tag:theconversation.com,2011:/au/topics/x-ray-crystallography-63011/articles
X-ray crystallography – The Conversation
2023-01-06T13:30:53Z
tag:theconversation.com,2011:article/195873
2023-01-06T13:30:53Z
2023-01-06T13:30:53Z
Visualizing the inside of cells at previously impossible resolutions provides vivid insights into how they work
<figure><img src="https://images.theconversation.com/files/501408/original/file-20221215-16-mtk39u.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C1078%2C913&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Cryo-electron tomography shows what molecules look like in high-resolution – in this case, the virus that causes COVID-19.</span> <span class="attribution"><a class="source" href="https://nanographics.at/projects/coronavirus-3d/">Nanographics</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span></figcaption></figure><p>All life is <a href="https://www.khanacademy.org/science/biology/intro-to-biology/what-is-biology/a/what-is-life">made up of cells</a> several magnitudes <a href="https://learn.genetics.utah.edu/content/cells/scale/">smaller than a grain of salt</a>. Their seemingly simple-looking structures mask the intricate and complex molecular activity that enables them to carry out the functions that sustain life. Researchers are beginning to be able to visualize this activity to a level of detail they haven’t been able to before.</p>
<p>Biological structures can be visualized by either starting at the level of the whole organism and working down, or starting at the level of single atoms and working up. However, there has been a resolution gap between a cell’s smallest structures, such as the cytoskeleton that supports the cell’s shape, and its largest structures, such as the ribosomes that make proteins in cells.</p>
<p>By analogy of Google Maps, while scientists have been able to see entire cities and individual houses, they did not have the tools to see how the houses came together to make up neighborhoods. Seeing these neighborhood-level details is essential to being able to understand how individual components work together in the environment of a cell.</p>
<p>New tools are steadily bridging this gap. And ongoing development of one particular technique, <a href="https://doi.org/10.1002/1873-3468.13948">cryo-electron tomography, or cryo-ET</a>, has the potential to deepen how researchers study and understand how cells function in health and disease. </p>
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<iframe width="440" height="260" src="https://www.youtube.com/embed/026rzTXb1zw?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Cryo-EM won the 2017 Nobel Prize in chemistry.</span></figcaption>
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<p>As the former <a href="https://www.science.org/content/article/jeremy-berg-named-science-editor-chief">editor-in-chief of Science magazine</a> and as a <a href="https://scholar.google.com/citations?user=MZ6qrPUAAAAJ&hl=en">researcher</a> who has studied hard-to-visualize large protein structures for decades, I have witnessed astounding progress in the development of tools that can determine biological structures in detail. Just as it becomes easier to understand how complicated systems work when you know what they look like, understanding how biological structures fit together in a cell is key to understanding how organisms function.</p>
<h2>A brief history of microscopy</h2>
<p>In the 17th century, <a href="https://doi.org/10.1098/rsob.150019">light microscopy</a> first revealed the existence of cells. In the 20th century, electron microscopy offered even greater detail, revealing the <a href="https://www.nobelprize.org/prizes/medicine/1974/summary/">elaborate structures within cells</a>, including organelles like the endoplasmic reticulum, a complex network of membranes that play key roles in protein synthesis and transport.</p>
<p>From the 1940s to 1960s, biochemists worked to separate cells into their molecular components and learn how to determine the 3D structures of proteins and other macromolecules at or near atomic resolution. This was first done using X-ray crystallography to visualize the structure of <a href="https://www.historyofinformation.com/detail.php?entryid=3015">myoglobin</a>, a protein that supplies oxygen to muscles. </p>
<p>Over the past decade, techniques based on <a href="https://www.nobelprize.org/prizes/chemistry/2002/press-release/">nuclear magnetic resonance</a>, which produces images based on how atoms interact in a magnetic field, and <a href="https://doi.org/10.1016/j.molcel.2015.02.019">cryo-electron microscopy</a> have rapidly increased the number and complexity of the structures scientists can visualize.</p>
<h2>What is cryo-EM and cryo-ET?</h2>
<p><a href="https://theconversation.com/scientists-uncovered-the-structure-of-the-key-protein-for-a-future-hepatitis-c-vaccine-heres-how-they-did-it-193705">Cryo-electron microscopy, or cryo-EM</a>, uses a camera to detect how a beam of electrons is deflected as the electrons pass through a sample to visualize structures at the molecular level. Samples are rapidly frozen to protect them from radiation damage. Detailed models of the structure of interest are made by taking multiple images of individual molecules and averaging them into a 3D structure.</p>
<p><a href="https://doi.org/10.1038/nmeth.4115">Cryo-ET</a> shares similar components with cryo-EM but uses different methods. Because most cells are too thick to be imaged clearly, a region of interest in a cell is first thinned by using an ion beam. The sample is then tilted to take multiple pictures of it at different angles, analogous to a CT scan of a body part – although in this case the imaging system itself is tilted, rather than the patient. These images are then combined by a computer to produce a 3D image of a portion of the cell. </p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/501410/original/file-20221215-27-mqhygu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Cryo-ET image of algal chloroplast" src="https://images.theconversation.com/files/501410/original/file-20221215-27-mqhygu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/501410/original/file-20221215-27-mqhygu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=932&fit=crop&dpr=1 600w, https://images.theconversation.com/files/501410/original/file-20221215-27-mqhygu.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=932&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/501410/original/file-20221215-27-mqhygu.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=932&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/501410/original/file-20221215-27-mqhygu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1172&fit=crop&dpr=1 754w, https://images.theconversation.com/files/501410/original/file-20221215-27-mqhygu.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1172&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/501410/original/file-20221215-27-mqhygu.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1172&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">This is a cryo-ET image of the chloroplast of an algal cell.</span>
<span class="attribution"><a class="source" href="https://dx.doi.org/10.7554/eLife.04889">Engel et al. (2015)</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
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<p>The resolution of this image is high enough that researchers – or computer programs – can identify the individual components of different structures in a cell. Researchers have used this approach, for example, to show how proteins move and are degraded inside an <a href="https://doi.org/10.1073/pnas.1905641117">algal cell</a>.</p>
<p>Many of the steps researchers once had to do manually to determine the structures of cells are becoming automated, allowing scientists to identify new structures at vastly higher speeds. For example, combining cryo-EM with artificial intelligence programs like <a href="https://doi.org/10.1038/s41586-021-03819-2">AlphaFold</a> can facilitate image interpretation by predicting protein structures that have not yet been characterized. </p>
<h2>Understanding cell structure and function</h2>
<p>As imaging methods and workflows improve, researchers will be able to tackle some key questions in cell biology with different strategies.</p>
<p>The first step is to decide what cells and which regions within those cells to study. Another visualization technique called <a href="https://doi.org/10.1002/1873-3468.14421">correlated light and electron microscopy, or CLEM</a>, uses fluorescent tags to help locate regions where interesting processes are taking place in living cells.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/501414/original/file-20221215-13-dadsmp.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Cryo-EM image of human T-cell leukemia virus type-1 (HTLV-1)" src="https://images.theconversation.com/files/501414/original/file-20221215-13-dadsmp.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/501414/original/file-20221215-13-dadsmp.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=406&fit=crop&dpr=1 600w, https://images.theconversation.com/files/501414/original/file-20221215-13-dadsmp.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=406&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/501414/original/file-20221215-13-dadsmp.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=406&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/501414/original/file-20221215-13-dadsmp.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=510&fit=crop&dpr=1 754w, https://images.theconversation.com/files/501414/original/file-20221215-13-dadsmp.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=510&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/501414/original/file-20221215-13-dadsmp.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=510&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">This is a cryo-EM image of a human T-cell leukemia virus type-1 (HTLV-1).</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/cryo-em-structure-of-human-t-cell-leukemia-virus-royalty-free-image/1300707029">vdvornyk/iStock via Getty Images Plus</a></span>
</figcaption>
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<p>Comparing the <a href="https://doi.org/10.1016/j.isci.2018.07.014">genetic difference between cells</a> can provide additional insight. Scientists can look at cells that are unable to carry out particular functions and see how this is reflected in their structure. This approach can also help researchers study how cells interact with each other.</p>
<p>Cryo-ET is likely to remain a specialized tool for some time. But further technological developments and increasing accessibility will allow the scientific community to examine the link between cellular structure and function at previously inaccessible levels of detail. I anticipate seeing new theories on how we understand cells, moving from disorganized bags of molecules to intricately organized and dynamic systems.</p><img src="https://counter.theconversation.com/content/195873/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Jeremy Berg does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>
Many microscopy techniques have won Nobel Prizes over the years. Advancements like cryo-ET that allow scientists to see the individual atoms of cells can reveal their biological functions.
