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    Matthew Shoulders named head of the Department of Chemistry

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    Matthew D. Shoulders, the Class of 1942 Professor of Chemistry, a MacVicar Faculty Fellow, and an associate member of the Broad Institute of MIT and Harvard, has been named head of the MIT Department of Chemistry, effective Jan. 16, 2026. “Matt has made pioneering contributions to the chemistry research community through his research on mechanisms of proteostasis and his development of next-generation techniques to address challenges in biomedicine and agriculture,” says Nergis Mavalvala, dean of the MIT School of Science and the Curtis and Kathleen Marble Professor of Astrophysics. “He is also a dedicated educator, beloved by undergraduates and graduates alike. I know the department will be in good hands as we double down on our commitment to world-leading research and education in the face of financial headwinds.”Shoulders succeeds Troy Van Voorhis, the Robert T. Haslam and Bradley Dewey Professor of Chemistry, who has been at the helm since October 2019.“I am tremendously grateful to Troy for his leadership the past six years, building a fantastic community here in our department. We face challenges, but also many exciting opportunities, as a department in the years to come,” says Shoulders. “One thing is certain: Chemistry innovations are critical to solving pressing global challenges. Through the research that we do and the scientists we train, our department has a huge role to play in shaping the future.”Shoulders studies how cells fold proteins, and he develops ​and applies novel protein engineering techniques to challenges in biotechnology. His work across chemistry and biochemistry fields including proteostasis, extracellular matrix biology, virology, evolution, and synthetic biology is yielding not just important insights into topics like how cells build healthy tissues and how proteins evolve, but also influencing approaches to disease therapy and biotechnology development.“Matt is an outstanding researcher whose work touches on fundamental questions about how the cell machinery directs the synthesis and folding of proteins. His discoveries about how that machinery breaks down as a result of mutations or in response to stress has a fundamental impact on how we think about and treat human diseases,” says Van Voorhis.In one part of Matt’s current research program, he is studying how protein folding systems in cells — known as chaperones — shape the evolution of their clients. Amongst other discoveries, his lab has shown that viral pathogens hijack human chaperones to enable their rapid evolution and escape from host immunity. In related recent work, they have discovered that these same chaperones can promote access to malignancy-driving mutations in tumors. Beyond fundamental insights into evolutionary biology, these findings hold potential to open new therapeutic strategies to target cancer and viral infections.“Matt’s ability to see both the details and the big picture makes him an outstanding researcher and a natural leader for the department,” says Timothy Swager, the John D. MacArthur Professor of Chemistry. “MIT Chemistry can only benefit from his dedication to understanding and addressing the parts and the whole.” Shoulders also leads a food security project through the Abdul Latif Jameel Water and Food Systems Lab (J-WAFS). Shoulders, along with MIT Research Scientist Robbie Wilson, assembled an interdisciplinary team based at MIT to enhance climate resilience in agriculture by improving one of the most inefficient aspects of photosynthesis, the carbon dioxide-fixing plant enzyme RuBisCO. J-WAFS funded this high-risk, high-reward MIT Grand Challenge project in 2023, and it has received further support from federal research agencies and the Grantham Foundation for the Protection of the Environment. “Our collaborative team of biochemists and synthetic biologists, computational biologists, and chemists is deeply integrated with plant biologists, creating a robust feedback loop for enzyme engineering,” Shoulders says. “Together, this team is making a concerted effort using state-of-the-art techniques to engineer crop RuBisCO with an eye to helping make meaningful gains in securing a stable crop supply, hopefully with accompanying improvements in both food and water security.”In addition to his research contributions, Shoulders has taught multiple classes for Course V, including 5.54 (Advances in Chemical Biology) and 5.111 (Principles of Chemical Science), along with a number of other key chemistry classes. His contributions to a 5.111 “bootcamp” through the MITx platform served to address gaps in the classroom curriculum by providing online tools to help undergraduate students better grasp the material in the chemistry General Institute Requirement (GIR). His development of Guided Learning Demonstrations to support first-year chemistry courses at MIT has helped bring the lab to the GIR, and also contributed to the popularity of 5.111 courses offered regularly via MITx.“I have had the pleasure of teaching with Matt on several occasions, and he is a fantastic educator. He is an innovator both inside and outside the classroom and has an unwavering commitment to his students’ success,” says Van Voorhis of Shoulders, who was named a 2022 MacVicar Faculty Fellow, and who received a Committed to Caring award through the Office of Graduate Education.Shoulders also founded the MIT Homeschool Internship Program for Science and Technology, which brings high school students to campus for paid summer research experiences in labs across the Institute.He is a founding member of the Department of Chemistry’s Quality of Life Committee and chair for the last six years, helping to improve all aspects of opportunity, professional development, and experience in the department: “countless changes that have helped make MIT a better place for all,” as Van Voorhis notes, including creating a peer mentoring program for graduate students and establishing universal graduate student exit interviews to collect data for department-wide assessment and improvement.At the Institute level, Shoulders has served on the Committee on Graduate Programs, Committee on Sexual Misconduct Prevention and Response (in which he co-chaired the provost’s working group on the Faculty and Staff Sexual Misconduct Survey), and the Committee on Assessment of Biohazards and Embryonic Stem Cell Research Oversight, among other roles.Shoulders graduated summa cum laude from Virginia Tech in 2004, earning a BS in chemistry with a minor in biochemistry. He earned a PhD in chemistry at the University of Wisconsin at Madison in 2009 under Professor Ronald Raines. Following an American Cancer Society Postdoctoral Fellowship at Scripps Research Institute, working with professors Jeffery Kelly and Luke Wiseman, Shoulders joined the MIT Department of Chemistry faculty as an assistant professor in 2012. Shoulders also serves as an associate member of the Broad Institute and an investigator at the Center for Musculoskeletal Research at Massachusetts General Hospital.Among his many awards, Shoulders has received a NIH Director’s New Innovator Award under the NIH High-Risk, High-Reward Research Program; an NSF CAREER Award; an American Cancer Society Research Scholar Award; the Camille Dreyfus Teacher-Scholar Award; and most recently the Ono Pharma Foundation Breakthrough Science Award. More

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      in Security

      A cysteine-rich diet may promote regeneration of the intestinal lining, study suggests

