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      in Environment

      Andrea Lo ’21 draws on ecological lessons for life, work, and education

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      Growing up in Los Angeles about 10 minutes away from the Ballona Wetlands, Andrea Lo ’21 has long been interested in ecology. She witnessed, in real-time, the effects of urbanization and the impacts that development had on the wetlands. 

      “In hindsight, it really helped shape my need for a career — and a life — where I can help improve my community and the environment,” she says.

      Lo, who majored in biology at MIT, says a recurring theme in her life has been the pursuit of balance, valuing both extracurricular and curricular activities. She always felt an equal pull toward STEM and the humanities, toward wet lab work and field work, and toward doing research and helping her community. 

      “One of the most important things I learned in 7.30[J] (Fundamentals of Ecology) was that there are always going to be trade-offs. That’s just the way of life,” she says. “The biology major at MIT is really flexible. I got a lot of room to explore what I was interested in and get a good balance overall, with humanities classes along with technical classes.” 

      Lo was drawn to MIT because of the focus on hands-on work — but many of the activities Lo was hoping to do, both extracurricular and curricular, were cut short because of the pandemic, including her lab-based Undergraduate Research Opportunities Program (UROP) project. 

      Instead, she pursued a UROP with MIT Sea Grant, working on a project in partnership with Northeastern University and the Charles River Conservancy with funding support from the MIT Community Service fund as part of STEAM Saturday.  

      She was involved in creating Floating Wetland kits, an educational activity directed at students in grades 4 to 6 to help students understand ecological concepts,the challenges the Charles River faces due to urbanization, and how floating wetlands improve the ecosystem. 

      “Our hope was to educate future generations of local students in Cambridge in order for them to understand the ecology surrounding where they live,” she says. 

      In recent years, many bodies of water in Massachusetts have become unusable during the warmer months due to the process of eutrophication: stormwater runoff picks up everything — from fertilizer and silt to animal excrement — and deposits it at the lowest point, which is often a body of water. This leads to an excess of nutrients in the body of water and, when combined with warm temperatures, can lead to harmful algal blooms, making the water sludgy, bright green, and dangerously toxic. 

      The wetland kits Lo worked with were mini ecosystems, replicating a full-sized floating wetland. One such floating wetland can be seen from the Longfellow Bridge at one end of MIT’s campus — the Charles River floating wetland is a patch of grass attached to a buoy like a boat, which is often visited by birds and inhabited by much smaller critters that cannot be seen from the shore.  

      The Charles River floating wetland has a variety of flora, but the kits Lo helped present use only wheat grass because it is easy to grow and has long, dangling roots that could penetrate the watery medium below. A water tray beneath the grass — the Charles river of the mini ecosystem — contains spirulina powder for replicating algae growth and daphnia, which are small, planktonic crustaceans that help keep freshwater clean and usable. 

      “This work was really fulfilling, but it’s also really important, because environmental sustainability relies on future generations to carry on the work that past generations have been doing,” she says. “MIT’s motto is ‘mens et manus’ — education for practical application, and applying theoretical knowledge to what we do in our daily lives. I think this project really helped reinforce that.” 

      Since 2021, Lo has been working in Denmark in a position she learned about through the MIT-Denmark program. 

      She chose Denmark because of its reputation for environmental and sustainability issues and because she didn’t know much about it except for it being one of the happiest countries in the world, often thought of synonymously with the word “hygge,” which has no direct translation but encapsulates coziness and comfort from the small joys in life. 

      “At MIT, we have a very strong work-hard, play-hard culture. I think we can learn a lot from the work-life balance that Denmark has a reputation for,” she says. “I really wanted to take the opportunity in between graduation and whatever came after to explore beyond my bubble. For me, it was important to step back, out of my comfort zone, step into a different environment — and just live.”

      Currently, her personal project is comparing the conditions of two lagoons on the island of Fyn in Denmark. Both are naturally occurring, but in different states of environmental health. 

      She’s been doing a mix of field work and lab work. She collects sediment and fauna samples using a steel corer, or “butter stick” in her lab’s slang. In the same way that one can use a metal tube-shaped tool to remove the core of an apple, she punches the steel corer into the ground, removing a plug of sample. She then sifts the sample through 1 millimeter mesh, preserves the filtered sample in formalin, and takes everything back to the lab. 

      Once there, she looks through the sample to find macrofauna — mollusks, barnacles, and polychaetes, a bristly-looking segmented worm, for example. Collected over time, sediment characteristics like organic matter content, sediment grain size, and the size and abundance of macrofauna, can reveal trends that can help determine the health of the ecosystem. 

      Lo doesn’t have any concrete results yet, but her data could help researchers project the recovery of a lagoon that was rehabilitated using a technique called managed realignment, where water is allowed to reclaim areas where it was once found. She says she’s glad she gets a mix of field work and lab work, even on Denmark’s stormiest days. 

      “Sometimes there are really cold days where it’s windy and I wish I was in the lab, but, at the same time, it’s nice to have a balance where I can be outside and really be hands-on with my work,” she says.  

