks. The data we generate speeds progress on other pathogens as well, and informs how we develop and test potential therapeutics and vaccines. The risk of not doing this work is to leave ourselves more vulnerable to emerging pathogens as they arise.</p>
<p>Professionals working on emerging infectious diseases are interested in solving problems that benefit the public’s health. We take pride in our work and are serious about our responsibility to perform our work safely and securely. We recognize that this research is often viewed skeptically and thus strive to keep the trust of the public by ensuring transparency around the work we do.</p>
<p>[<em>The Conversation’s science, health and technology editors pick their favorite stories.</em> <a href="https://theconversation.com/us/newsletters/science-editors-picks-71/?utm_source=TCUS&utm_medium=inline-link&utm_campaign=newsletter-text&utm_content=science-favorite">Weekly on Wednesdays</a>.]</p><img src="https://counter.theconversation.com/content/163197/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Ronald Corley receives funding from the National Institutes of Health, and the Massachusetts Consortium on Pathogen Readiness. </span></em></p>The microbiologist who directs the National Emerging Infectious Diseases Laboratories at Boston University explains all the biosafety precautions in place that help him feel safer in the lab than out.Ronald Corley, Director of the National Emerging Infectious Diseases Laboratories and Chair of Microbiology, Boston UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1387942020-05-31T19:50:33Z2020-05-31T19:50:33ZLab experiments in the pandemic moved online or mailed home to uni students<figure><img src="https://images.theconversation.com/files/338458/original/file-20200529-51449-15pz5hk.jpg?ixlib=rb-1.1.0&rect=29%2C29%2C4542%2C2807&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">hxdbzxy/Shutterstock</span></span></figcaption></figure><p>The COVID-19 pandemic has shaken university education, with most teaching moved off campus and students learning online at home.</p>
<p>But a cornerstone of undergraduate science education has been a challenge: the laboratory class.</p>
<p>The real joy of science is in discovery and the links between knowledge and understanding crystallise when conducting experiments in the laboratory.</p>
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Read more:
<a href="https://theconversation.com/no-big-packed-lectures-allowed-if-were-to-safely-bring-uni-students-back-to-campus-138945">No big packed lectures allowed if we're to safely bring uni students back to campus</a>
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<p>Lab classes solidify both the practical skills needed by future scientists and the intellectual culture of their discipline.</p>
<h2>Labs put theory into practice</h2>
<p>For many students, it’s only when they put theoretical concepts into physical practice in the lab that they really understand them. </p>
<p>Although restrictions are easing, the need to maintain social distancing in crowded laboratory classes creates a range of challenges for lab education.</p>
<p>How should university educators address this? </p>
<p>Some universities, including <a href="https://www.farlabs.edu.au/">La Trobe</a>, <a href="https://opus.lib.uts.edu.au/bitstream/10453/7122/1/2006011911.pdf">University of Technology Sydney</a>, <a href="https://www.handbook.unsw.edu.au/undergraduate/courses/2020/PHYS1110">UNSW</a>, <a href="https://az659834.vo.msecnd.net/eventsairseasiaprod/production-conlog-public/dcef1570f6534af9b7818c6754225104">Monash</a> and <a href="https://openjournals.library.sydney.edu.au/index.php/IISME/article/view/4821">Murdoch</a>, have rolled out pilot projects trying to give students a laboratory experience off-campus.</p>
<p>The idea is attractive, not least because lab classes represent a significant cost to universities. Dedicated lab buildings, casual teaching assistants, technicians and safety compliance are all overheads unique to lab classes even before equipment is purchased and maintained.</p>
<p>So what are the options for students who want to gain a laboratory experience but are challenged with accessing the lab? Broadly speaking there are currently three models being trialled. </p>
<h2>The mail order lab</h2>
<p>The first and simplest idea is the mail order experiment model. In this approach, laboratory kits would be assembled at the university and sent direct to the students to conduct experiments in their own home.</p>
<p>This has the distinct advantage of providing students with a tactile lab experience with no specific time limits set on how long they get to learn with the equipment. </p>
<p>But sending equipment by post is expensive and who would cover the costs if things go wrong? For example, if equipment gets lost in the mail or accidentally damaged at home.</p>
<p>In addition, there are health and safety issues with trying to perform experiments without a trained demonstrator on hand to oversee the work. </p>
<h2>The home lab</h2>
<p>A second approach is to design experiments <a href="https://openjournals.library.sydney.edu.au/index.php/IISME/article/view/8826" title="A contextualised, online, introductory physics course">around what can be readily found at home</a>. A huge amount of physics, chemistry and biology can be investigated using regular everyday items.</p>
<p>For example, students can measure the force of gravity with a simple pendulum, or find the latent heat of ice by observing the temperature change when added to a glass of water. </p>
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<a href="https://images.theconversation.com/files/338462/original/file-20200529-51462-gtaoue.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/338462/original/file-20200529-51462-gtaoue.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/338462/original/file-20200529-51462-gtaoue.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=509&fit=crop&dpr=1 600w, https://images.theconversation.com/files/338462/original/file-20200529-51462-gtaoue.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=509&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/338462/original/file-20200529-51462-gtaoue.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=509&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/338462/original/file-20200529-51462-gtaoue.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=640&fit=crop&dpr=1 754w, https://images.theconversation.com/files/338462/original/file-20200529-51462-gtaoue.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=640&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/338462/original/file-20200529-51462-gtaoue.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=640&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
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<span class="attribution"><a class="source" href="https://www.flickr.com/photos/nep/101939154/">Flickr/Travis Nep Smith</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
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<p>This has enormous appeal as it not only saves costs but also may improve learning outcomes for the students by making experiments more relatable to the world around us.</p>
<p>The downside is that some key experiments might require specialist, expensive apparatus, such as a decent optical microscope, well beyond what could be expected to be performed at home. </p>