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      A diet rich in the amino acid cysteine may have rejuvenating effects in the small intestine, according to a new study from MIT. This amino acid, the researchers discovered, can turn on an immune signaling pathway that helps stem cells to regrow new intestinal tissue.This enhanced regeneration may help to heal injuries from radiation, which often occur in patients undergoing radiation therapy for cancer. The research was conducted in mice, but if future research shows similar results in humans, then delivering elevated quantities of cysteine, through diet or supplements, could offer a new strategy to help damaged tissue heal faster, the researchers say.“The study suggests that if we give these patients a cysteine-rich diet or cysteine supplementation, perhaps we can dampen some of the chemotherapy or radiation-induced injury,” says Omer Yilmaz, director of the MIT Stem Cell Initiative, an associate professor of biology at MIT, and a member of MIT’s Koch Institute for Integrative Cancer Research. “The beauty here is we’re not using a synthetic molecule; we’re exploiting a natural dietary compound.”While previous research has shown that certain types of diets, including low-calorie diets, can enhance intestinal stem cell activity, the new study is the first to identify a single nutrient that can help intestinal cells to regenerate.Yilmaz is the senior author of the study, which appears today in Nature. Koch Institute postdoc Fangtao Chi is the paper’s lead author.Boosting regenerationIt is well-established that diet can affect overall health: High-fat diets can lead to obesity, diabetes, and other health problems, while low-calorie diets have been shown to extend lifespans in many species. In recent years, Yilmaz’s lab has investigated how different types of diets influence stem cell regeneration, and found that high-fat diets, as well as short periods of fasting, can enhance stem cell activity in different ways.“We know that macro diets such as high-sugar diets, high-fat diets, and low-calorie diets have a clear impact on health. But at the granular level, we know much less about how individual nutrients impact stem cell fate decisions, as well as tissue function and overall tissue health,” Yilmaz says.In their new study, the researchers began by feeding mice a diet high in one of 20 different amino acids, the building blocks of proteins. For each group, they measured how the diet affected intestinal stem cell regeneration. Among these amino acids, cysteine had the most dramatic effects on stem cells and progenitor cells (immature cells that differentiate into adult intestinal cells).Further studies revealed that cysteine initiates a chain of events leading to the activation of a population of immune cells called CD8 T cells. When cells in the lining of the intestine absorb cysteine from digested food, they convert it into CoA, a cofactor that is released into the mucosal lining of the intestine. There, CD8 T cells absorb CoA, which stimulates them to begin proliferating and producing a cytokine called IL-22.IL-22 is an important player in the regulation of intestinal stem cell regeneration, but until now, it wasn’t known that CD8 T cells can produce it to boost intestinal stem cells. Once activated, those IL-22-releasing T cells are primed to help combat any kind of injury that could occur within the intestinal lining.“What’s really exciting here is that feeding mice a cysteine-rich diet leads to the expansion of an immune cell population that we typically don’t associate with IL-22 production and the regulation of intestinal stemness,” Yilmaz says. “What happens in a cysteine-rich diet is that the pool of cells that make IL-22 increases, particularly the CD8 T-cell fraction.”These T cells tend to congregate within the lining of the intestine, so they are already in position when needed. The researchers found that the stimulation of CD8 T cells occurred primarily in the small intestine, not in any other part of the digestive tract, which they believe is because most of the protein that we consume is absorbed by the small intestine.Healing the intestineIn this study, the researchers showed that regeneration stimulated by a cysteine-rich diet could help to repair radiation damage to the intestinal lining. Also, in work that has not been published yet, they showed that a high-cysteine diet had a regenerative effect following treatment with a chemotherapy drug called 5-fluorouracil. This drug, which is used to treat colon and pancreatic cancers, can also damage the intestinal lining.Cysteine is found in many high-protein foods, including meat, dairy products, legumes, and nuts. The body can also synthesize its own cysteine, by converting the amino acid methionine to cysteine — a process that takes place in the liver. However, cysteine produced in the liver is distributed through the entire body and doesn’t lead to a buildup in the small intestine the way that consuming cysteine in the diet does.“With our high-cysteine diet, the gut is the first place that sees a high amount of cysteine,” Chi says.Cysteine has been previously shown to have antioxidant effects, which are also beneficial, but this study is the first to demonstrate its effect on intestinal stem cell regeneration. The researchers now hope to study whether it may also help other types of stem cells regenerate new tissues. In one ongoing study, they are investigating whether cysteine might stimulate hair follicle regeneration.They also plan to further investigate some of the other amino acids that appear to influence stem cell regeneration.“I think we’re going to uncover multiple new mechanisms for how these amino acids regulate cell fate decisions and gut health in the small intestine and colon,” Yilmaz says.The research was funded, in part, by the National Institutes of Health, the V Foundation, the Kathy and Curt Marble Cancer Research Award, the Koch Institute-Dana-Farber/Harvard Cancer Center Bridge Project, the American Federation for Aging Research, the MIT Stem Cell Initiative, and the Koch Institute Support (core) Grant from the National Cancer Institute. More

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      in Energy

      MIT engineers develop a magnetic transistor for more energy-efficient electronics