Jeremy Berg, Professor of Computational and Systems Biology, Associate Senior Vice Chancellor for Science Strategy and Planning, University of Pittsburgh
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/182031
2022-06-16T18:39:25Z
2022-06-16T18:39:25Z
A celebrated AI has learned a new trick: How to do chemistry
<figure><img src="https://images.theconversation.com/files/469287/original/file-20220616-12-dmwhkp.jpg?ixlib=rb-1.1.0&rect=2%2C0%2C1794%2C840&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Figuring out what makes some proteins glow requires an understanding of chemistry.</span> <span class="attribution"><a class="source" href="https://www.flickr.com/photos/128643624@N07/16652974221/">eLife - the journal</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span></figcaption></figure><p>Artificial intelligence has changed the way science is done by allowing researchers to analyze the massive amounts of data modern scientific instruments generate. It can find a needle in a million haystacks of information and, using <a href="https://www.techtarget.com/searchenterpriseai/definition/deep-learning-deep-neural-network">deep learning</a>, it can learn from the data itself. AI is accelerating advances in <a href="https://doi.org/10.1186/s13073-021-00965-0">gene hunting</a>, <a href="https://doi.org/10.1038/s41591-020-01197-2">medicine</a>, <a href="https://news.mit.edu/2021/drug-discovery-binding-affinity-0315">drug design</a> and <a href="https://doi.org/10.1038/nature25978">the creation of organic compounds</a>.</p>
<p>Deep learning uses algorithms, often neural networks that are trained on large amounts of data, to extract information from new data. It is very different from traditional computing with its step-by-step instructions. Rather, it learns from data. Deep learning is far less transparent than traditional computer programming, leaving important questions – what has the system learned, what does it know?</p>
<p>As a <a href="https://scholar.google.ca/citations?user=RpiSPiwAAAAJ&hl=en">chemistry professor</a> I like to design tests that have at least one difficult question that stretches the students’ knowledge to establish whether they can combine different ideas and synthesize new ideas and concepts. We have devised such a question for the poster child of AI advocates, AlphaFold, which has solved the <a href="https://doi.org/10.1146%2Fannurev.biophys.37.092707.153558">protein-folding problem</a>.</p>
<h2>Protein folding</h2>
<p>Proteins are present in all living organisms. They provide the cells with structure, catalyze reactions, transport small molecules, digest food and do much more. They are made up of long chains of amino acids like beads on a string. But for a protein to do its job in the cell, it must twist and bend into a complex three-dimensional structure, a process called protein folding. Misfolded proteins can lead to disease.</p>
<p>In his chemistry Nobel acceptance speech in 1972, <a href="https://www.nobelprize.org/prizes/chemistry/1972/anfinsen/biographical/">Christiaan Anfinsen</a> postulated that it should be possible to <a href="https://directorsblog.nih.gov/tag/christian-anfinsen/">calculate the three-dimensional structure of a protein from the sequence of its building blocks</a>, the amino acids. </p>
<p>Just as the order and spacing of the letters in this article give it sense and message, so the order of the amino acids determines the protein’s identity and shape, which results in its function. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/462041/original/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="a graphic showing a thread-like line on the left and a coiled structure on the right" src="https://images.theconversation.com/files/462041/original/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/462041/original/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=266&fit=crop&dpr=1 600w, https://images.theconversation.com/files/462041/original/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=266&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/462041/original/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=266&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/462041/original/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=334&fit=crop&dpr=1 754w, https://images.theconversation.com/files/462041/original/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=334&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/462041/original/file-20220509-23-mkr8t2.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=334&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Within milliseconds of the exit of an amino acid chain (left) from the ribosome, it is folded into the lowest-energy 3D shape (right), which is required for the protein’s function.</span>
<span class="attribution"><span class="source">Marc Zimmer</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>Because of the inherent flexibility of the amino acid building blocks, a typical protein can adopt an estimated <a href="https://web.archive.org/web/20110523080407/http:/www-miller.ch.cam.ac.uk/levinthal/levinthal.html">10 to the power of 300 different forms</a>. This is a massive number, more than the <a href="https://educationblog.oup.com/secondary/maths/numbers-of-atoms-in-the-universe">number of atoms in the universe</a>. Yet within a millisecond every protein in an organism will fold into its very own specific shape – the lowest-energy arrangement of all the chemical bonds that make up the protein. Change just one amino acid in the hundreds of amino acids typically found in a protein and it may misfold and no longer work. </p>
<h2>AlphaFold</h2>
<p>For 50 years computer scientists have tried to solve the protein-folding problem – with little success. Then in 2016 <a href="https://www.deepmind.com/">DeepMind</a>, an AI subsidiary of Google parent Alphabet, initiated its <a href="https://www.deepmind.com/blog/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology">AlphaFold</a> program. It used the <a href="https://www.rcsb.org/">protein databank</a> as its training set, which contains the experimentally determined structures of over 150,000 proteins. </p>
<p>In less than five years AlphaFold had <a href="https://www.deepmind.com/blog/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology">the protein-folding problem beat</a> – at least the most useful part of it, namely, determining the protein structure from its amino acid sequence. AlphaFold does not explain how the proteins fold so quickly and accurately. It was a major win for AI, because it not only accrued huge scientific prestige, it also was a major scientific advance that could affect everyone’s lives.</p>
<p>Today, thanks to programs like <a href="https://www.deepmind.com/blog/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology">AlphaFold2</a> and <a href="https://www.ipd.uw.edu/2021/07/rosettafold-accurate-protein-structure-prediction-accessible-to-all/">RoseTTAFold</a>, researchers like me can determine the three-dimensional structure of proteins from the sequence of amino acids that make up the protein – at no cost – in an hour or two. Before AlphaFold2 we had to crystallize the proteins and solve the structures using <a href="https://doi.org/10.1136%2Fmp.53.1.8">X-ray crystallography</a>, a process that took months and cost tens of thousands of dollars per structure. </p>