<h2>The online lab</h2>
<p>The third and perhaps the most ambitious approach is to try to <a href="https://www.latrobe.edu.au/news/announcements/2020/free-science,-done-remotely">recreate the lab experience entirely online</a>.</p>
<p>This would involve a combination of virtual reality and remote control over lab equipment that can be operated from the safety and comfort of a student’s home.</p>
<p>This approach enables key concepts to be explored in a practical way that can be live streamed to a student’s monitor or even to a virtual environment. It also maintains a high degree of interactivity since multiple students can be logged onto the same experiment at once.</p>
<p>But there are downsides to this approach too, even aside from the fact that the “hands on” element is removed. </p>
<p>Such online facilities are expensive to set up and maintain, involving expertise in engineering and computing as well as laboratory teaching. Academics need to carefully design and monitor the experiments. </p>
<h2>The lab of the future</h2>
<p>So what does the future hold for the lab class? Some of the experiments performed today have little changed for hundreds of years. For example, every physics student splits light with a prism, and every chemistry student neutralises an acid with a base.</p>
<p>It was perhaps only a matter of time until the way in which we educate our students in the laboratory received scrutiny.</p>
<p>One thing is certain: given how much financial pressure they are currently under, universities will be looking to cut costs wherever possible. Critical as it is to learning outcomes, the lab class will no doubt be examined closely. </p>
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Read more:
<a href="https://theconversation.com/australian-universities-could-lose-19-billion-in-the-next-3-years-our-economy-will-suffer-with-them-136251">Australian universities could lose $19 billion in the next 3 years. Our economy will suffer with them</a>
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<p>Universities may be tempted to save money by adopting some of the new and exciting ways of teaching labs beyond the face-to-face model. But a better motivator should be achieving improved learning outcomes for all students.</p>
<p>Often changing to online delivery just moves costs from one sort of infrastructure to another rather than allowing simple cuts to jobs and buildings. </p>
<p>It’s the duty of academics to clearly articulate why the laboratory experience is central to teaching and learning, and be open to new and unconventional ways of achieving this experience.</p><img src="https://counter.theconversation.com/content/138794/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Brian Abbey receives funding from the Australian Research Council and the Australian Maths and Science Partnerships Program (AMSPP).</span></em></p><p class="fine-print"><em><span>David Hoxley receives funding from the Australian Research Council and the Australian Maths and Science Partnerships Program (AMSPP).</span></em></p>Many university teaching labs are empty as students have been moved off campus during the pandemic. There are other ways to put theory into practice, at home and online.Brian Abbey, Professor of Physics, La Trobe UniversityDavid Hoxley, Senior Lecturer, Physics, La Trobe UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/946662018-05-08T13:55:27Z2018-05-08T13:55:27ZPrivate lab tests in Uganda are costly. But price doesn’t equal quality<figure><img src="https://images.theconversation.com/files/217945/original/file-20180507-46356-fy1v70.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Very few laboratories in Uganda are accredited. </span> <span class="attribution"><span class="source">Arne Hoel / World Bank</span></span></figcaption></figure><p>Laboratory tests are the <a href="https://scholar.google.com/scholar_lookup?author=Ngo%2C+et+al&title=Frequency+that+laboratory+tests+influence+medical+decisions&publication_year=2016&journal=J+Appl+Lab+Med&volume=1%3B4&pages=410-4">backbone of clinical care</a>. They are used to screen patients, to diagnose diseases and to manage conditions ranging from anaemia and diabetes to HIV and malaria. </p>
<p>Considerable effort has gone into improving laboratory services in many African countries. But, as many <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064661">previous studies</a> have shown, the quality of laboratory tests in much of sub-Saharan Africa is poor. </p>
<p>This is because most of these <a href="http://www.afro.who.int/sites/default/files/2017-06/afro-guidance-lab-systems-final_dec2014.pdf">laboratories don’t have</a> the necessary infrastructure nor enough competent staff who are adequately trained or the adequate management systems in place.</p>
<p>In many African countries laboratory testing is provided both as a free service in the public health sector and for a fee <a href="https://www.mm3admin.co.za/documents/docmanager/f447b607-3c8f-4eb7-8da4-11bca747079f/00060290.pdf">by private companies</a>. In some countries the majority of lab tests are done in the private sector; for instance, <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064661">more than 90%</a> of the laboratories in Uganda’s capital city Kampala are privately owned.</p>
<p><a href="https://www.ncbi.nlm.nih.gov/pubmed/26226183">Research shows</a> that these services, for which patients pay out of their own pockets, tend to be costlier than those offered in the public sector. But there’s been no evaluation of whether the more expensive tests provide better, more accurate results. </p>
<p>We tried to answer this question in <a href="https://doi.org/10.1093/ajcp/aqy017">our study</a> which looked at the costs and accuracy of tests at laboratories in Kampala. We randomly selected close to 80 laboratories and ordered 13 of the most commonly ordered laboratory tests – among them tests for malaria, pregnancy, HIV, syphilis, glucose; complete blood counts, and liver and kidney function tests.</p>
<p>We found that people are paying up to 36 times more for private laboratory tests than they do in the public sector. And, most importantly, test prices do not predict their quality. Higher costs don’t mean more accurate or clinically useful results. </p>
<p>The findings suggest that Uganda should put an external system in place to ensure that the public gets what they pay for.</p>
<h2>Global standards</h2>
<p>There are two broad sets of measures where the quality of laboratories can be checked against. </p>
<p>Firstly, countries are obliged to set up guidelines for both public sector and private laboratories. </p>
<p>But many countries around the world failed to follow these prescriptions, leading to the World Health Organisation also creating <a href="http://www.afro.who.int/sites/default/files/2017-06/afro-guidance-lab-systems-final_dec2014.pdf">guidelines</a> to help them set up their laboratory systems.</p>
<p>Although this has improved the quality of a few laboratories, the challenge is that the vast majority of laboratories are still not meeting the lowest bar of the guidelines. </p>