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      Transistors, the building blocks of modern electronics, are typically made of silicon. Because it’s a semiconductor, this material can control the flow of electricity in a circuit. But silicon has fundamental physical limits that restrict how compact and energy-efficient a transistor can be.MIT researchers have now replaced silicon with a magnetic semiconductor, creating a magnetic transistor that could enable smaller, faster, and more energy-efficient circuits. The material’s magnetism strongly influences its electronic behavior, leading to more efficient control of the flow of electricity. The team used a novel magnetic material and an optimization process that reduces the material’s defects, which boosts the transistor’s performance.The material’s unique magnetic properties also allow for transistors with built-in memory, which would simplify circuit design and unlock new applications for high-performance electronics.“People have known about magnets for thousands of years, but there are very limited ways to incorporate magnetism into electronics. We have shown a new way to efficiently utilize magnetism that opens up a lot of possibilities for future applications and research,” says Chung-Tao Chou, an MIT graduate student in the departments of Electrical Engineering and Computer Science (EECS) and Physics, and co-lead author of a paper on this advance.Chou is joined on the paper by co-lead author Eugene Park, a graduate student in the Department of Materials Science and Engineering (DMSE); Julian Klein, a DMSE research scientist; Josep Ingla-Aynes, a postdoc in the MIT Plasma Science and Fusion Center; Jagadeesh S. Moodera, a senior research scientist in the Department of Physics; and senior authors Frances Ross, TDK Professor in DMSE; and Luqiao Liu, an associate professor in EECS, and a member of the Research Laboratory of Electronics; as well as others at the University of Chemistry and Technology in Prague. The paper appears today in Physical Review Letters.Overcoming the limitsIn an electronic device, silicon semiconductor transistors act like tiny light switches that turn a circuit on and off, or amplify weak signals in a communication system. They do this using a small input voltage.But a fundamental physical limit of silicon semiconductors prevents a transistor from operating below a certain voltage, which hinders its energy efficiency.To make more efficient electronics, researchers have spent decades working toward magnetic transistors that utilize electron spin to control the flow of electricity. Electron spin is a fundamental property that enables electrons to behave like tiny magnets.So far, scientists have mostly been limited to using certain magnetic materials. These lack the favorable electronic properties of semiconductors, constraining device performance.“In this work, we combine magnetism and semiconductor physics to realize useful spintronic devices,” Liu says.The researchers replace the silicon in the surface layer of a transistor with chromium sulfur bromide, a two-dimensional material that acts as a magnetic semiconductor.Due to the material’s structure, researchers can switch between two magnetic states very cleanly. This makes it ideal for use in a transistor that smoothly switches between “on” and “off.”“One of the biggest challenges we faced was finding the right material. We tried many other materials that didn’t work,” Chou says.They discovered that changing these magnetic states modifies the material’s electronic properties, enabling low-energy operation. And unlike many other 2D materials, chromium sulfur bromide remains stable in air.To make a transistor, the researchers pattern electrodes onto a silicon substrate, then carefully align and transfer the 2D material on top. They use tape to pick up a tiny piece of material, only a few tens of nanometers thick, and place it onto the substrate.“A lot of researchers will use solvents or glue to do the transfer, but transistors require a very clean surface. We eliminate all those risks by simplifying this step,” Chou says.Leveraging magnetismThis lack of contamination enables their device to outperform existing magnetic transistors. Most others can only create a weak magnetic effect, changing the flow of current by a few percent or less. Their new transistor can switch or amplify the electric current by a factor of 10.They use an external magnetic field to change the magnetic state of the material, switching the transistor using significantly less energy than would usually be required.The material also allows them to control the magnetic states with electric current. This is important because engineers cannot apply magnetic fields to individual transistors in an electronic device. They need to control each one electrically.The material’s magnetic properties could also enable transistors with built-in memory, simplifying the design of logic or memory circuits.A typical memory device has a magnetic cell to store information and a transistor to read it out. Their method can combine both into one magnetic transistor.“Now, not only are transistors turning on and off, they are also remembering information. And because we can switch the transistor with greater magnitude, the signal is much stronger so we can read out the information faster, and in a much more reliable way,” Liu says.Building on this demonstration, the researchers plan to further study the use of electrical current to control the device. They are also working to make their method scalable so they can fabricate arrays of transistors.This research was supported, in part, by the Semiconductor Research Corporation, the U.S. Defense Advanced Research Projects Agency (DARPA), the U.S. National Science Foundation (NSF), the U.S. Department of Energy, the U.S. Army Research Office, and the Czech Ministry of Education, Youth, and Sports. The work was partially carried out at the MIT.nano facilities. More