      Reflecting her dual interests in the technical and the innovative, she will be back in the Greater Boston area in the fall, pursuing a master of science in innovation and management and an MS in civil and environmental engineering at the Tufts Gordon Institute.

      “So much has happened and changed due to the pandemic that it’s easy to dwell on what could’ve been, but I tell myself to be optimistic and take the positive aspects that have come out of the circumstances,” Lo says. “My opportunities with the Sea Grant, MISTI, and Tufts definitely wouldn’t have happened if the pandemic hadn’t happened.” More

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      in Energy

      Chemists discover why photosynthetic light-harvesting is so efficient

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      When photosynthetic cells absorb light from the sun, packets of energy called photons leap between a series of light-harvesting proteins until they reach the photosynthetic reaction center. There, cells convert the energy into electrons, which eventually power the production of sugar molecules.

      This transfer of energy through the light-harvesting complex occurs with extremely high efficiency: Nearly every photon of light absorbed generates an electron, a phenomenon known as near-unity quantum efficiency.

      A new study from MIT chemists offers a potential explanation for how proteins of the light-harvesting complex, also called the antenna, achieve that high efficiency. For the first time, the researchers were able to measure the energy transfer between light-harvesting proteins, allowing them to discover that the disorganized arrangement of these proteins boosts the efficiency of the energy transduction.

      “In order for that antenna to work, you need long-distance energy transduction. Our key finding is that the disordered organization of the light-harvesting proteins enhances the efficiency of that long-distance energy transduction,” says Gabriela Schlau-Cohen, an associate professor of chemistry at MIT and the senior author of the new study.

      MIT postdocs Dihao Wang and Dvir Harris and former MIT graduate student Olivia Fiebig PhD ’22 are the lead authors of the paper, which appears this week in the Proceedings of the National Academy of Sciences. Jianshu Cao, an MIT professor of chemistry, is also an author of the paper.

      Energy capture

      For this study, the MIT team focused on purple bacteria, which are often found in oxygen-poor aquatic environments and are commonly used as a model for studies of photosynthetic light-harvesting.

      Within these cells, captured photons travel through light-harvesting complexes consisting of proteins and light-absorbing pigments such as chlorophyll. Using ultrafast spectroscopy, a technique that uses extremely short laser pulses to study events that happen on timescales of femtoseconds to nanoseconds, scientists have been able to study how energy moves within a single one of these proteins. However, studying how energy travels between these proteins has proven much more challenging because it requires positioning multiple proteins in a controlled way.

      To create an experimental setup where they could measure how energy travels between two proteins, the MIT team designed synthetic nanoscale membranes with a composition similar to those of naturally occurring cell membranes. By controlling the size of these membranes, known as nanodiscs, they were able to control the distance between two proteins embedded within the discs.

      For this study, the researchers embedded two versions of the primary light-harvesting protein found in purple bacteria, known as LH2 and LH3, into their nanodiscs. LH2 is the protein that is present during normal light conditions, and LH3 is a variant that is usually expressed only during low light conditions.

      Using the cryo-electron microscope at the MIT.nano facility, the researchers could image their membrane-embedded proteins and show that they were positioned at distances similar to those seen in the native membrane. They were also able to measure the distances between the light-harvesting proteins, which were on the scale of 2.5 to 3 nanometers.

      Disordered is better

      Because LH2 and LH3 absorb slightly different wavelengths of light, it is possible to use ultrafast spectroscopy to observe the energy transfer between them. For proteins spaced closely together, the researchers found that it takes about 6 picoseconds for a photon of energy to travel between them. For proteins farther apart, the transfer takes up to 15 picoseconds.

      Faster travel translates to more efficient energy transfer, because the longer the journey takes, the more energy is lost during the transfer.

      “When a photon gets absorbed, you only have so long before that energy gets lost through unwanted processes such as nonradiative decay, so the faster it can get converted, the more efficient it will be,” Schlau-Cohen says.

      The researchers also found that proteins arranged in a lattice structure showed less efficient energy transfer than proteins that were arranged in randomly organized structures, as they usually are in living cells.

      “Ordered organization is actually less efficient than the disordered organization of biology, which we think is really interesting because biology tends to be disordered. This finding tells us that that may not just be an inevitable downside of biology, but organisms may have evolved to take advantage of it,” Schlau-Cohen says.

      Now that they have established the ability to measure inter-protein energy transfer, the researchers plan to explore energy transfer between other proteins, such as the transfer between proteins of the antenna to proteins of the reaction center. They also plan to study energy transfer between antenna proteins found in organisms other than purple bacteria, such as green plants.

      The research was funded primarily by the U.S. Department of Energy. More

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      in Energy

      A new mathematical “blueprint” is accelerating fusion device development

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      Developing commercial fusion energy requires scientists to understand sustained processes that have never before existed on Earth. But with so many unknowns, how do we make sure we’re designing a device that can successfully harness fusion power?

      We can fill gaps in our understanding using computational tools like algorithms and data simulations to knit together experimental data and theory, which allows us to optimize fusion device designs before they’re built, saving much time and resources.