<p>The second set of measures are international accreditation standards that monitor laboratory quality. There are two. One is <a href="http://www.cms.gov/clia/">US-based</a> and the other are standards created by the International Organisation for Standardisation <a href="http://www.iso.org/iso/home/standards.htm">based in Europe</a>. Laboratories that meet these standards are considered accredited and recognised as meeting international performance standards. But laboratories are not obliged to go through this accreditation. </p>
<p>There are thousands of laboratories across Africa. Ideally, each of these should be accredited. But a 2014 study shows that in <a href="https://doi.org/10.1309/AJCPQ5KTKAGSSCFN">37 of 49 sub-Saharan African countries</a> there was not a single accredited clinical laboratory. Only 380 laboratories accredited to international standards in the region – and 91% of these were in South Africa, Namibia and Botswana.</p>
<p>Uganda has both accredited and non-accredited laboratories. We included both in our study to try and gauge whether the relevant “stamp of approval” affected the tests’ accuracy.</p>
<p>To establish how accurate and expensive the tests were we sent real, but unknown samples, to all the laboratories in our study. And we then also recorded how much they charged us for performing the tests. To establish accuracy, we used results on the same samples from specialised laboratories both in Uganda and Australia to determine the correct results. </p>
<p>We made three important observations. </p>
<h2>Our findings</h2>
<p>Firstly, accuracy varied widely. About 98% of the samples from accredited laboratories were correct while only 66% of the samples from the unaccredited laboratories were correct. </p>
<p>Secondly, accuracy depended on the type of test that was being done. For example, about 90% of test results for HIV, malaria, and syphilis were correct. But only 38% of the tests for urine pregnancy screenings, blood counts, and liver and kidney function tests were accurate.</p>
<p>And test prices ranged widely for an individual test performed in different laboratories. Some labs in the private sector were charging 36 times more than others. Yet we found no relationship between price and quality. </p>
<p>Our findings show that both accreditation and the test being done matters. Tests done by an accredited laboratory is likely to produce correct results 98% of the time. The figure plummets in unaccredited labs.</p>
<p>The quality is likely to be acceptable at all the laboratories for common tests such as HIV and malaria. But for people who had kidney or liver disease, the quality of test is generally not good. These problems stem from a lack of clear and enforced laboratory quality requirements. They have real impact on what diagnoses and treatments patients receive, and must be fixed. </p>
<h2>The way forward</h2>
<p>The way to address this problem is to make the market more transparent by making quality measurable and obvious to the public. </p>
<p>Based on our study, there are two practical approaches that could work. The first is ensuring that laboratories in Africa have international accreditation. The second involves doing quality checks such as those used in this study. </p>
<p>Some countries –like South Africa and Namibia – have bodies that monitor the quality of the laboratories but this is not a uniform practise across the continent. The responsibility to enforce such a practice could emerge from bodies like the World Health Organisation or the <a href="http://www.aslm.org/">African Society for Laboratory Medicine</a> which aims to strengthen laboratories.</p>
<p>Achieving international accreditation should be the goal for every laboratory. </p>
<p>But accreditation is an expensive and challenging task in the short term, especially for small private laboratories. In the meanwhile countries that still have challenges with the quality of their laboratories could use the testing of unknown samples as an achievable, affordable, and effective way to monitor their laboratories and reestablish the public’s trust.</p><img src="https://counter.theconversation.com/content/94666/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Timothy Amukele does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Considerable effort has gone into improving laboratory services in many African countries. But the quality of tests is questionable.Timothy Amukele, Assistant Professor Johns Hopkins University, and Director of the Hopkins Bayview Medical Center Clinical Laboratories, Johns Hopkins UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/633632016-08-15T15:01:28Z2016-08-15T15:01:28ZWe’re holding an amoeba Olympics to uncover the mechanisms behind human diseases<figure><img src="https://images.theconversation.com/files/133551/original/image-20160809-20932-1b39fuy.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Dictyostelium discoideum at work.</span> <span class="attribution"><a class="source" href="https://upload.wikimedia.org/wikipedia/commons/thumb/5/5a/Dictyostelium_discoideum_43.jpg/1280px-Dictyostelium_discoideum_43.jpg">Usman Bashir/Wikimedia</a></span></figcaption></figure><p>There are 10,000 competitors and a variety of events to test their abilities. You would be forgiven for thinking that I am about to talk about the Rio Olympics.</p>
<p>But approximately 5,600 miles away from the games, our lab in Cardiff will be training amoeba participants to take part in various tests – but rather than gold medals, the legacy of these competitions will be new understanding of human diseases, such as bacterial infections, cancer and psychiatric disorders. </p>
<p>Humans and amoeba are distant evolutionary cousins and rather fortuitously have comparable genetic makeups. In fact, the amoeba we are using, <em>Dictyostelium discoideum</em>, played an important role in finding the mechanism of the <a href="http://www.nature.com/nature/journal/v417/n6886/full/417292a.html">mood stabilising drug lithium</a>. Despite lithium having been used as a medicine to <a href="http://www.mind.org.uk/information-support/drugs-and-treatments/lithium-and-other-mood-stabilisers/about-lithium/#.V7GVHbgrLIU">treat psychiatric disorders</a> for more than a century, the way it worked was previously unknown. But now that the key pathway has been <a href="https://books.google.co.uk/books?id=BKwkonZwZD0C&pg=PA264&lpg=PA264&dq=how+lithium+affects+amoeba&source=bl&ots=caKM53WxDW&sig=bhXFsID7yhiCShQONfARXCukeGA&hl=en&sa=X&ved=0ahUKEwjKl8evzrTOAhVDSBQKHWV4CvIQ6AEIMTAD#v=onepage&q=how%20lithium%20affects%20amoeba&f=false">found and characterised in amoeba</a>, and we know how these single-cell organisms are affected by it, researchers can move on to investigating how it works in human cells. </p>
<p><em>Dictyostelium discoideum</em> is a <a href="http://modelorganisms.nih.gov/d_discoideum/">soil-dwelling social amoeba</a>, more affectionately known as “Dicty”. Dicty was plucked from a forest in North Carolina in 1935 and now resides in hundreds of labs across the world. To date, it has helped us track the movement of neutrophils, one of the most abundant white blood cells in the human body; the mechanism behind the rare “smooth brain” disorder Lissencephaly; resistance to the cancer chemotherapy drug cisplatin; and infections of the harmful bacteria that cause Legionnaire’s disease and TB. </p>
<h2>Starting line</h2>