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      in Environment

      MIT geologists discover where energy goes during an earthquake

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      The ground-shaking that an earthquake generates is only a fraction of the total energy that a quake releases. A quake can also generate a flash of heat, along with a domino-like fracturing of underground rocks. But exactly how much energy goes into each of these three processes is exceedingly difficult, if not impossible, to measure in the field.Now MIT geologists have traced the energy that is released by “lab quakes” — miniature analogs of natural earthquakes that are carefully triggered in a controlled laboratory setting. For the first time, they have quantified the complete energy budget of such quakes, in terms of the fraction of energy that goes into heat, shaking, and fracturing.They found that only about 10 percent of a lab quake’s energy causes physical shaking. An even smaller fraction — less than 1 percent — goes into breaking up rock and creating new surfaces. The overwhelming portion of a quake’s energy — on average 80 percent — goes into heating up the immediate region around a quake’s epicenter. In fact, the researchers observed that a lab quake can produce a temperature spike hot enough to melt surrounding material and turn it briefly into liquid melt.The geologists also found that a quake’s energy budget depends on a region’s deformation history — the degree to which rocks have been shifted and disturbed by previous tectonic motions. The fractions of quake energy that produce heat, shaking, and rock fracturing can shift depending on what the region has experienced in the past.“The deformation history — essentially what the rock remembers — really influences how destructive an earthquake could be,” says Daniel Ortega-Arroyo, a graduate student in MIT’s Department of Earth, Atmospheric and Planetary Sciences (EAPS). “That history affects a lot of the material properties in the rock, and it dictates to some degree how it is going to slip.”The team’s lab quakes are a simplified analog of what occurs during a natural earthquake. Down the road, their results could help seismologists predict the likelihood of earthquakes in regions that are prone to seismic events. For instance, if scientists have an idea of how much shaking a quake generated in the past, they might be able to estimate the degree to which the quake’s energy also affected rocks deep underground by melting or breaking them apart. This in turn could reveal how much more or less vulnerable the region is to future quakes.“We could never reproduce the complexity of the Earth, so we have to isolate the physics of what is happening, in these lab quakes,” says Matěj Peč, associate professor of geophysics at MIT. “We hope to understand these processes and try to extrapolate them to nature.”Peč (pronounced “Peck”) and Ortega-Arroyo reported their results on Aug. 28 in the journal AGU Advances. Their MIT co-authors are Hoagy O’Ghaffari and Camilla Cattania, along with Zheng Gong and Roger Fu at Harvard University and Markus Ohl and Oliver Plümper at Utrecht University in the Netherlands.Under the surfaceEarthquakes are driven by energy that is stored up in rocks over millions of years. As tectonic plates slowly grind against each other, stress accumulates through the crust. When rocks are pushed past their material strength, they can suddenly slip along a narrow zone, creating a geologic fault. As rocks slip on either side of the fault, they produce seismic waves that ripple outward and upward.We perceive an earthquake’s energy mainly in the form of ground shaking, which can be measured using seismometers and other ground-based instruments. But the other two major forms of a quake’s energy — heat and underground fracturing — are largely inaccessible with current technologies.“Unlike the weather, where we can see daily patterns and measure a number of pertinent variables, it’s very hard to do that very deep in the Earth,” Ortega-Arroyo says. “We don’t know what’s happening to the rocks themselves, and the timescales over which earthquakes repeat within a fault zone are on the century-to-millenia timescales, making any sort of actionable forecast challenging.”To get an idea of how an earthquake’s energy is partitioned, and how that energy budget might affect a region’s seismic risk, he and Peč went into the lab. Over the last seven years, Peč’s group at MIT has developed methods and instrumentation to simulate seismic events, at the microscale, in an effort to understand how earthquakes at the macroscale may play out.“We are focusing on what’s happening on a really small scale, where we can control many aspects of failure and try to understand it before we can do any scaling to nature,” Ortega-Arroyo says.MicroshakesFor their new study, the team generated miniature lab quakes that simulate a seismic slipping of rocks along a fault zone. They worked with small samples of granite, which are representative of rocks in the seismogenic layer — the geologic region in the continental crust where earthquakes typically originate. They ground up the granite into a fine powder and mixed the crushed granite with a much finer powder of magnetic particles, which they used as a sort of internal temperature gauge. (A particle’s magnetic field strength will change in response to a fluctuation in temperature.)The researchers placed samples of the powdered granite — each about 10 square millimeters and 1 millimeter thin — between two small pistons and wrapped the ensemble in a gold jacket. They then applied a strong magnetic field to orient the powder’s magnetic particles in the same initial direction and to the same field strength. They reasoned that any change in the particles’ orientation and field strength afterward should be a sign of how much heat that region experienced as a result of any seismic event.Once samples were prepared, the team placed them one at a time into a custom-built apparatus that the researchers tuned to apply steadily increasing pressure, similar to the pressures that rocks experience in the Earth’s seismogenic layer, about 10 to 20 kilometers below the surface. They used custom-made piezoelectric sensors, developed by co-author O’Ghaffari, which they attached to either end of a sample to measure any shaking that occurred as they increased the stress on the sample.They observed that at certain stresses, some samples slipped, producing a microscale seismic event similar to an earthquake. By analyzing the magnetic particles in the samples after the fact, they obtained an estimate of how much each sample was temporarily heated — a method developed in collaboration with Roger Fu’s lab at Harvard University. They also estimated the amount of shaking each sample experienced, using measurements from the piezoelectric sensor and numerical models. The researchers also examined each sample under the microscope, at different magnifications, to assess how the size of the granite grains changed — whether and how many grains broke into smaller pieces, for instance.From all these measurements, the team was able to estimate each lab quake’s energy budget. On average, they found that about 80 percent of a quake’s energy goes into heat, while 10 percent generates shaking, and less than 1 percent goes into rock fracturing, or creating new, smaller particle surfaces. “In some instances we saw that, close to the fault, the sample went from room temperature to 1,200 degrees Celsius in a matter of microseconds, and then immediately cooled down once the motion stopped,” Ortega-Arroyo says. “And in one sample, we saw the fault move by about 100 microns, which implies slip velocities essentially about 10 meters per second. It moves very fast, though it doesn’t last very long.”The researchers suspect that similar processes play out in actual, kilometer-scale quakes.“Our experiments offer an integrated approach that provides one of the most complete views of the physics of earthquake-like ruptures in rocks to date,” Peč says. “This will provide clues on how to improve our current earthquake models and natural hazard mitigation.”This research was supported, in part, by the National Science Foundation. More