<p>We now also have access to the <a href="https://alphafold.ebi.ac.uk/">AlphaFold Protein Structure Database</a>, where Deepmind has deposited the 3D structures of nearly all the proteins found in humans, mice and more than 20 other species. To date they it has solved more than a million structures and plan to add another 100 million structures this year alone. Knowledge of proteins has skyrocketed. The structure of half of all known proteins is likely to be documented by the end of 2022, among them many new unique structures associated with new useful functions.</p>
<h2>Thinking like a chemist</h2>
<p>AlphaFold2 was not designed to predict how proteins would interact with one another, yet it has been able to model how individual proteins combine to <a href="https://www.nature.com/articles/d41586-022-00997-5">form large complex units composed of multiple proteins</a>. We had a challenging question for AlphaFold – had its structural training set taught it some chemistry? Could it tell whether amino acids would react with one another – a rare yet important occurrence?</p>
<p>I am a computational chemist interested in <a href="https://theconversation.com/fluorescent-proteins-light-up-science-by-making-the-invisible-visible-39272">fluorescent proteins</a>. These are proteins found in hundreds of marine organisms like jellyfish and coral. Their glow can be used <a href="https://theconversation.com/from-crispr-to-glowing-proteins-to-optogenetics-scientists-most-powerful-technologies-have-been-borrowed-from-nature-164459">to illuminate</a> and <a href="https://global.oup.com/academic/product/illuminating-disease-9780199362813?cc=us&lang=en&">study diseases</a>.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/468852/original/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="two multicolored blobs with bright lines inside them against a black background" src="https://images.theconversation.com/files/468852/original/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/468852/original/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=302&fit=crop&dpr=1 600w, https://images.theconversation.com/files/468852/original/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=302&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/468852/original/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=302&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/468852/original/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=379&fit=crop&dpr=1 754w, https://images.theconversation.com/files/468852/original/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=379&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/468852/original/file-20220614-12-84y9j5.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=379&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Neurons expressing fluorescent proteins reveal the brain structures of two fruit fly larvae.</span>
<span class="attribution"><a class="source" href="https://images.nigms.nih.gov/pages/DetailPage.aspx?imageid2=6808">Wen Lu and Vladimir I. Gelfand, Feinberg School of Medicine, Northwestern University</a></span>
</figcaption>
</figure>
<p>There are 578 fluorescent proteins in the <a href="https://www.rcsb.org/search?request=%7B%22query%22%3A%7B%22type%22%3A%22group%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22group%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22group%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22terminal%22%2C%22service%22%3A%22text%22%2C%22parameters%22%3A%7B%22attribute%22%3A%22struct_keywords.pdbx_keywords%22%2C%22operator%22%3A%22contains_phrase%22%2C%22value%22%3A%22FLUORESCENT%20PROTEIN%22%7D%7D%5D%2C%22logical_operator%22%3A%22and%22%7D%5D%2C%22logical_operator%22%3A%22and%22%2C%22label%22%3A%22text%22%7D%5D%2C%22logical_operator%22%3A%22and%22%7D%2C%22return_type%22%3A%22entry%22%2C%22request_options%22%3A%7B%22paginate%22%3A%7B%22start%22%3A0%2C%22rows%22%3A25%7D%2C%22scoring_strategy%22%3A%22combined%22%2C%22sort%22%3A%5B%7B%22sort_by%22%3A%22score%22%2C%22direction%22%3A%22desc%22%7D%5D%7D%2C%22request_info%22%3A%7B%22query_id%22%3A%223e70236cf383b26f27688c5c79c6eb2b%22%7D%7D">protein databank</a>, of which 10 are “broken” and don’t fluoresce. Proteins rarely attack themselves, a process called autocatalytic posttranslation modification, and it is very difficult to predict which proteins will react with themselves and which ones won’t. </p>
<p>Only a chemist with a significant amount of fluorescent protein knowledge would be able to use the amino acid sequence to find the fluorescent proteins that have the right amino acid sequence to undergo the chemical transformations required to make them fluorescent. When we presented AlphaFold2 with the sequences of 44 fluorescent proteins that are not in the protein databank, <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0267560">it folded the fixed fluorescent proteins differently from the broken ones</a>.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/462050/original/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="a diagram showing a light bulb on the left and the stem only of a light bulb on the right" src="https://images.theconversation.com/files/462050/original/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/462050/original/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=333&fit=crop&dpr=1 600w, https://images.theconversation.com/files/462050/original/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=333&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/462050/original/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=333&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/462050/original/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=419&fit=crop&dpr=1 754w, https://images.theconversation.com/files/462050/original/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=419&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/462050/original/file-20220509-12-fxhj9p.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=419&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">AlphaFold2 can take the amino acid sequence of fluorescent proteins (letters at the top) and predict their 3D barrel shapes (middle). This isn’t surprising. What is totally unexpected is that it can also predict which fluorescent proteins are ‘broken’ and can’t fluoresce.</span>
<span class="attribution"><span class="source">Marc Zimmer</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>The result stunned us: AlphaFold2 had learned some chemistry. It had figured out which amino acids in fluorescent proteins do the chemistry that makes them glow. We suspect that the protein databank training set and <a href="https://samfordubioinformatics.wordpress.com/bioinformatics-techniques/multiple-sequence-alignment/">multiple sequence alignments</a> enable AlphaFold2 to “think” like chemists and look for the amino acids required to react with one another to make the protein fluorescent. </p>
<p>A folding program learning some chemistry from its training set also has wider implications. By asking the right questions, what else can be gained from other deep learning algorithms? Could facial recognition algorithms find hidden markers for diseases? Could algorithms designed to predict spending patterns among consumers also find a propensity for minor theft or deception? And most important, is this capability – and <a href="https://www.technologyreview.com/2019/09/17/75427/open-ai-algorithms-learned-tool-use-and-cooperation-after-hide-and-seek-games/">similar leaps in ability</a> in other AI systems – desirable?</p><img src="https://counter.theconversation.com/content/182031/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Marc Zimmer does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>
The AI AlphaFold can figure out the three-dimensional protein structure any string of amino acids will become. It has now exceeded its training by figuring out what makes some proteins glow.