<p>Dicty won’t need to throw a javelin or run 100m to win an event: the winner will be the “athlete” who is able to multiply the fastest – although slow growth is just as interesting. Each one of the athletes has a unique feature to contend with; they are each missing a different gene, but otherwise they are all genetically identical. Without the gene, the cell will lose a specific function and so its performance will be affected. Thousands of amoeba with different function handicaps will be observed side-by-side. </p>
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<p>Our goal is to challenge the cells to grow in the presence of lithium and see which ones thrive and which struggle. By taking away a specific gene, we can see whether the amoeba performs better than its competitors who have other genes taken away.</p>
<p>We have spent the past two years bringing together and cultivating these miniature athletes for this project in a bid to create a powerful new resource for the scientific community. Shortly these tiny athletes will be put into stasis and shipped around the world to take part in competitions and help other researchers explore molecular mechanisms.</p>
<p>As the 2016 amoeba games open, the thousands of amoeba will be placed in about 3⅓ tablespoons of nutrient rich broth and compete simultaneously in the first lithium challenge. It is easy to imagine now that the whole human genome has been sequenced that we know the role of every A, T, C and G – but in truth our genome is vast and this is far from the case. We hope the winners (and the losers) will reveal further new components and pathways.</p>
<p>One key element that has made this possible today has been the affordability and capacity of next-generation sequencing technology. Less than £1,000 will buy us a mind-boggling 400m sequencing reads. Each amoeba has a unique athlete number and so can be detected by sequencing and counted. This would have been impossible 10 years ago, but it has now given us the ability to monitor thousands of individuals simultaneously and detect changes in abundance. Plus 400m sequencing reads is enough to run three heats so we will make sure the true winners reach the podium.</p>
<p>Each event will reveal how different genomes are affected in the presence of lithium and so help us study the processes of human health and disease. This simple yet powerful model organism will play an important role in discovering how our genomes function and allow us to develop better medications.</p><img src="https://counter.theconversation.com/content/63363/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Amy Baldwin is employed by a Wellcome Trust grant awarded to Cardiff University and The University of Manchester. </span></em></p>They may be single-celled organisms, but as our distant cousins amoeba can tell us a lot about ourselves.Amy Baldwin, Research associate, Cardiff UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/572712016-07-25T03:34:43Z2016-07-25T03:34:43ZWelcome to Lab 2.0 where computers replace experimental science<figure><img src="https://images.theconversation.com/files/119816/original/image-20160422-17369-1osfhnh.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C1198%2C896&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The Titan Supercomputer, in the US, has allowed scientists to study ice formation on wind turbines at a molecular level.</span> <span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Titan_supercomputer_at_the_Oak_Ridge_National_Laboratory.jpg">Wikimedia/Oak Ridge National LaboratoryOak Ridge National Laboratory</a></span></figcaption></figure><p>We spend our lives surrounded by hi-tech materials and chemicals that make our batteries, solar cells and mobile phones work. But developing new technologies requires time-consuming, <a href="https://www.cheaptubes.com/product-category/single-walled-double-walled-carbon-nanotubes/">expensive</a> and even <a href="http://www.chemistry.auckland.ac.nz/en/for/current-students/cs-health-and-safety/examples-of-real-incidents.html">dangerous</a> experiments.</p>
<p>Luckily we now have a secret weapon that allows us to <a href="https://www.whitehouse.gov/blog/2011/06/24/materials-genome-initiative-renaissance-american-manufacturing">save time, money and risk</a> by avoiding some of these experiments: computers.</p>
<p>Thanks to <a href="https://www-ssl.intel.com/content/www/us/en/silicon-innovations/moores-law-technology.html">Moore’s law</a> and a number of developments in physics, chemistry, computer science and mathematics over the past 50 years (leading to Nobel Prizes in Chemistry in <a href="https://www.nobelprize.org/nobel_prizes/chemistry/laureates/1998/">1998</a> and <a href="https://www.nobelprize.org/nobel_prizes/chemistry/laureates/2013/">2013</a>) we can now carry out many experiments entirely on computers using modelling.</p>
<p>This lets us test chemicals, drugs and hi-tech materials on a computer before ever making them in a lab, which saves time and money and reduces risks. But to dispense with labs entirely we need computer models that will reliably give us the right answers. That’s a difficult task.</p>
<h2>A grand challenge</h2>
<p>Why so difficult? Because chemistry is the quantum mechanics of interacting electrons – usually based on <a href="https://plus.maths.org/content/schrodinger-1">Schrodinger’s equation</a> – which require enormous amounts of memory and time to model. </p>
<p>For example, to study the interaction of three water molecules, we need to store around 10<sup>80</sup> pieces of data, and do at least 10<sup>320</sup> <a href="http://infocenter.arm.com/help/topic/com.arm.doc.faqs/ka9805.html">mathematical operations</a>.</p>
<p>This basically means that when the universe ends we’d still be waiting for an answer. This is somewhat of a bottleneck.</p>
<p>But this bottleneck was broken by three major advances that allow modern computer models to approximate reality pretty well without taking billions of years.</p>
<p>Firstly, Pierre Hohenberg, Walter Kohn and Lu Jeu Sham turned the interaction problem on its head in the 1960s, <a href="http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1998/kohn-lecture.pdf">greatly simplifying and improving theory</a>. </p>
<p>They showed that the electronic density – a quantum mechanical probability that is fairly easy to calculate – is all you need to determine all properties of any quantum system.</p>
<p>This is a truly remarkable result. In the case of three water molecules, their approach needs only 3,000 pieces of data and around 100 billion maths operations.</p>
<p>Secondly, in the 1970s John Pople and co-workers found a very clever way to simplify the computing method by employing mathematical and computational shortcuts. </p>
<p>This lets us use just 300 pieces of data for three water molecules. Calculations need around 100 million operations, which would take a 1975 supercomputer two seconds but can be solved <a href="http://www.phonearena.com/news/A-modern-smartphone-or-a-vintage-supercomputer-which-is-more-powerful_id57149">500 times in a second on a modern phone</a>.</p>
<p>And finally, the 1990s saw a bunch of people come up with some simple methods to approximate very complex interaction physics with surprisingly high accuracy.</p>
<p>Modern computer models are now mostly fast and mostly accurate, most of the time, for most chemistry.</p>
<h2>Quantum mechanical modelling takes off</h2>