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      in Environment

      Simpler models can outperform deep learning at climate prediction

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      Environmental scientists are increasingly using enormous artificial intelligence models to make predictions about changes in weather and climate, but a new study by MIT researchers shows that bigger models are not always better.The team demonstrates that, in certain climate scenarios, much simpler, physics-based models can generate more accurate predictions than state-of-the-art deep-learning models.Their analysis also reveals that a benchmarking technique commonly used to evaluate machine-learning techniques for climate predictions can be distorted by natural variations in the data, like fluctuations in weather patterns. This could lead someone to believe a deep-learning model makes more accurate predictions when that is not the case.The researchers developed a more robust way of evaluating these techniques, which shows that, while simple models are more accurate when estimating regional surface temperatures, deep-learning approaches can be the best choice for estimating local rainfall.They used these results to enhance a simulation tool known as a climate emulator, which can rapidly simulate the effect of human activities onto a future climate.The researchers see their work as a “cautionary tale” about the risk of deploying large AI models for climate science. While deep-learning models have shown incredible success in domains such as natural language, climate science contains a proven set of physical laws and approximations, and the challenge becomes how to incorporate those into AI models.“We are trying to develop models that are going to be useful and relevant for the kinds of things that decision-makers need going forward when making climate policy choices. While it might be attractive to use the latest, big-picture machine-learning model on a climate problem, what this study shows is that stepping back and really thinking about the problem fundamentals is important and useful,” says study senior author Noelle Selin, a professor in the MIT Institute for Data, Systems, and Society (IDSS) and the Department of Earth, Atmospheric and Planetary Sciences (EAPS).Selin’s co-authors are lead author Björn Lütjens, a former EAPS postdoc who is now a research scientist at IBM Research; senior author Raffaele Ferrari, the Cecil and Ida Green Professor of Oceanography in EAPS and co-director of the Lorenz Center; and Duncan Watson-Parris, assistant professor at the University of California at San Diego. Selin and Ferrari are also co-principal investigators of the Bringing Computation to the Climate Challenge project, out of which this research emerged. The paper appears today in the Journal of Advances in Modeling Earth Systems.Comparing emulatorsBecause the Earth’s climate is so complex, running a state-of-the-art climate model to predict how pollution levels will impact environmental factors like temperature can take weeks on the world’s most powerful supercomputers.Scientists often create climate emulators, simpler approximations of a state-of-the art climate model, which are faster and more accessible. A policymaker could use a climate emulator to see how alternative assumptions on greenhouse gas emissions would affect future temperatures, helping them develop regulations.But an emulator isn’t very useful if it makes inaccurate predictions about the local impacts of climate change. While deep learning has become increasingly popular for emulation, few studies have explored whether these models perform better than tried-and-true approaches.The MIT researchers performed such a study. They compared a traditional technique called linear pattern scaling (LPS) with a deep-learning model using a common benchmark dataset for evaluating climate emulators.Their results showed that LPS outperformed deep-learning models on predicting nearly all parameters they tested, including temperature and precipitation.“Large AI methods are very appealing to scientists, but they rarely solve a completely new problem, so implementing an existing solution first is necessary to find out whether the complex machine-learning approach actually improves upon it,” says Lütjens.Some initial results seemed to fly in the face of the researchers’ domain knowledge. The powerful deep-learning model should have been more accurate when making predictions about precipitation, since those data don’t follow a linear pattern.They found that the high amount of natural variability in climate model runs can cause the deep learning model to perform poorly on unpredictable long-term oscillations, like El Niño/La Niña. This skews the benchmarking scores in favor of LPS, which averages out those oscillations.Constructing a new evaluationFrom there, the researchers constructed a new evaluation with more data that address natural climate variability. With this new evaluation, the deep-learning model performed slightly better than LPS for local precipitation, but LPS was still more accurate for temperature predictions.“It is important to use the modeling tool that is right for the problem, but in order to do that you also have to set up the problem the right way in the first place,” Selin says.Based on these results, the researchers incorporated LPS into a climate emulation platform to predict local temperature changes in different emission scenarios.“We are not advocating that LPS should always be the goal. It still has limitations. For instance, LPS doesn’t predict variability or extreme weather events,” Ferrari adds.Rather, they hope their results emphasize the need to develop better benchmarking techniques, which could provide a fuller picture of which climate emulation technique is best suited for a particular situation.“With an improved climate emulation benchmark, we could use more complex machine-learning methods to explore problems that are currently very hard to address, like the impacts of aerosols or estimations of extreme precipitation,” Lütjens says.Ultimately, more accurate benchmarking techniques will help ensure policymakers are making decisions based on the best available information.The researchers hope others build on their analysis, perhaps by studying additional improvements to climate emulation methods and benchmarks. Such research could explore impact-oriented metrics like drought indicators and wildfire risks, or new variables like regional wind speeds.This research is funded, in part, by Schmidt Sciences, LLC, and is part of the MIT Climate Grand Challenges team for “Bringing Computation to the Climate Challenge.” More

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      in Security

      MIT chemists boost the efficiency of a key enzyme in photosynthesis

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      During photosynthesis, an enzyme called rubisco catalyzes a key reaction — the incorporation of carbon dioxide into organic compounds to create sugars. However, rubisco, which is believed to be the most abundant enzyme on Earth, is very inefficient compared to the other enzymes involved in photosynthesis.MIT chemists have now shown that they can greatly enhance a version of rubisco found in bacteria from a low-oxygen environment. Using a process known as directed evolution, they identified mutations that could boost rubisco’s catalytic efficiency by up to 25 percent.The researchers now plan to apply their technique to forms of rubisco that could be used in plants to help boost their rates of photosynthesis, which could potentially improve crop yields.“This is, I think, a compelling demonstration of successful improvement of a rubisco’s enzymatic properties, holding out a lot of hope for engineering other forms of rubisco,” says Matthew Shoulders, the Class of 1942 Professor of Chemistry at MIT.Shoulders and Robert Wilson, a research scientist in the Department of Chemistry, are the senior authors of the new study, which appears this week in the Proceedings of the National Academy of Sciences. MIT graduate student Julie McDonald is the paper’s lead author.Evolution of efficiencyWhen plants or photosynthetic bacteria absorb energy from the sun, they first convert it into energy-storing molecules such as ATP. In the next phase of photosynthesis, cells use that energy to transform a molecule known as ribulose bisphosphate into glucose, which requires several additional reactions. Rubisco catalyzes the first of those reactions, known as carboxylation. During that reaction, carbon from CO2 is added to ribulose bisphosphate.Compared to the other enzymes involved in photosynthesis, rubisco is very slow, catalyzing only one to 10 reactions per second. Additionally, rubisco can also interact with oxygen, leading to a competing reaction that incorporates oxygen instead of carbon — a process that wastes some of the energy absorbed from sunlight.“For protein engineers, that’s a really attractive set of problems because those traits seem like things that you could hopefully make better by making changes to the enzyme’s amino acid sequence,” McDonald says.Previous research has led to improvement in rubisco’s stability and solubility, which resulted in small gains in enzyme efficiency. Most of those studies used directed evolution — a technique in which a naturally occurring protein is randomly mutated and then screened for the emergence of new, desirable features.This process is usually done using error-prone PCR, a technique that first generates mutations in vitro (outside of the cell), typically introducing only one or two mutations in the target gene. In past studies on rubisco, this library of mutations was then introduced into bacteria that grow at a rate relative to rubisco activity. Limitations in error-prone PCR and in the efficiency of introducing new genes restrict the total number of mutations that can be generated and screened using this approach. Manual mutagenesis and selection steps also add more time to the process over multiple rounds of evolution.The MIT team instead used a newer mutagenesis technique that the Shoulders Lab previously developed, called MutaT7. This technique allows the researchers to perform both mutagenesis and screening in living cells, which dramatically speeds up the process. Their technique also enables them to mutate the target gene at a higher rate.“Our continuous directed evolution technique allows you to look at a lot more mutations in the enzyme than has been done in the past,” McDonald says.Better rubiscoFor this study, the researchers began with a version of rubisco, isolated from a family of semi-anaerobic bacteria known as Gallionellaceae, that is one of the fastest rubisco found in nature. During the directed evolution experiments, which were conducted in E. coli, the researchers kept the microbes in an environment with atmospheric levels of oxygen, creating evolutionary pressure to adapt to oxygen.After six rounds of directed evolution, the researchers identified three different mutations that improved the rubisco’s resistance to oxygen. Each of these mutations are located near the enzyme’s active site (where it performs carboxylation or oxygenation). The researchers believe that these mutations improve the enzyme’s ability to preferentially interact with carbon dioxide over oxygen, which leads to an overall increase in carboxylation efficiency.“The underlying question here is: Can you alter and improve the kinetic properties of rubisco to operate better in environments where you want it to operate better?” Shoulders says. “What changed through the directed evolution process was that rubisco began to like to react with oxygen less. That allows this rubisco to function well in an oxygen-rich environment, where normally it would constantly get distracted and react with oxygen, which you don’t want it to do.”In ongoing work, the researchers are applying this approach to other forms of rubisco, including rubisco from plants. Plants are believed to lose about 30 percent of the energy from the sunlight they absorb through a process called photorespiration, which occurs when rubisco acts on oxygen instead of carbon dioxide.“This really opens the door to a lot of exciting new research, and it’s a step beyond the types of engineering that have dominated rubisco engineering in the past,” Wilson says. “There are definite benefits to agricultural productivity that could be leveraged through a better rubisco.”The research was funded, in part, by the National Science Foundation, the National Institutes of Health, an Abdul Latif Jameel Water and Food Systems Lab Grand Challenge grant, and a Martin Family Society Fellowship for Sustainability. More