Marc Zimmer, Professor of Chemistry, Connecticut College
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/167660
2021-09-26T08:35:21Z
2021-09-26T08:35:21Z
Want to develop vaccines in Africa? Then invest in expertise and infrastructure
<figure><img src="https://images.theconversation.com/files/421630/original/file-20210916-13-u7asg4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Aerial view of the UK’s national synchrotron, Diamond Light Source Ltd (Diamond) on the Harwell Science and Innovation Campus in Oxfordshire,</span> <span class="attribution"><span class="source"> ©Diamond Light Source</span></span></figcaption></figure><p>In <a href="https://theconversation.com/oxford-scientists-how-we-developed-our-covid-19-vaccine-in-record-time-153135">little more than a year</a> from the onset of COVID-19, scientists successfully developed vaccines against the SARS-CoV-2 virus for world-wide use.</p>
<p>Three main factors contributed to this extraordinary feat.</p>
<p>One, unprecedented collaboration between international scientists. Two, scientists were able to obtain exquisitely detailed images of the virus proteins and the human proteins that they interact with – right down to the positions of the atoms.</p>
<p>Three, expertise and infrastructure, developed over many years, involving tens of thousands of scientists supported by national governments and substantial private investment. Developing this skilled workforce was only possible because societies agreed to sponsor their best researchers to solve acute problems by providing appropriate tools and resources.</p>
<p>The African contribution to this massive achievement proved quite small. African researchers remain challenged by the lack of sustainable and accessible funding, infrastructure and expertise.</p>
<p>In late May President Cyril Ramaphosa <a href="https://www.gov.za/speeches/president-cyril-ramaphosa-high-level-dialogue-future-vaccine-manufacturing-africa-28-may">announced</a> that South Africa was “developing a local vaccine manufacturing plan to produce vaccines locally through strategic partnerships and technology transfer”. The goal, he said, was to cover the entire vaccine production value chain. He said Africa wants to do things for itself and that</p>
<blockquote>
<p>we must also look at how vaccine manufacturing capacity developed during COVID-19 can be repurposed for the future production of other vaccines and related technologies.</p>
</blockquote>
<p>In this article we unpack how the three-year <a href="https://start-project.org/">START programme (Synchrotron Techniques for African Research and Technology)</a> – funded with a grant from the UK Research and Innovations’ Science and Technology Facilities Council – substantially prepared South Africa’s capacity to do this type of work. It trained students and postdoctoral research assistants at eight South African universities and the country’s National Institute for Communicable Disease (NICD). It also <a href="https://www.diamond.ac.uk/Home.htm">allowed access</a> to the UK’s national synchrotron, <a href="https://www.diamond.ac.uk/Home.html">Diamond Light Source</a>. Funded through a £3.7 million (about US$5million) Global Challenges Research Fund grant, the initiative provided an exceptional combination of expertise and experimental resources.</p>
<h2>Innovative technologies</h2>
<p>Understanding biological systems is critical to the prosperity, and possibly, survival of the human race. Without it, we are threatened by disease, energy and food insecurity, pollution and climate change. Studying biological macromolecules – such as proteins at atomic resolution – empowers us to develop drugs, vaccines, herbicides and pesticides. And it helps us design non-polluting industrial processes to create the chemicals that we need.</p>
<p>The branch of science that deals with this is called Structural Biology.</p>
<p>Structural biologists unravel the intricacies of protein structures using highly brilliant synchrotron radiation in a technique called X-ray crystallography or by cryo-electron microscopy (cryo-EM). These structures form the basis for developing new drugs or vaccines to stop diseases. In particular, the recently developed, <a href="https://www.nobelprize.org/prizes/chemistry/2017/summary/">Nobel prize-winning</a>, technique of cryo-EM was essential for the development of the COVID-19 vaccines.</p>
<p>However, Africa largely remains a spectator in the race to build these innovative technologies despite START showing how it could be done. The programme has yielded extraordinary impact with relatively modest investment over a short space of time. It has triggered a step change in structural biology research in Africa, demonstrating what is needed and that it works. Existing research hubs and networks were strengthened, and new ones developed. Young career scientists grew in confidence and skills through international collaborations, mentoring, writing proposals and crunching data.</p>
<p>The South African groups regularly collected data at synchrotrons and electron microscopes to augment our understanding of potential treatments. These have included SARS-CoV-2 (COVID-19), snakebite venom, HIV, tuberculosis, malaria, human papilloma virus, cardiovascular disease, as well as equine diseases. Work has also been done to create industrial enzymes for the manufacture of medicines and commodity chemicals.</p>
<p>The structural biology laboratory at the NICD, for example, focused on understanding the antibody response to communicable diseases such as HIV and COVID-19 to guide the search for effective vaccines. In addition, the NICD has developed structural biology projects to understand how antibodies recognise and stop SARS-CoV-2 variants of concern.</p>
<p>The START grant has contributed to:</p>
<ul>
<li><p>research papers in leading international journals,</p></li>
<li><p>the development of a small but growing network of suitably equipped labs across South Africa,</p></li>
<li><p>vibrant international collaborations, and</p></li>
<li><p>numerous early career scientists trained in world class Structural Biology, including synchrotron and cryo-EM techniques.</p></li>
</ul>
<p>Unfortunately, the funding for START has ended.</p>
<h2>Now what?</h2>
<p>National government must build on the foundations of the START programme. Only a sustained national policy will ensure that structural biology can achieve world-class science and grow relevant research across Africa.</p>
<p>Structural biology remains a niche science on the continent, largely ignored by the infrastructure roadmaps. Ramaphosa’s vision of African vaccines needs to be supported by a national strategy for structural biology. The aim would be to grow the community of scientists. This, in turn, would massively impact vaccine and drug development as well as other regional challenges.</p>
<p>Teaching, training and infrastructure in protein crystallography and cryo-EM need to expand dramatically from a tiny base.</p>
<p>The structural biology community requires a modern cryo-EM centre in South Africa. This would require substantial investment beyond the means of critically stressed tertiary education institutions.</p>
<p>The support of the international community is crucial.</p>
<p>The COVID-19 pandemic has shown how important it is to have both national and international approaches to research and development with access to the right type of world class equipment, training and expertise.</p>
<p>Vaccines need to be developed in Africa against diseases arising in Africa. This makes financial sense and places emphasis on Africa solving Africa’s problems. The World Bank has estimated that the slow rollout of COVID-19 vaccines could cost the continent <a href="https://www.reuters.com/world/us/us-will-donate-substantial-portion-vaccines-through-covax-us-official-2021-05-19/">$14 billion a month</a>. Even this pales in comparison to the long-term cost of malaria, tuberculosis, HIV, and other poverty-related diseases.</p>
<p>Required steps involve:</p>
<ul>
<li><p>Local infrastructure and capacity. The infrastructure put in place by the START programme needs to be expanded to national reference laboratories, sustainably funded, well-equipped and staffed by experts.</p></li>
<li><p>Capacity retention. Early career researchers trained in South Africa need to be retained to prevent loss of knowledge and expertise. The need to provide all young researchers opportunities to further develop their careers is obvious. But this cannot be done without growth. It is therefore urgent to implement policies that stimulate the structural biology research environment and create new posts. This is key to ensuring that diversity, fresh ideas and novel approaches relevant to Africa are brought into the local and international scientific community.</p></li>
<li><p>Access to international infrastructure. Synchrotrons, neutron sources and cryo-EM facilities around the world are open to African researchers. The challenge is to produce world-class research and competitive proposals to gain access. Funding for this must come from the South African Treasury. This should be enhanced by membership of international organisations.</p></li>
</ul>
<p>START has boosted the skills and enthusiasm of South African bioscientists. They have seen the benefit of a structural approach in designing medicines for African diseases. The programme has opened doors to international co-operation and technology that Africa can’t afford. Young researchers have committed to careers in structural biology, hoping to practice their skills locally. Local research into both vaccines and medicines has started.</p>
<p>Ramaphosa’s desire to develop vaccines in South Africa could be realised by building on the foundation that has been laid. But only if there’s substantial and sustained investment in both human resources and infrastructure.</p>
<p><em>Rebekka Stredwick from Diamond Light Source also contributed to this article. She has been responsible for creating content for <a href="https://start-project.org/">START’s website</a></em>.</p><img src="https://counter.theconversation.com/content/167660/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Bryan Trevor Sewell receives funding from SA MRC, GCRF START</span></em></p><p class="fine-print"><em><span>Ed Sturrock owns shares in AngioDesign (UK) Ltd. He has received government-funded grants. He is affiliated to AngioDesign (UK) Ltd, an industry association.
</span></em></p><p class="fine-print"><em><span>Erick Strauss received funding from the GRCF in the form of the START grant.</span></em></p><p class="fine-print"><em><span>Jeremy David Woodward received funding from GCRF START. </span></em></p><p class="fine-print"><em><span>Lauren B. Arendse receives funding from The Future Leaders − African Independent Research (FLAIR) Fellowship Programme, a partnership between the African Academy of Sciences and the Royal Society funded by the UK Government’s Global Challenges Research Fund.</span></em></p><p class="fine-print"><em><span>Thandeka Moyo-Gwete receives funding from GCRF START programme.</span></em></p><p class="fine-print"><em><span>Wolf-Dieter Schubert 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>
Making vaccines in South Africa by building on the foundation that’s been laid is possible. But only if substantial and sustained investment in human resources and infrastructure becomes a reality.