<p>As a result, computer modelling has transformed chemistry. A quick glance through any recent chemistry journal shows that many experimental papers now include results from modelling.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/119809/original/image-20160422-17409-1uasf3y.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/119809/original/image-20160422-17409-1uasf3y.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/119809/original/image-20160422-17409-1uasf3y.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=553&fit=crop&dpr=1 600w, https://images.theconversation.com/files/119809/original/image-20160422-17409-1uasf3y.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=553&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/119809/original/image-20160422-17409-1uasf3y.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=553&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/119809/original/image-20160422-17409-1uasf3y.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=694&fit=crop&dpr=1 754w, https://images.theconversation.com/files/119809/original/image-20160422-17409-1uasf3y.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=694&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/119809/original/image-20160422-17409-1uasf3y.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=694&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Computers can show quantum mechanical details no experiment can probe. Here modelling has been used to calculate and plot the electron density of a C60 bucky ball.</span>
<span class="attribution"><span class="source">Itamblyn/Wikipedia</span></span>
</figcaption>
</figure>
<p>Density functional theory (the technical name for the most common modelling method) is a feature in more than <a href="http://journals.aps.org/rmp/pdf/10.1103/RevModPhys.87.897">15,000 scientific papers</a> published in 2015. Its impact will only continue to grow as computers and theory improve.</p>
<p>Modelling is now used to <a href="http://www.nature.com/nchem/journal/v6/n12/full/nchem.2099.html">uncover chemical mechanisms</a>, to reveal details about systems that are <a href="http://science.sciencemag.org/content/351/6279/1310.abstract">hidden from experiments</a>, and <a href="http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.102.236804">to propose novel materials</a> that can later be <a href="http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.108.155501">made in a lab</a>. </p>
<p>In a particularly exciting case, computers were able to predict that a molecule C<sub>3</sub>H+ (propynylidynium) was responsible for some <a href="http://www.scientificamerican.com/article/the-hunt-for-alien-molecules/">strange astronomical observations</a>.</p>
<p>C<sub>3</sub>H+ had never before been seen on Earth. When it was later made in a lab it behaved just as the modelling predicted.</p>
<h2>New challenges need new solutions</h2>
<p>However, the rise of graphene exposed a major flaw in existing models. </p>
<p>Graphene and similar 2D materials do not stick together in the same way as most chemicals. They are instead held together by what are known as <a href="https://www.britannica.com/science/van-der-Waals-forces">van der Waals forces</a> that are not included in standard models, making them fail in 2D systems. </p>
<p>This <a href="http://arxiv.org/abs/1206.3542">failure</a> has led to a surge of interest in computer modelling of van der Waals forces. </p>
<p>For example, I was involved in an international project that used sophisticated modelling to <a href="http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.105.196401">determine the energy gained</a> by forming graphite out of layers of graphene. This energy still cannot be determined by experiments.</p>
<p>Even more usefully, 2D materials can potentially be <a href="http://www.nature.com/nature/journal/v499/n7459/abs/nature12385.html">stacked like LEGO</a>, offering vast technological promise. But there are basically an infinite number of ways to arrange these stacks. </p>
<p>We recently developed a <a href="http://link.aps.org/doi/10.1103/PhysRevB.93.165436">fast and reliable model</a> so that a computer can churn through different arrangements very quickly to find the best stacks for a given purpose. This would be impossible in a real lab.</p>
<p>On another front, electrical charge transfer in solar cells is also difficult to study with existing techniques, making the models unreliable for an important field of green technology. </p>
<p>Even worse, highly promising (but dangerous) <a href="http://www.gizmag.com/cheap-durable-perovskite-solar-cells/41618/">lead based perovskite solar cells</a> involve van der Waals forces and charge transfer together, <a href="http://pubs.rsc.org/en/content/articlelanding/cp/2014/c3cp54479f">as shown by some colleagues and me</a>.</p>
<p>A substantial effort is underway to deal with this difficult problem, and the equally difficult (and related) magnetism and conduction problems.</p>
<h2>Things will only get better</h2>
<p>The ultimate goal of computer modelling is to replace experiments almost entirely. We can then build experiments on a computer in the same way people build things in Minecraft.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/LGkkyKZVzug?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
</figure>
<p>The computer would model the real world to allow us to save real time and money and avoid real dangerous experiments. </p>
<p>For example, the <a href="https://web.archive.org/web/20130226173844/http://www.olcf.ornl.gov/wp-content/themes/olcf/titan/Titan_BuiltForScience.pdf">Titan supercomputer</a> (pictured top) has recently been used to study non-icing surface materials at the molecular level to improve the efficiency of wind power turbines in cold climates.</p>
<p>This ultimate goal was almost met in the 1990s until the experimental scientists came up with graphene and perovskites that showed flaws in existing theories. Researchers like me continue to study, anticipate and fix these flaws so that computers can replace more challenging experiments.</p>
<p>Perhaps the 2020s will be the last decade when experiments are carried out before knowing what the answer will be. That is a certainly a model worth striving for.</p><img src="https://counter.theconversation.com/content/57271/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Timothy Gould does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Developing new technologies requires time-consuming, expensive and even dangerous experiments. But now we can carry out many experiments entirely on computers using modelling.Timothy Gould, Lecturer in Physics, Griffith UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/553692016-04-25T10:03:32Z2016-04-25T10:03:32ZIt bears repeating: how scientists are addressing the ‘reproducibility problem’<figure><img src="https://images.theconversation.com/files/119903/original/image-20160422-17401-1yrvxy2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">In scientific research, repetition is good.</span> <span class="attribution"><a class="source" href="https://www.flickr.com/photos/w4nd3rl0st/5855396656/">w4nd3rl0st/flickr</a>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span></figcaption></figure><p>Recently a friend of mine on Facebook posted a link whose headline quoted a scientist saying “Most cancer research is largely a fraud.” The quote is both out of context and many decades old. But its appearance still makes a strong point: the general public has a <a href="https://www.washingtonpost.com/posteverything/wp/2015/01/30/even-in-2015-the-public-doesnt-trust-scientists/">growing distrust</a> of science and research. </p>