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      in Environment

      Island rivers carve passageways through coral reefs

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      Volcanic islands, such as the islands of Hawaii and the Caribbean, are surrounded by coral reefs that encircle an island in a labyrinthine, living ring. A coral reef is punctured at points by reef passes — wide channels that cut through the coral and serve as conduits for ocean water and nutrients to filter in and out. These watery passageways provide circulation throughout a reef, helping to maintain the health of corals by flushing out freshwater and transporting key nutrients.Now, MIT scientists have found that reef passes are shaped by island rivers. In a study appearing today in the journal Geophysical Research Letters, the team shows that the locations of reef passes along coral reefs line up with where rivers funnel out from an island’s coast.Their findings provide the first quantitative evidence of rivers forming reef passes.  Scientists and explorers had speculated that this may be the case: Where a river on a volcanic island meets the coast, the freshwater and sediment it carries flows toward the reef, where a strong enough flow can tunnel into the surrounding coral. This idea has been proposed from time to time but never quantitatively tested, until now.“The results of this study help us to understand how the health of coral reefs depends on the islands they surround,” says study author Taylor Perron, the Cecil and Ida Green Professor of Earth, Atmospheric and Planetary Sciences at MIT.“A lot of discussion around rivers and their impact on reefs today has been negative because of human impact and the effects of agricultural practices,” adds lead author Megan Gillen, a graduate student in the MIT-WHOI Joint Program in Oceanography. “This study shows the potential long-term benefits rivers can have on reefs, which I hope reshapes the paradigm and highlights the natural state of rivers interacting with reefs.”The study’s other co-author is Andrew Ashton of the Woods Hole Oceanographic Institution.Drawing the linesThe new study is based on the team’s analysis of the Society Islands, a chain of islands in the South Pacific Ocean that includes Tahiti and Bora Bora. Gillen, who joined the MIT-WHOI program in 2020, was interested in exploring connections between coral reefs and the islands they surround. With limited options for on-site work during the Covid-19 pandemic, she and Perron looked to see what they could learn through satellite images and maps of island topography. They did a quick search using Google Earth and zeroed in on the Society Islands for their uniquely visible reef and island features.“The islands in this chain have these iconic, beautiful reefs, and we kept noticing these reef passes that seemed to align with deeply embayed portions of the coastline,” Gillen says. “We started asking ourselves, is there a correlation here?”Viewed from above, the coral reefs that circle some islands bear what look to be notches, like cracks that run straight through a ring. These breaks in the coral are reef passes — large channels that run tens of meters deep and can be wide enough for some boats to pass through. On first look, Gillen noticed that the most obvious reef passes seemed to line up with flooded river valleys — depressions in the coastline that have been eroded over time by island rivers that flow toward the ocean. She wondered whether and to what extent island rivers might shape reef passes.“People have examined the flow through reef passes to understand how ocean waves and seawater circulate in and out of lagoons, but there have been no claims of how these passes are formed,” Gillen says. “Reef pass formation has been mentioned infrequently in the literature, and people haven’t explored it in depth.”Reefs unraveledTo get a detailed view of the topography in and around the Society Islands, the team used data from the NASA Shuttle Radar Topography Mission — two radar antennae that flew aboard the space shuttle in 1999 and measured the topography across 80 percent of the Earth’s surface.The researchers used the mission’s topographic data in the Society Islands to create a map of every drainage basin along the coast of each island, to get an idea of where major rivers flow or once flowed. They also marked the locations of every reef pass in the surrounding coral reefs. They then essentially “unraveled” each island’s coastline and reef into a straight line, and compared the locations of basins versus reef passes.“Looking at the unwrapped shorelines, we find a significant correlation in the spatial relationship between these big river basins and where the passes line up,” Gillen says. “So we can say that statistically, the alignment of reef passes and large rivers does not seem random. The big rivers have a role in forming passes.”As for how rivers shape the coral conduits, the team has two ideas, which they call, respectively, reef incision and reef encroachment. In reef incision, they propose that reef passes can form in times when the sea level is relatively low, such that the reef is exposed above the sea surface and a river can flow directly over the reef. The water and sediment carried by the river can then erode the coral, progressively carving a path through the reef.When sea level is relatively higher, the team suspects a reef pass can still form, through reef encroachment. Coral reefs naturally live close to the water surface, where there is light and opportunity for photosynthesis. When sea levels rise, corals naturally grow upward and inward toward an island, to try to “catch up” to the water line.“Reefs migrate toward the islands as sea levels rise, trying to keep pace with changing average sea level,” Gillen says.However, part of the encroaching reef can end up in old river channels that were previously carved out by large rivers and that are lower than the rest of the island coastline. The corals in these river beds end up deeper than light can extend into the water column, and inevitably drown, leaving a gap in the form of a reef pass.“We don’t think it’s an either/or situation,” Gillen says. “Reef incision occurs when sea levels fall, and reef encroachment happens when sea levels rise. Both mechanisms, occurring over dozens of cycles of sea-level rise and island evolution, are likely responsible for the formation and maintenance of reef passes over time.”The team also looked to see whether there were differences in reef passes in older versus younger islands. They observed that younger islands were surrounded by more reef passes that were spaced closer together, versus older islands that had fewer reef passes that were farther apart.As islands age, they subside, or sink, into the ocean, which reduces the amount of land that funnels rainwater into rivers. Eventually, rivers are too weak to keep the reef passes open, at which point, the ocean likely takes over, and incoming waves could act to close up some passes.Gillen is exploring ideas for how rivers, or river-like flow, can be engineered to create paths through coral reefs in ways that would promote circulation and benefit reef health.“Part of me wonders: If you had a more persistent flow, in places where you don’t naturally have rivers interacting with the reef, could that potentially be a way to increase health, by incorporating that river component back into the reef system?” Gillen says. “That’s something we’re thinking about.”This research was supported, in part, by the WHOI Watson and Von Damm fellowships. More