Bryan Trevor Sewell, Senior Scholar (former Director of the Electron Microscope Unit and Professor in the Department of Integrative Biomedical Sciences), University of Cape Town
Ed Sturrock, Professor of Chemical and Systems Biology, University of Cape Town
Erick Strauss, Professor of Biochemistry, Stellenbosch University
Jeremy David Woodward, Chief Scientific Officer, University of Cape Town
Lauren B. Arendse, FLAIR Fellow, Drug Discovery and Development (H3D) Centre, University of Cape Town
Thandeka Moyo-Gwete, Senior Medical Scientist, National Institute for Communicable Diseases
Wolf-Dieter Schubert, Professor of Biochemistry, University of Pretoria
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/139249
2020-07-20T15:23:17Z
2020-07-20T15:23:17Z
Sexism pushed Rosalind Franklin toward the scientific sidelines during her short life, but her work still shines on her 100th birthday
<figure><img src="https://images.theconversation.com/files/347997/original/file-20200716-27-pvrhh0.jpg?ixlib=rb-1.1.0&rect=13%2C62%2C508%2C414&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Rosalind Franklin at age 25.</span> <span class="attribution"><a class="source" href="https://www.npg.org.uk/collections/search/portrait/mw62981/Rosalind-Franklin?">Elliott & Fry/© National Portrait Gallery, London</a>, <a class="license" href="http://creativecommons.org/licenses/by-nc-nd/4.0/">CC BY-NC-ND</a></span></figcaption></figure><p>What do coal, viruses and DNA have in common? The structures of each – the predominant power source of the early 20th century, one of the most remarkable forms of life on Earth and the master molecule of heredity – were all elucidated by one person. Her name was Rosalind Franklin, and the story of her triumph over sexism and rise to scientific greatness is made even more remarkable by the fact that she lived only 37 years.</p>
<p>In Franklin’s day, <a href="https://www.stsci.edu/stsci/meetings/WiA/schieb.pdf">sexism ran rampant</a> in science. <a href="https://www.harpercollins.com/9780060985080/rosalind-franklin/">Her own father</a>, judging science no career for a woman, actively discouraged her aspirations. Her doctoral supervisor at Cambridge, eventual Nobel Laureate <a href="https://www.harpercollins.com/9780060985080/rosalind-franklin/">Ronald G.W. Norrish</a>, called her “stubborn and difficult to supervise” and offered little support. <a href="https://wwnorton.com/books/9780393950755">James Watson</a>, whose Nobel Prize hinged in large part on her work, referred to her in his <a href="http://sites.bu.edu/manove-ec101/files/2017/09/Watson_The_Double_Helix.pdf">memoir</a> as “Rosy” (against her preference), and stated that, because of her “belligerent moods,” colleagues knew she “either had to go or be put in her place.” </p>
<p>Despite the attitudes of those around her, Franklin maintained her scientific acumen and thirst for knowledge, crucially contributing to one of the greatest discoveries of the 20th century.</p>
<h2>Becoming a chemist</h2>
<p>Franklin was <a href="https://www.wwnorton.co.uk/books/9780393320442-rosalind-franklin-and-dna">born in London on July 25, 1920</a> to a prominent family. Her great uncle served in the British Cabinet, and her father was a banker and science educator.</p>
<p>Franklin was an outstanding student. She received a scholarship to Cambridge, where she earned honors on her examinations and won a research fellowship. A lack of rapport with her supervisor, Norrish, drove her from his lab, and she ended up conducting groundbreaking research for her Ph.D. thesis on the <a href="https://profiles.nlm.nih.gov/spotlight/kr/feature/coal">molecular structure of coal</a>. </p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/348007/original/file-20200716-27-1d05cs2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Woman looking into microscope" src="https://images.theconversation.com/files/348007/original/file-20200716-27-1d05cs2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/348007/original/file-20200716-27-1d05cs2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=721&fit=crop&dpr=1 600w, https://images.theconversation.com/files/348007/original/file-20200716-27-1d05cs2.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=721&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/348007/original/file-20200716-27-1d05cs2.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=721&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/348007/original/file-20200716-27-1d05cs2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=906&fit=crop&dpr=1 754w, https://images.theconversation.com/files/348007/original/file-20200716-27-1d05cs2.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=906&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/348007/original/file-20200716-27-1d05cs2.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=906&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Rosalind Franklin in the lab.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Rosalind_Franklin.jpg">MRC Laboratory of Molecular Biology/Jenifer Glynn</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<p>Franklin then moved to Paris, where she studied X-ray crystallography, a powerful means of inferring the structure of molecules from how they bend beams of X-rays. She produced a <a href="https://wellcomelibrary.org/collections/digital-collections/makers-of-modern-genetics/digitised-archives/rosalind-franklin/">number of important articles</a> before returning to the U.K.</p>
<p>[<em>Deep knowledge, daily.</em> [Sign up for The Conversation’s newsletter]</p>
<p>Assigned to work on the structure of DNA in her new position at King’s College London, she applied her knowledge of X-ray diffraction and created crucial images of its molecular structure. At the time, determining DNA’s structure was one of science’s holy grails.</p>
<h2>Structure of life’s molecule</h2>
<p>Recalling a moment in 1953, <a href="https://wwnorton.com/books/9780393950755">Watson described</a> first seeing one of Franklin’s images of the DNA molecule, known as “Photograph 51”:</p>
<blockquote>
<p>The instant I saw the picture my mouth fell open and my pulse began to race. The pattern was unbelievably simpler from those obtained previously. Moreover, the black cross of reflections which dominated the picture could only arise from a helical structure.</p>
</blockquote>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/348143/original/file-20200717-23-ryev4o.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Sketch of X-ray shining through DNA sample with resulting crystallograph and double helix structure" src="https://images.theconversation.com/files/348143/original/file-20200717-23-ryev4o.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/348143/original/file-20200717-23-ryev4o.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=318&fit=crop&dpr=1 600w, https://images.theconversation.com/files/348143/original/file-20200717-23-ryev4o.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=318&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/348143/original/file-20200717-23-ryev4o.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=318&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/348143/original/file-20200717-23-ryev4o.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=400&fit=crop&dpr=1 754w, https://images.theconversation.com/files/348143/original/file-20200717-23-ryev4o.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=400&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/348143/original/file-20200717-23-ryev4o.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=400&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Diagram of Franklin’s experimental setup aiming X-ray through DNA sample with resulting ‘Photograph 51’ that implied the double-helix structure of the molecule.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/wiki/File:Experimental_setup_of_Photo_51.svg">MagentaGreen/Wikimedia Commons</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<p>Watson and his Cambridge collaborator and eventual fellow Nobel Laureate Francis Crick were not doing laboratory research on the structure of DNA, but they were actively attempting to build a model of it. Franklin’s image provided them with a breakthrough. Franklin was a <a href="https://www.sciencemag.org/careers/2018/08/rosalind-franklin-and-damage-gender-harassment">cautious scientist</a>, believing that modeling should await airtight scientific evidence. But Watson and Crick were less hesitant and became convinced that their double helix model must be correct.</p>
<p>In 1953, when Watson and Crick <a href="https://doi.org/10.1038/171737a0">announced their now famous double helix model</a> for DNA, tensions at King’s College were driving Franklin to Birkbeck College. She joined John Bernal, an X-ray crystallographer known for <a href="https://doi.org/10.1088/1742-6596/57/1/006">promoting the careers of women</a>. </p>
<p>There Franklin worked on characterizing the structure of RNA, another key information-bearing molecule in living organisms. She also studied the tobacco mosaic virus, the first virus shown to be harmful to a living organism, the tobacco plant.</p>