<figure class="align-left zoomable">
<a href="https://images.theconversation.com/files/119891/original/image-20160422-17417-18j842g.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/119891/original/image-20160422-17417-18j842g.png?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/119891/original/image-20160422-17417-18j842g.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=1130&fit=crop&dpr=1 600w, https://images.theconversation.com/files/119891/original/image-20160422-17417-18j842g.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=1130&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/119891/original/image-20160422-17417-18j842g.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=1130&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/119891/original/image-20160422-17417-18j842g.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1420&fit=crop&dpr=1 754w, https://images.theconversation.com/files/119891/original/image-20160422-17417-18j842g.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1420&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/119891/original/image-20160422-17417-18j842g.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1420&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Seeking reproducibility: a difference between scientists and normal people.</span>
<span class="attribution"><a class="source" href="https://xkcd.com/242/">Randall Munroe/XKCD</a>, <a class="license" href="http://creativecommons.org/licenses/by-nc/4.0/">CC BY-NC</a></span>
</figcaption>
</figure>
<p>Recent reports in the <a href="https://www.washingtonpost.com/news/speaking-of-science/wp/2015/08/27/trouble-in-science-massive-effort-to-reproduce-100-experimental-results-succeeds-only-36-times/">Washington Post</a> and the <a href="http://www.economist.com/news/leaders/21588069-scientific-research-has-changed-world-now-it-needs-change-itself-how-science-goes-wrong">Economist,</a> among others, raise the concern that <a href="https://theconversation.com/we-found-only-one-third-of-published-psychology-research-is-reliable-now-what-46596">relatively few</a> scientists’ experimental findings <a href="https://theconversation.com/real-crisis-in-psychology-isnt-that-studies-dont-replicate-but-that-we-usually-dont-even-try-47249">can be replicated</a>. This is worrying: replicating an experiment is a main foundation of the scientific method. </p>
<p>As scientists, we build on knowledge gained and published by others. We develop new experiments and questions based on the knowledge we gain from those published reports. If those papers are valid, our work is supported and knowledge advances.</p>
<p>On the other hand, if published research is not actually valid, if it can’t be replicated, it delivers only an incidental finding, not scientific knowledge. Any subsequent questions will either be wrong or flawed in important ways. Identifying which reports are invalid is critical to prevent wasting money and time pursuing an incorrect idea based on bad data. How can we know which findings to trust? </p>
<h2>Why would a repeat fail?</h2>
<p>Repeating a result is not always a simple task. Say you flip a coin three times and get heads each time. You may conclude that coins always land on heads. As an independent test, your friend flips a coin five more times and gets four tails and one heads. The friend concludes your results were incorrect, not reproducible and that coins usually land on tails. Repeating the research can both correct inaccuracies and deepen our understanding of the real truth: the coin lands on heads and tails equally.</p>
<p>This is much harder in studies that are more complex than coin-flipping. In a recent <a href="http://dx.doi.org/10.1126/science.aad7243">commentary</a> in Science, lead author and Harvard psychologist Daniel Gilbert notes that the 2015 study that reported low reproducibility of psychology research <a href="http://news.harvard.edu/gazette/story/2016/03/study-that-undercut-psych-research-got-it-wrong/">did not correctly replicate</a> the methods or approaches of the original studies. For example, a study of race and affirmative action performed at Stanford University was “replicated” at the University of Amsterdam in the Netherlands, in another country with different racial diversity. When the study was later repeated at Stanford, the original published results were indeed replicated.</p>
<p>Gilbert’s analysis suggests that the reproducibility “problem” may be more complex. Perhaps some studies cannot be repeated due to problems with the initial study, while others aren’t replicable because the follow-up research did not follow the methods or use the same tools as the original study. Likely both contribute to the reproducibility problem.</p>
<h2>Focusing on the details</h2>
<p>The scientific community is addressing this challenge in several ways. For example, scholarly journals are requiring much more detailed explanations of how we did our experiments. More detail allows scholars to better evaluate and understand what parts of the experiment could <a href="http://www.nature.com/news/journals-unite-for-reproducibility-1.16259">influence the result</a>. </p>
<p>Also, when reviewing requests for government research grant money, the National Institutes of Health now <a href="http://www.nature.com/news/repetitive-flaws-1.19192">requires</a> scientists to detail both the tools they will use and the tests they used to confirm the tools are exactly what they should be.</p>
<p>One way scientists can get results that can’t be reproduced is if one or more of the tools used doesn’t work as the researchers assume or intend. Researchers have <a href="http://www.nature.com/news/announcement-time-to-tackle-cells-mistaken-identity-1.17316">found</a> that tools such as cell lines can become contaminated, mislabeled or mixed up. Antibodies used to identify one protein may actually identify the <a href="http://www.nature.com/news/reproducibility-crisis-blame-it-on-the-antibodies-1.17586">wrong protein</a> or more than one protein. Even variations in the type of food given to lab mice have shown to significantly <a href="http://www.nature.com/news/chow-down-1.19378">change experiment results</a>.</p>
<p>To combat this type of problem, researchers have begun sequencing DNA to ensure they are working with the cell lines they intend to be. Some lab supply companies are <a href="http://www.nature.com/nature/journal/v527/n7579/full/527545a.html">testing their antibodies in-house</a> to confirm they work as expected. Other companies are using the <a href="https://theconversation.com/the-sharing-economy-comes-to-scientific-research-55368">online lab-services marketplace</a> <a href="http://www.scienceexchange.com">Science Exchange</a> to find expert labs like mine to independently test their antibodies. (I am on Science Exchange’s Lab Advisory Board, but have no financial interest in the company.) The results of those tests can “validate” an antibody as good or bad for a particular experiment, letting future scientists know which antibodies are the best tools for their research.</p>
<h2>Finding time to reproduce important studies</h2>