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      in Environment

      When Earth iced over, early life may have sheltered in meltwater ponds

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      When the Earth froze over, where did life shelter? MIT scientists say one refuge may have been pools of melted ice that dotted the planet’s icy surface.In a study appearing today in Nature Communications, the researchers report that 635 million to 720 million years ago, during periods known as “Snowball Earth,” when much of the planet was covered in ice, some of our ancient cellular ancestors could have waited things out in meltwater ponds.The scientists found that eukaryotes — complex cellular lifeforms that eventually evolved into the diverse multicellular life we see today — could have survived the global freeze by living in shallow pools of water. These small, watery oases may have persisted atop relatively shallow ice sheets present in equatorial regions. There, the ice surface could accumulate dark-colored dust and debris from below, which enhanced its ability to melt into pools. At temperatures hovering around 0 degrees Celsius, the resulting meltwater ponds could have served as habitable environments for certain forms of early complex life.The team drew its conclusions based on an analysis of modern-day meltwater ponds. Today in Antarctica, small pools of melted ice can be found along the margins of ice sheets. The conditions along these polar ice sheets are similar to what likely existed along ice sheets near the equator during Snowball Earth.The researchers analyzed samples from a variety of meltwater ponds located on the McMurdo Ice Shelf in an area that was first described by members of Robert Falcon Scott’s 1903 expedition as “dirty ice.” The MIT researchers discovered clear signatures of eukaryotic life in every pond. The communities of eukaryotes varied from pond to pond, revealing a surprising diversity of life across the setting. The team also found that salinity plays a key role in the kind of life a pond can host: Ponds that were more brackish or salty had more similar eukaryotic communities, which differed from those in ponds with fresher waters.“We’ve shown that meltwater ponds are valid candidates for where early eukaryotes could have sheltered during these planet-wide glaciation events,” says lead author Fatima Husain, a graduate student in MIT’s Department of Earth, Atmospheric and Planetary Sciences (EAPS). “This shows us that diversity is present and possible in these sorts of settings. It’s really a story of life’s resilience.”The study’s MIT co-authors include Schlumberger Professor of Geobiology Roger Summons and former postdoc Thomas Evans, along with Jasmin Millar of Cardiff University, Anne Jungblut at the Natural History Museum in London, and Ian Hawes of the University of Waikato in New Zealand.Polar plunge“Snowball Earth” is the colloquial term for periods of time in Earth history during which the planet iced over. It is often used as a reference to the two consecutive, multi-million-year glaciation events which took place during the Cryogenian Period, which geologists refer to as the time between 635 and 720 million years ago. Whether the Earth was more of a hardened snowball or a softer “slushball” is still up for debate. But scientists are certain of one thing: Most of the planet was plunged into a deep freeze, with average global temperatures of minus 50 degrees Celsius. The question has been: How and where did life survive?“We’re interested in understanding the foundations of complex life on Earth. We see evidence for eukaryotes before and after the Cryogenian in the fossil record, but we largely lack direct evidence of where they may have lived during,” Husain says. “The great part of this mystery is, we know life survived. We’re just trying to understand how and where.”There are a number of ideas for where organisms could have sheltered during Snowball Earth, including in certain patches of the open ocean (if such environments existed), in and around deep-sea hydrothermal vents, and under ice sheets. In considering meltwater ponds, Husain and her colleagues pursued the hypothesis that surface ice meltwaters may also have been capable of supporting early eukaryotic life at the time.“There are many hypotheses for where life could have survived and sheltered during the Cryogenian, but we don’t have excellent analogs for all of them,” Husain notes. “Above-ice meltwater ponds occur on Earth today and are accessible, giving us the opportunity to really focus in on the eukaryotes which live in these environments.”Small pond, big lifeFor their new study, the researchers analyzed samples taken from meltwater ponds in Antarctica. In 2018, Summons and colleagues from New Zealand traveled to a region of the McMurdo Ice Shelf in East Antarctica, known to host small ponds of melted ice, each just a few feet deep and a few meters wide. There, water freezes all the way to the seafloor, in the process trapping dark-colored sediments and marine organisms. Wind-driven loss of ice from the surface creates a sort of conveyer belt that brings this trapped debris to the surface over time, where it absorbs the sun’s warmth, causing ice to melt, while surrounding debris-free ice reflects incoming sunlight, resulting in the formation of shallow meltwater ponds.The bottom of each pond is lined with mats of microbes that have built up over years to form layers of sticky cellular communities.“These mats can be a few centimeters thick, colorful, and they can be very clearly layered,” Husain says.These microbial mats are made up of cyanobacteria, prokaryotic, single-celled photosynthetic organisms that lack a cell nucleus or other organelles. While these ancient microbes are known to survive within some of the the harshest environments on Earth including meltwater ponds, the researchers wanted to know whether eukaryotes — complex organisms that evolved a cell nucleus and other membrane bound organelles — could also weather similarly challenging circumstances. Answering this question would take more than a microscope, as the defining characteristics of the microscopic eukaryotes present among the microbial mats are too subtle to distinguish by eye.To characterize the eukaryotes, the team analyzed the mats for specific lipids they make called sterols, as well as genetic components called ribosomal ribonucleic acid (rRNA), both of which can be used to identify organisms with varying degrees of specificity. These two independent sets of analyses provided complementary fingerprints for certain eukaryotic groups. As part of the team’s lipid research, they found many sterols and rRNA genes closely associated with specific types of algae, protists, and microscopic animals among the microbial mats. The researchers were able to assess the types and relative abundance of lipids and rRNA genes from pond to pond, and found the ponds hosted a surprising diversity of eukaryotic life.“No two ponds were alike,” Husain says. “There are repeating casts of characters, but they’re present in different abundances. And we found diverse assemblages of eukaryotes from all the major groups in all the ponds studied. These eukaryotes are the descendants of the eukaryotes that survived the Snowball Earth. This really highlights that meltwater ponds during Snowball Earth could have served as above-ice oases that nurtured the eukaryotic life that enabled the diversification and proliferation of complex life — including us — later on.”This research was supported, in part, by the NASA Exobiology Program, the Simons Collaboration on the Origins of Life, and a MISTI grant from MIT-New Zealand. More