<p>During a trip to the U.S. in 1956, Franklin <a href="https://www.harpercollins.com/9780060985080/rosalind-franklin/">first noticed</a> that she was having difficulty fitting into her clothes. Upon her return to London, she was diagnosed with ovarian cancer, the result of mutations in the DNA of her own cells. Yet she did not let her illness interfere with her work and published a half dozen or more scientific papers in both 1956 and 1957. She died in April of 1958.</p>
<p>Franklin faced sexism for much of her professional life in science. Watson repeatedly described her in sexist terms in “<a href="https://wwnorton.com/books/9780393950755">The Double Helix</a>,” criticizing her “choice” not to “emphasize her feminine qualities” and her lack of “even a mild interest in clothes.” Moreover, he and Crick chose not to reveal the extent to which their model depended on her DNA photograph.</p>
<p>Even in this atmosphere, Franklin was a great scientist, as captured in this passage from her <a href="https://www.nature.com/articles/182154a0">obituary</a>, composed by her mentor, Bernal:</p>
<blockquote>
<p>She was distinguished by extreme clarity and perfection in everything she undertook. Her photographs are among the most beautiful X-ray photographs of any substance ever taken…. Her early death is a great loss to science.</p>
</blockquote>
<h2>Franklin’s reputation grew after death</h2>
<p>Franklin certainly did not sink into obscurity.</p>
<p>One of her students, eventual Nobelist <a href="https://www.nobelprize.org/prizes/chemistry/1982/summary/">Aaron Klug</a>, continued her work, helping to develop a new form of crystallography that relies on electrons instead of X-rays and advancing the understanding of the structure of viruses.</p>
<p>And of course initial skepticism about a double helix structure for DNA waned. Watson, Crick and another X-ray crystallography researcher at King’s College, Maurice Wilkins, received the <a href="https://www.nobelprize.org/prizes/medicine/1962/summary/">Nobel Prize in Physiology or Medicine</a> in 1962 for its identification. </p>
<p>Many have wondered why Franklin did not receive the Nobel Prize. First, she was never nominated, perhaps in part because of her gender. Another problem was the fact that the prize cannot be divided among more than three people, though <a href="https://www.sciencehistory.org/historical-profile/james-watson-francis-crick-maurice-wilkins-and-rosalind-franklin">some historians have argued</a> that she deserved it more than Wilkins. Perhaps the most decisive reason is that Nobel Prizes are not awarded posthumously.</p>
<p>Franklin has been memorialized in many ways. <a href="https://www.kcl.ac.uk/aboutkings/history/famouspeople/wilkinsfranklin">King’s College</a> and <a href="https://www.alliesandmorrison.com/projects/rosalind-franklin-building">Cambridge University</a> both created residence halls in her name, and <a href="http://www.bbk.ac.uk/biology/our-research/research-facilities/rosalind-franklin">Birkbeck</a> established the Rosalind Franklin Laboratory. Her portrait now hangs next to those of Watson, Crick and Wilkins in the <a href="https://www.npg.org.uk/collections/search/person/mp58704/rosalind-elsie-franklin">National Portrait Gallery</a> in London.</p>
<p><div data-react-class="InstagramEmbed" data-react-props="{"url":"https://www.instagram.com/p/BziZMHeBvAM/?igshid=1ufwhujl34l0y","accessToken":"127105130696839|b4b75090c9688d81dfd245afe6052f20"}"></div></p>
<p>And outside of Chicago is the <a href="https://www.rosalindfranklin.edu/">Rosalind Franklin University of Medicine and Science</a>, which uses photograph 51 as its logo.</p>
<p>Franklin saw herself less as a <a href="https://www.nature.com/articles/nature01399">female scientific pioneer</a> than as a researcher whose work should be assessed purely in the light of her scientific contributions. Although she was not focused on gender, perhaps her greatest and most <a href="https://www.rosalindfranklin.edu/about/facts-figures/dr-rosalind-franklin/">enduring legacy</a> is the many women who have been inspired by her example to pursue scientific careers.</p><img src="https://counter.theconversation.com/content/139249/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Richard Gunderman does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>
Franklin was born a century ago, and her X-ray crystallography work crucially contributed to determining the structure of DNA.
Richard Gunderman, Chancellor's Professor of Medicine, Liberal Arts, and Philanthropy, Indiana University
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/104297
2018-12-03T11:45:17Z
2018-12-03T11:45:17Z
Scientist at work: To take atomic-scale pictures of tiny crystals, use a huge, kilometer-long synchrotron
<figure><img src="https://images.theconversation.com/files/247512/original/file-20181127-76752-130m1ub.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C4200%2C3444&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">It takes a giant piece of equipment to look deep inside a tiny atom.</span> <span class="attribution"><a class="source" href="https://www.aps.anl.gov/About/Welcome">Advanced Photon Source at Argonne National Lab</a></span></figcaption></figure><p>It’s 4 a.m., and I’ve been up for about 20 hours straight. A loud alarm is blaring, accompanied by red strobe lights flashing. A stern voice announces, “Searching station B. Exit immediately.” It feels like an emergency, but it’s not. In fact, the alarm has already gone off 60 or 70 times today. It is a warning, letting everyone in the vicinity know I’m about to blast a high-powered X-ray beam into a small room full of electronic equipment and plumes of vaporizing liquid nitrogen.</p>
<p>In the center of this room, which is called station B, I have placed a crystal no thicker than a human hair on the tip of a tiny glass fiber. I have prepared dozens of these crystals, and am attempting to analyze all of them. </p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/240005/original/file-20181010-72110-13t1boh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/240005/original/file-20181010-72110-13t1boh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/240005/original/file-20181010-72110-13t1boh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=311&fit=crop&dpr=1 600w, https://images.theconversation.com/files/240005/original/file-20181010-72110-13t1boh.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=311&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/240005/original/file-20181010-72110-13t1boh.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=311&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/240005/original/file-20181010-72110-13t1boh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=391&fit=crop&dpr=1 754w, https://images.theconversation.com/files/240005/original/file-20181010-72110-13t1boh.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=391&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/240005/original/file-20181010-72110-13t1boh.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=391&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 author and her colleagues preparing crystalline samples to take to the synchrotron, in hopes of determining their atomic-level structures.</span>
<span class="attribution"><span class="source">Courtesy of Kerry Rippy</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>These crystals are made of <a href="https://theconversation.com/smart-windows-could-combine-solar-panels-and-tvs-too-95352">organic semiconducting materials</a>, which are used to make computer chips, LED lights, smartphone screens and solar panels. I want to find out precisely where each atom inside the crystals is located, how densely packed they are and how they interact with each other. This information will help me predict how well electricity will flow through them.</p>
<p>To see these atoms and determine their structure, I need the help of a synchrotron, which is a massive scientific instrument containing a kilometer-long loop of electrons zooming around at near the speed of light. I also need a microscope, a gyroscope, liquid nitrogen, a bit of luck, a gifted colleague and a tricycle.</p>
<h2>Getting the crystal in place</h2>
<p>The first step of this experiment involves placing the super-tiny crystals on the tip of the glass fiber. I use a needle to scrape a pile of them together onto a glass slide and put them under a microscope. The crystals are beautiful – colorful and faceted like little gemstones. I often find myself transfixed, staring with sleep-deprived eyes into the microscope, and refocusing my gaze before painstakingly coaxing one onto the tip of a glass fiber. </p>