<p>Those steps address future and ongoing research. But how do we know which already published experiments are reproducible and which are not? Most journals focus on publishing new and groundbreaking findings, rather than publishing a replication of a previous study. Further, research that finds a study’s results can’t be replicated – getting what are called “negative results” – can also be difficult for scientists and journals to publish. Collaboration and support from colleagues are key to academic success; publishing data that contradict a fellow researcher’s results risks alienating peers. </p>
<p>In 2012, the biopharmaceutical company Amgen <a href="http://www.nature.com/news/biotech-giant-publishes-failures-to-confirm-high-profile-science-1.19269">reported</a> that it had been unable to reproduce 47 of 53 “landmark” cancer papers. For confidentiality reasons, however, the company did not release which papers it could not replicate and thus did not provide details about how it repeated the experiments. As with the psychology studies, this leaves the possibility that Amgen got different results because the experiments were not performed the same way as the original study. It opens the door to doubt about which result – the first or the repeat test – was correct. </p>
<p><a href="http://validation.scienceexchange.com/">Several initiatives</a> are addressing this problem in multiple disciplines. Science Exchange; the <a href="https://cos.io/">Center for Open Science</a>, a group dedicated to “openness, integrity and reproducibility of scientific research”; and <a href="http://f1000research.com/">F1000Research</a>, a team focused on <a href="http://f1000research.com/channels/PRR">immediate and transparent publishing</a> have all introduced initiatives along this line. </p>
<p>Science Exchange and the Center for Open Science have launched a specific effort in this direction regarding cancer research. Their effort, the <a href="https://osf.io/e81xl/">Reproducibility Project: Cancer Biology</a>, has received US$1.3 million from the <a href="http://www.arnoldfoundation.org/">Arnold Foundation</a> to repeat selected experiments from a number of high-profile cancer biology papers. The project will publish comprehensive details of how scientists attempted to reproduce each study, and will report results whether they confirm, contradict or change the findings of the study being repeated.</p>
<p>In addition, Science Exchange, the open-access journal <a href="https://www.plos.org/">PLoS</a>, the data management site <a href="https://figshare.com/">figshare</a> and the reference management site <a href="https://www.mendeley.com/">Mendeley</a> joined forces in 2012 to identify and document high-quality reproducible research. This effort, called the <a href="https://www.scienceexchange.com/applications/reproducibility">Reproducibility Initiative</a>, allows scientists to apply to have key parts of their projects repeated in independent expert labs identified by Science Exchange. </p>
<p>The results of the repeat tests can be published in the special PLoS <a href="http://journals.plos.org/plosone/browse/reproducibility">reproducibility collection</a>. The data are made openly available through figshare and the impact the work has on future studies and publications can be tracked in the Mendeley reproducibility <a href="https://www.mendeley.com/groups/2473351/reproducibility-initiative/">collection</a>. Many journals have agreed to add an <a href="http://www.slate.com/articles/health_and_science/science/2012/08/reproducing_scientific_studies_a_good_housekeeping_seal_of_approval_.html">“Independently Validated” badge</a> to original articles that are successfully repeated, indicating their high quality.</p>
<h2>Doing it right again and again</h2>
<p>To prevent problems in the repetition of the experiments, the Reproducibility Initiative spends months reviewing the details of an experiment with the original author to ensure the project is repeated accurately. Once reviewed, Science Exchange splits the project into types of experiments and outsources each type to a lab with that expertise. By dividing and outsourcing the project, the testing labs do not know the original paper, results, or authors, eliminating chances for bias in testing. </p>
<p>Testing labs like mine create a detailed report of the experiments to be done. Every step, every reagent down to the catalog number and company, is carefully documented and published in an <a href="http://dx.doi.org/10.1371/journal.pone.0114614">independent report</a> in “PLoS One.” That way, whether the result of the repetition is positive or negative, the full details of the experiment are available for review. Upon completion of the repeat testing, the results are published in “PLoS One,” whether they validate or contradict the original findings. The results of the first full replication of a study are expected to be published later this year.</p>
<p>As scientists, we are working to dispel concerns about scientific research like those raised by my Facebook friend. With improved reporting and tools for future research, the science community can counter and reduce existing problems of reproducibility, which will help us build a strong and valid foundation for future scientific studies.</p><img src="https://counter.theconversation.com/content/55369/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Deborah Berry is a member of the Laboratory Advisory Board for Science Exchange. </span></em></p>Scientists build on knowledge gained and published by others. How can we know which findings to trust?Deborah Berry, Assistant Professor and Co-Director of the Histopathology and Tissue Shared Resource, Georgetown UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/449952015-07-23T10:08:43Z2015-07-23T10:08:43ZExplainer: biosafety and biosecurity in South Africa<figure><img src="https://images.theconversation.com/files/89350/original/image-20150722-1479-8qygt2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">South Africa needs to ensure that it is equipped to deal with bioterrorism attacks and possible laboratory outbreaks.</span> <span class="attribution"><span class="source">Mariana Bazo/Reuters</span></span></figcaption></figure><p>In the scientific world, laboratories provide the crucial space for scientists to work and test hypotheses that they are working on. There are dangers involved, though. Laboratories may contain many hazardous chemicals and the spread of these could have devastating effects on the environment, humans, livestock and agriculture. </p>
<p>It is imperative that the necessary precautions are taken to ensure that hazardous material and potentially dangerous pathogens are handled safely and securely.</p>
<p>Biosafety generally means the adherence to good laboratory practices and <a href="http://www.medicinenet.com/script/main/art.asp?articlekey=33817">procedures</a>. It also refers to the use of appropriate safety equipment and facilities in order to ensure the safe handling, storage and disposal of biological material. This includes <a href="http://www.phac-aspc.gc.ca/publicat/lbg-ldmbl-04/ch2-eng.php">pathogens</a> – infectious agents that cause disease. </p>
<p>Measures to prevent harm caused by the accidental exposure to harmful pathogens and toxins fall under the term biosafety. Physical containment barriers and practices are <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2493080/">mandatory</a>. This is to prevent unintentional exposure to biological agents. They are also required to prevent accidental release into the environment.</p>