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      in Environment

      After more than a decade of successes, ESI’s work will spread out across the Institute

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      MIT’s Environmental Solutions Initiative (ESI), a pioneering cross-disciplinary body that helped give a major boost to sustainability and solutions to climate change at MIT, will close as a separate entity at the end of June. But that’s far from the end for its wide-ranging work, which will go forward under different auspices. Many of its key functions will become part of MIT’s recently launched Climate Project. John Fernandez, head of ESI for nearly a decade, will return to the School of Architecture and Planning, where some of ESI’s important work will continue as part of a new interdisciplinary lab.When the ideas that led to the founding of MIT’s Environmental Solutions Initiative first began to be discussed, its founders recall, there was already a great deal of work happening at MIT relating to climate change and sustainability. As Professor John Sterman of the MIT Sloan School of Management puts it, “there was a lot going on, but it wasn’t integrated. So the whole added up to less than the sum of its parts.”ESI was founded in 2014 to help fill that coordinating role, and in the years since it has accomplished a wide range of significant milestones in research, education, and communication about sustainable solutions in a wide range of areas. Its founding director, Professor Susan Solomon, helmed it for its first year, and then handed the leadership to Fernandez, who has led it since 2015.“There wasn’t much of an ecosystem [on sustainability] back then,” Solomon recalls. But with the help of ESI and some other entities, that ecosystem has blossomed. She says that Fernandez “has nurtured some incredible things under ESI,” including work on nature-based climate solutions, and also other areas such as sustainable mining, and reduction of plastics in the environment.Desiree Plata, director of MIT’s Climate and Sustainability Consortium and associate professor of civil and environmental engineering, says that one key achievement of the initiative has been in “communication with the external world, to help take really complex systems and topics and put them in not just plain-speak, but something that’s scientifically rigorous and defensible, for the outside world to consume.”In particular, ESI has created three very successful products, which continue under the auspices of the Climate Project. These include the popular TIL Climate Podcast, the Webby Award-winning Climate Portal website, and the online climate primer developed with Professor Kerry Emanuel. “These are some of the most frequented websites at MIT,” Plata says, and “the impact of this work on the global knowledge base cannot be overstated.”Fernandez says that ESI has played a significant part in helping to catalyze what has become “a rich institutional landscape of work in sustainability and climate change” at MIT. He emphasizes three major areas where he feels the ESI has been able to have the most impact: engaging the MIT community, initiating and stewarding critical environmental research, and catalyzing efforts to promote sustainability as fundamental to the mission of a research university.Engagement of the MIT community, he says, began with two programs: a research seed grant program and the creation of MIT’s undergraduate minor in environment and sustainability, launched in 2017.ESI also created a Rapid Response Group, which gave students a chance to work on real-world projects with external partners, including government agencies, community groups, nongovernmental organizations, and businesses. In the process, they often learned why dealing with environmental challenges in the real world takes so much longer than they might have thought, he says, and that a challenge that “seemed fairly straightforward at the outset turned out to be more complex and nuanced than expected.”The second major area, initiating and stewarding environmental research, grew into a set of six specific program areas: natural climate solutions, mining, cities and climate change, plastics and the environment, arts and climate, and climate justice.These efforts included collaborations with a Nobel Peace Prize laureate, three successive presidential administrations from Colombia, and members of communities affected by climate change, including coal miners, indigenous groups, various cities, companies, the U.N., many agencies — and the popular musical group Coldplay, which has pledged to work toward climate neutrality for its performances. “It was the role that the ESI played as a host and steward of these research programs that may serve as a key element of our legacy,” Fernandez says.The third broad area, he says, “is the idea that the ESI as an entity at MIT would catalyze this movement of a research university toward sustainability as a core priority.” While MIT was founded to be an academic partner to the industrialization of the world, “aren’t we in a different world now? The kind of massive infrastructure planning and investment and construction that needs to happen to decarbonize the energy system is maybe the largest industrialization effort ever undertaken. Even more than in the recent past, the set of priorities driving this have to do with sustainable development.”Overall, Fernandez says, “we did everything we could to infuse the Institute in its teaching and research activities with the idea that the world is now in dire need of sustainable solutions.”Fernandez “has nurtured some incredible things under ESI,” Solomon says. “It’s been a very strong and useful program, both for education and research.” But it is appropriate at this time to distribute its projects to other venues, she says. “We do now have a major thrust in the Climate Project, and you don’t want to have redundancies and overlaps between the two.”Fernandez says “one of the missions of the Climate Project is really acting to coalesce and aggregate lots of work around MIT.” Now, with the Climate Project itself, along with the Climate Policy Center and the Center for Sustainability Science and Strategy, it makes more sense for ESI’s climate-related projects to be integrated into these new entities, and other projects that are less directly connected to climate to take their places in various appropriate departments or labs, he says.“We did enough with ESI that we made it possible for these other centers to really flourish,” he says. “And in that sense, we played our role.”As of June 1, Fernandez has returned to his role as professor of architecture and urbanism and building technology in the School of Architecture and Planning, where he directs the Urban Metabolism Group. He will also be starting up a new group called Environment ResearchAction (ERA) to continue ESI work in cities, nature, and artificial intelligence.  More