<p>Once I’ve gotten the crystal attached to the fiber, I begin the often frustrating task of centering the crystal on the tip of a gyroscope inside station B. This device will spin the crystal around, slowly and continuously, allowing me to get X-ray images of it from all sides. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/240002/original/file-20181010-72113-1aubjn9.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/240002/original/file-20181010-72113-1aubjn9.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/240002/original/file-20181010-72113-1aubjn9.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=211&fit=crop&dpr=1 600w, https://images.theconversation.com/files/240002/original/file-20181010-72113-1aubjn9.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=211&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/240002/original/file-20181010-72113-1aubjn9.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=211&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/240002/original/file-20181010-72113-1aubjn9.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=265&fit=crop&dpr=1 754w, https://images.theconversation.com/files/240002/original/file-20181010-72113-1aubjn9.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=265&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/240002/original/file-20181010-72113-1aubjn9.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=265&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">On the left is the gyroscope, designed to rotate the crystal through a series of different angles as the X-ray beam hits it. Behind it is the detector panel which records the diffraction spots. On the right is a zoomed in picture of a single crystal, mounted on a glass fiber attached to the tip of the gyroscope.</span>
<span class="attribution"><span class="source">Kerry Rippy</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>As it spins, liquid nitrogen vapor is used to cool it down: Even at room temperature, atoms vibrate back and forth, making it hard to get clear images of them. Cooling the crystal to minus 196 degrees Celsius, the temperature of liquid nitrogen, makes the atoms stop moving so much.</p>
<h2>X-ray photography</h2>
<p>Once I have the crystal centered and cooled, I close off station B, and from a computer control hub outside of it, blast the sample with X-rays. The resulting image, called a diffraction pattern, is displayed as bright spots on an orange background. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/247144/original/file-20181125-149332-prb8n6.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/247144/original/file-20181125-149332-prb8n6.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/247144/original/file-20181125-149332-prb8n6.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=608&fit=crop&dpr=1 600w, https://images.theconversation.com/files/247144/original/file-20181125-149332-prb8n6.PNG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=608&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/247144/original/file-20181125-149332-prb8n6.PNG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=608&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/247144/original/file-20181125-149332-prb8n6.PNG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=764&fit=crop&dpr=1 754w, https://images.theconversation.com/files/247144/original/file-20181125-149332-prb8n6.PNG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=764&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/247144/original/file-20181125-149332-prb8n6.PNG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=764&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">This is a diffraction pattern that results when you shoot an X-ray beam at a single crystal.</span>
<span class="attribution"><span class="source">Kerry Rippy</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>What I am doing is not very different from taking photographs with a camera and a flash. I’m about to send light rays at an object and record how the light bounces off it. But I can’t use visible light to photograph atoms – they’re too small, and the wavelengths of light in the visible part of the spectrum are too big. X-rays have shorter wavelengths, so they will diffract, or bounce off atoms. </p>
<p>However, unlike with a camera, diffracted X-rays can’t be focused with a simple lens. Instead of a photograph-like image, the data I collect are an unfocused pattern of where the X-rays went after they bounced off the atoms in my crystal. A full set of data about one crystal is made up of these images taken from every angle all around the crystal as the gyroscope spins it. </p>
<h2>Advanced math</h2>
<p>My colleague, <a href="https://www.linkedin.com/in/nicholasjohndeweerd/">Nicholas DeWeerd</a>, sits nearby, analyzing data sets I’ve already collected. He has managed to ignore the blaring alarms and flashing lights for hours, staring at diffraction images on his screen to, in effect, turn the X-ray images from all sides of the crystal into a picture of the atoms inside the crystal itself.</p>
<p>In years past, this process might have taken years of careful calculations done by hand, but now he uses computer modeling to put all the pieces together. He is our research group’s unofficial expert at this part of the puzzle, and he loves it. “It’s like Christmas!” I hear him mutter, as he flips through twinkling images of diffraction patterns.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/247152/original/file-20181126-149338-1sjgkjx.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/247152/original/file-20181126-149338-1sjgkjx.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/247152/original/file-20181126-149338-1sjgkjx.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=332&fit=crop&dpr=1 600w, https://images.theconversation.com/files/247152/original/file-20181126-149338-1sjgkjx.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=332&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/247152/original/file-20181126-149338-1sjgkjx.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=332&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/247152/original/file-20181126-149338-1sjgkjx.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=418&fit=crop&dpr=1 754w, https://images.theconversation.com/files/247152/original/file-20181126-149338-1sjgkjx.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=418&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/247152/original/file-20181126-149338-1sjgkjx.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=418&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Solving a set of diffraction patterns produces an atomic-level picture of a crystal, showing individual molecules (left) and how they pack together to form a crystalline structure.</span>
<span class="attribution"><a class="source" href="https://doi.org/10.1002/cplu.201800451">Kerry Rippy</a>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>I smile at the enthusiasm he’s managed to maintain so late into the night, as I fire up the synchotron to get my pictures of the crystal perched in station B. I hold my breath as diffraction patterns from the first few angles pop up on the screen. Not all crystals diffract, even if I’ve set everything up perfectly. Often that’s because each crystal is made up of lots of even smaller crystals stuck together, or crystals containing too many impurities to form a repeating crystalline pattern that we can mathematically solve. </p>
<p>If this one doesn’t deliver clear images, I’ll have to start over and set up another. Luckily, in this case, the first few images that pop up show bright, clear diffraction spots. I smile and sit back to collect the rest of the data set. Now as the gyroscope whirls and the X-ray beam blasts the sample, I have a few minutes to relax.</p>
<p>I would drink some coffee to stay alert, but my hands are already shaking from caffeine overload. Instead, I call over to Nick: “I’m gonna take a lap.” I walk over to a group of tricycles sitting nearby. Normally used just to get around the large building containing the synchrotron, I find them equally helpful for a desperate attempt to wake up with some exercise. </p>
<p>As I ride, I think about the crystal mounted on the gyroscope. I’ve spent months synthesizing it, and soon I’ll have a picture of it. With the picture, I’ll gain understanding of whether the modifications that I have made to it, which make it slightly different than other materials I have made in the past, have improved it at all. If I see evidence of better packing or increased intermolecular interactions, that could mean the molecule is a good candidate for testing in electronic devices. </p>
<p>Exhausted, but happy because I’m collecting useful data, I slowly pedal around the loop, noting that the synchrotron is in high demand. When the beamline is running, it is used 24/7, which is why I’m working through the night. I was lucky to get a time slot at all. At other stations, other researchers like me are working late into the night. </p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/zfhJgY2Begk?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Taking a tricycle for a ride at the Advanced Photon Source.</span></figcaption>
</figure><img src="https://counter.theconversation.com/content/104297/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Kerry Rippy does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>
It turns out to be fairly complicated to figure out how electricity will flow through materials – a crucial question for designing new electronics and semiconductor materials.