<p><a href="http://www.epa.gov/agriculture/tbis.html">Biosecurity</a> refers to the misuse or abuse of biological material. This includes pathogens and their products. There need to be ways to protect their misuse from causing harm to humans, livestock or crops. </p>
<p>Measures need to be implemented to control any harm in the event of exposure. This includes the protection, control and accountability for harmful biological materials – specifically in <a href="http://www.who.int/csr/resources/publications/biosafety/WHO_CDS_EPR_2006_6.pdf">laboratories</a>, in order to prevent their unauthorised access, loss or theft.</p>
<p>Bio-risk assessment is the quantitative and/or qualitative assessment of the possibility of a particular biological event. This includes natural disease outbreaks such as Ebola, accidents or the deliberate misuse of biological agents. The type of biological event that may adversely affect the health of humans, animals and crops. </p>
<h2>Why it is relevant to South Africa</h2>
<p>The use of biological material for harmful purposes is becoming an increasing threat. Even though it is not widely publicised, there have been incidents of both unintentional and deliberate exposure to harmful biological agents. Some of the most common agents used in bioterrorism include <a href="http://gulfnews.com/news/americas/usa/sarin-how-nazis-developed-deadly-neurotoxin-1.1179868">sarin neurotoxin</a>, <a href="http://www.bbc.co.uk/news/uk-england-merseyside-33607623">ricin</a> and <a href="http://www.npr.org/2011/02/15/93170200/timeline-how-the-anthrax-terror-unfolded">anthrax</a>. </p>
<p>Existing legislation and capacity to monitor and deal with these types of problems is <a href="http://uctscholar.uct.ac.za/R/?func=dbin-jump-full&object_id=1277&local_base=GEN01">fragmented</a> in South Africa. This is scattered across a number of <a href="http://www.acgt.co.za/wp-content/uploads/2014/07/South-Africa-status-with-respect-to-biotechnology-and-biosafety_Hennie-Groenewald.pdf">departments</a> such as Agriculture, Health, and Trade and Industry. This makes reporting and monitoring very difficult. </p>
<p>It would be appropriate for one department, such as Science and Technology, to take overall responsibility for the implementation of biorisk assessment legislation in South Africa. </p>
<p>South Africa has excellent ethical guidelines in place for human and animal <a href="http://www.kznhealth.gov.za/research/ethics3.pdf">experimentation</a>. But there is a lack of education and training in research ethics for life scientists working with harmful biological <a href="http://sabioriskassociation.org/">material</a>. </p>
<p>There is a conspicuous absence of a database of both public and commercial laboratories working on such material within South Africa. There is generally a disconcerting low level of awareness among life scientists about national and international conventions, laws and regulations related to their research.</p>
<h2>How vulnerable is South Africa?</h2>
<p>South Africa has largely been spared the threats of bioterrorism. But given that South Africa is the <a href="http://www.southafrica.info/africa/">gateway</a> to Africa and the transit route to many Western and Eastern destinations, we will not be immune from such threats forever. </p>
<figure class="align-right ">
<img alt="" src="https://images.theconversation.com/files/89349/original/image-20150722-1473-lfqsa.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/89349/original/image-20150722-1473-lfqsa.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=389&fit=crop&dpr=1 600w, https://images.theconversation.com/files/89349/original/image-20150722-1473-lfqsa.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=389&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/89349/original/image-20150722-1473-lfqsa.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=389&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/89349/original/image-20150722-1473-lfqsa.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=489&fit=crop&dpr=1 754w, https://images.theconversation.com/files/89349/original/image-20150722-1473-lfqsa.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=489&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/89349/original/image-20150722-1473-lfqsa.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=489&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">All scientists in South Africa need to be aware of the dangers that stem from laboratories.</span>
<span class="attribution"><span class="source">Wolfgang Rattay/Reuters</span></span>
</figcaption>
</figure>
<p>Research and development in the life sciences are crucial in driving the bio-economy in South Africa. It is also imperative that such research is conducted in a safe, secure and ethically sound manner. There is a general attitude that “this does not apply to me or my work” or “my work cannot be used for harmful purposes by <a href="http://www.gov.za/minister-naledi-pandor-international-symposium-bio-safety-genetically-modified-organisms">scientists”</a>. </p>
<p>Creating awareness and accepting that the misuse of scientific technology is a reality is in the interest of both South Africans and the life science community.</p>
<p>Although the South African legislative framework is robust and comprehensive, it suffers from several <a href="http://innovationsymposium.wits.ac.za/usrfiles/users/1/pdfs/Pamela_Andanda.pdf">limitations and challenges</a>. These include:</p>
<ul>
<li><p>Lack of coherence in the categorisation of pathogens;</p></li>
<li><p>The lack of harmonisation of guidelines; and</p></li>
<li><p>The deficiency in infrastructure and capacity to meet the challenges for implementation of the legislation. </p></li>
</ul>
<p>South Africa also has a complex set of regulations governing the detection, identification, control, and prevention of human, animal and plant diseases caused by infectious agents. There is a definite need to develop a single, locally relevant list of infectious agents. There is also a need for their control and eradication. This list should be dynamic and regularly updated. </p>
<p>One should not be alarmist, but given the increasing threats elsewhere in the world, South Africa should not be complacent. The country should rather be proactive in putting in place preventative measures to protect its population. Criminal elements intending to use technology for harmful purposes are always a threat anywhere in the word. </p>
<hr>
<p><em>Find the official Academy of Science of South Africa report <a href="http://www.assaf.co.za/wp-content/uploads/2011/10/Final-WEB-K-12423-ASSAF-Biosafety-and-Biosecurity-Report_DevV11LR.pdf">here</a>.</em></p><img src="https://counter.theconversation.com/content/44995/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Iqbal Parker receives research funding from the South African Medical Research Council (MRC) and the National Research Foundation (NRF)</span></em></p>In the science world, laboratories are essential but safety precautions should be taken to prevent any incidents like the Ebola outbreak or biochemical attacks.Iqbal Parker, Director, International Centre for Genetic Engineering and Biotechnology, University of Cape TownLicensed as Creative Commons – attribution, no derivatives.