Kerry Rippy, Ph.D. Candidate in Chemistry, Colorado State University
Licensed as Creative Commons – attribution, no derivatives.
tag:theconversation.com,2011:article/107360
2018-11-29T19:08:21Z
2018-11-29T19:08:21Z
X-rays of rocks show their super-fluid past, and reveal mineral deposits vital for batteries
<figure><img src="https://images.theconversation.com/files/247454/original/file-20181127-130878-5vud0d.png?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The green blob is metal-rich molten sulfide in an ore from the Norilsk area in Siberia, the most valuable accumulation of metals of any kind on the planet. </span> <span class="attribution"><span class="source">Steve Barnes </span>, <span class="license">Author provided</span></span></figcaption></figure><p>New X-ray technologies reveal some of the incredible processes that took place in Earth’s geological history – and should help us <a href="https://pubs.geoscienceworld.org/msa/ammin/article-abstract/102/3/473/277863/sulfide-silicate-textures-in-magmatic-ni-cu-pge?redirectedFrom=fulltext">identify new high value ores</a>.</p>
<p>We see that some of the most valuable accumulations of metals ever mined by humans formed from molten rocks, and particularly from molten sulfide minerals (those that feature sulfur as a major compenent).</p>
<p>These metal accumulations, called ore deposits, contain nickel, copper and cobalt – metals that are critical components of lithium-ion batteries. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/how-to-make-batteries-that-last-almost-forever-79750">How to make batteries that last (almost) forever</a>
</strong>
</em>
</p>
<hr>
<p>Even at present prices, large examples of such once-molten orebodies contain hundreds of billions of dollars worth of nickel, usually with valuable by-products copper, cobalt, platinum and palladium.</p>
<p>We need to keep finding new, high-grade deposits – like the recently discovered <a href="http://www.igo.com.au/irm/content/nova-project.aspx?RID=503">Nova-Bollinger orebody</a> east of Kalgoorlie in Western Australia – to keep up with the inevitable increase in demand. On current projections, a new one of these is needed every year to keep up with <a href="https://www.visualcapitalist.com/nickel-secret-driver-battery-revolution/">demand for nickel</a> in lithium-ion batteries.</p>
<p>A better understanding of how these deposits formed, deep in the Earth’s crust millions of year ago, will help us improve our exploration success rate.</p>
<h2>Plumbing system in ancient volcanoes</h2>
<p>The geological process that formed ores from molten sulfides have a lot in common with smelting (the procedure used by people for millennia to extract pure metals from sulfur-bearing minerals). </p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/247626/original/file-20181127-32236-11w1irw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/247626/original/file-20181127-32236-11w1irw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/247626/original/file-20181127-32236-11w1irw.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/247626/original/file-20181127-32236-11w1irw.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/247626/original/file-20181127-32236-11w1irw.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=425&fit=crop&dpr=1 754w, https://images.theconversation.com/files/247626/original/file-20181127-32236-11w1irw.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=425&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/247626/original/file-20181127-32236-11w1irw.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=425&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Smelting iron ore to produce steel.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/hard-work-foundry-liquid-metal-melting-792262471?src=mAgzc3ytKA0r_nN1yj10uw-1-7">from www.shutterstock.com</a></span>
</figcaption>
</figure>
<p>Millions of years ago, molten iron sulfide minerals reacted with magma in the plumbing system of ancient volcanoes – in effect scavenging the essential metals nickel, copper, cobalt and platinum. These minerals accumulated in sufficient concentrations such that they could be mined once erosion had exposed the ore at the surface.</p>
<p>Over the past few years, we have greatly improved our understanding of how these remarkable ore deposits formed. This understanding has been built up using new techniques in imaging the ores in two and three dimensions, using <a href="https://www.csiro.au/en/Research/MRF/Areas/Orebody-knowledge/Maia">X-ray technologies at CSIRO</a> and the <a href="http://archive.synchrotron.org.au/">Australian Synchrotron</a> .</p>
<p>We have been using a technique called microbeam X-ray element mapping to make detailed 2D images of the ores and the rocks they sit in. </p>
<p>Some of these images – such as the one at the top of this story – are created on the X-ray fluorescence microscopy beamline at the Australian Synchrotron, applying the <a href="https://publications.csiro.au/rpr/pub?pid=csiro:EP1311783">Maia detector system</a>. This enables gigapixel images to be collected in a matter of minutes.</p>
<h2>Like turning on the light</h2>
<p>Complementing this technique, we’ve also applied high-resolution 3D X-ray tomography – the equivalent of a hospital CT scan – to reveal in 3D details on the shape and size of the droplets of sulfide liquid that formed the ores. </p>
<p>The effect has been to turn on a light in a dark room: we have seen features inside solid rocks that have not previously been revealed.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/247456/original/file-20181127-130884-sebjs6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/247456/original/file-20181127-130884-sebjs6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=413&fit=crop&dpr=1 600w, https://images.theconversation.com/files/247456/original/file-20181127-130884-sebjs6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=413&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/247456/original/file-20181127-130884-sebjs6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=413&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/247456/original/file-20181127-130884-sebjs6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=519&fit=crop&dpr=1 754w, https://images.theconversation.com/files/247456/original/file-20181127-130884-sebjs6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=519&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/247456/original/file-20181127-130884-sebjs6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=519&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">An X-ray tomography image (CT scan) of an ore sample showing frozen droplets of sulfide liquid as red blobs.</span>
<span class="attribution"><span class="source">Steve Barnes</span>, <span class="license">Author provided</span></span>
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<p>Sulfide liquids, it turns out, have remarkable physical properties. They behave like a hot knife through butter: so corrosive that they can melt their way through solid rocks, ending up in some cases tens of metres away from their original host rocks.</p>
<p>We now know that orebodies form in very particular parts of the ancient “plumbing systems” that fed magmas to the volcanoes above. The ores formed where the flowing magma was so hot that it melted the rocks around it. </p>
<p>The “hot knife” sulfide liquid then continued to melt its way into the floor, such that the ores are now found injected into the underlying non-igneous rocks.</p>
<p>In the case of the supergiant nickel ores of the Norilsk region in Siberia, the rocks that melted also supplied the sulfur to form the orebodies. </p>
<p>In fact, so much sulfur was released by this process that much of it, along with vast amounts of nickel, was actually erupted into the atmosphere, contributing to the <a href="https://theconversation.com/death-metal-how-nickel-played-a-role-in-the-worlds-worst-mass-extinction-74754">greatest mass extinction in Earth history</a>.</p>
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Read more:
<a href="https://theconversation.com/death-metal-how-nickel-played-a-role-in-the-worlds-worst-mass-extinction-74754">Death metal: how nickel played a role in the world's worst mass extinction</a>
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<h2>Needle in haystack targets</h2>
<p>This type of work helps us improve geological models the exploration industry uses to explore for new deposits. </p>
<p>Nickel sulfide ores are notoriously difficult “needle in haystack” targets, and we need to bring our best combination of geophysical detection techniques and predictive geological models.</p>
<p>So where next? </p>
<p>Research is ongoing: both into the fundamental processes of ore formation and into the implications of this understanding for where and how to look for new deposits. </p>
<p>Some of the minerals that form along with the sulfide ores can be dispersed by erosion, and rivers transport them long distances from the deposits themselves. </p>
<p>We are learning how to recognise these chemically distinctive grains, in the same way diamond explorers use “indicator minerals” to find fertile kimberlites (the source rock for diamonds). </p>
<p>We’re also doing more fundamental research, such as using analogue material (salt water and olive oil work very well, it turns out) and computational fluid dynamic models on supercomputers to look into the physics of how magmatic ores come to look the way they do.</p><img src="https://counter.theconversation.com/content/107360/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Steve Barnes receives funding from the CSIRO Research Office Science Leader fund. The synchrotron XRF mapping was carried out on the XFM beamline of the Australian Synchrotron, Clayton, Victoria, operated by ANSTO.</span></em></p>
Liquid minerals containing sulfur behave like a hot knife through butter – they’re so corrosive they can melt their way through solid rock.
Steve Barnes, Geologist, CSIRO
Licensed as Creative Commons – attribution, no derivatives.