      Currently, classical supercomputers are used to run simulations of plasma physics and fusion energy scenarios, but to address the many design and operating challenges that still remain, more powerful computers are a necessity, and of great interest to plasma researchers and physicists.

      Quantum computers’ exponentially faster computing speeds have offered plasma and fusion scientists the tantalizing possibility of vastly accelerated fusion device development. Quantum computers could reconcile a fusion device’s many design parameters — for example, vessel shape, magnet spacing, and component placement — at a greater level of detail, while also completing the tasks faster. However, upgrading to a quantum computer is no simple task.

      In a paper, “Dyson maps and unitary evolution for Maxwell equations in tensor dielectric media,” recently published in Physics Review A, Abhay K. Ram, a research scientist at the MIT Plasma Science and Fusion Center (PSFC), and his co-authors Efstratios Koukoutsis, Kyriakos Hizanidis, and George Vahala present a framework that would facilitate the use of quantum computers to study electromagnetic waves in plasma and its manipulation in magnetic confinement fusion devices.

      Quantum computers excel at simulating quantum physics phenomena, but many topics in plasma physics are predicated on the classical physics model. A plasma (which is the “dielectric media” referenced in the paper’s title) consists of many particles — electrons and ions — the collective behaviors of which are effectively described using classic statistical physics. In contrast, quantum effects that influence atomic and subatomic scales are averaged out in classical plasma physics.  

      Furthermore, the descriptive limitations of quantum mechanics aren’t suited to plasma. In a fusion device, plasmas are heated and manipulated using electromagnetic waves, which are one of the most important and ubiquitous occurrences in the universe. The behaviors of electromagnetic waves, including how waves are formed and interact with their surroundings, are described by Maxwell’s equations — a foundational component of classical plasma physics, and of general physics as well. The standard form of Maxwell’s equations is not expressed in “quantum terms,” however, so implementing the equations on a quantum computer is like fitting a square peg in a round hole: it doesn’t work.

      Consequently, for plasma physicists to take advantage of quantum computing’s power for solving problems, classical physics must be translated into the language of quantum mechanics. The researchers tackled this translational challenge, and in their paper, they reveal that a Dyson map can bridge the translational divide between classical physics and quantum mechanics. Maps are mathematical functions that demonstrate how to take an input from one kind of space and transform it to an output that is meaningful in a different kind of space. In the case of Maxwell’s equations, a Dyson map allows classical electromagnetic waves to be studied in the space utilized by quantum computers. In essence, it reconfigures the square peg so it will fit into the round hole without compromising any physics.

      The work also gives a blueprint of a quantum circuit encoded with equations expressed in quantum bits (“qubits”) rather than classical bits so the equations may be used on quantum computers. Most importantly, these blueprints can be coded and tested on classical computers.

      “For years we have been studying wave phenomena in plasma physics and fusion energy science using classical techniques. Quantum computing and quantum information science is challenging us to step out of our comfort zone, thereby ensuring that I have not ‘become comfortably numb,’” says Ram, quoting a Pink Floyd song.

      The paper’s Dyson map and circuits have put quantum computing power within reach, fast-tracking an improved understanding of plasmas and electromagnetic waves, and putting us that much closer to the ideal fusion device design.    More

    • 88 Shares149 Views

      in Environment

      Q&A: Are far-reaching fires the new normal?

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      Where there’s smoke, there is fire. But with climate change, larger and longer-burning wildfires are sending smoke farther from their source, often to places that are unaccustomed to the exposure. That’s been the case this week, as smoke continues to drift south from massive wildfires in Canada, prompting warnings of hazardous air quality, and poor visibility in states across New England, the mid-Atlantic, and the Midwest.

      As wildfire season is just getting going, many may be wondering: Are the air-polluting effects of wildfires a new normal?

      MIT News spoke with Professor Colette Heald of the Department of Civil and Environmental Engineering and the Department of Earth, Atmospheric and Planetary Sciences, and Professor Noelle Selin of the Institute for Data, Systems and Society and the Department of Earth, Atmospheric and Planetary Sciences. Heald specializes in atmospheric chemistry and has studied the climate and health effects associated with recent wildfires, while Selin works with atmospheric models to track air pollutants around the world, which she uses to inform policy decisions on mitigating  pollution and climate change. The researchers shared some of their insights on the immediate impacts of Canada’s current wildfires and what downwind regions may expect in the coming months, as the wildfire season stretches into summer.  

      Q: What role has climate change and human activity played in the wildfires we’ve seen so far this year?

      Heald: Unusually warm and dry conditions have dramatically increased fire susceptibility in Canada this year. Human-induced climate change makes such dry and warm conditions more likely. Smoke from fires in Alberta and Nova Scotia in May, and Quebec in early June, has led to some of the worst air quality conditions measured locally in Canada. This same smoke has been transported into the United States and degraded air quality here as well. Local officials have determined that ignitions have been associated with lightning strikes, but human activity has also played a role igniting some of the fires in Alberta.

      Q: What can we expect for the coming months in terms of the pattern of wildfires and their associated air pollution across the United States?

      Heald: The Government of Canada is projecting higher-than-normal fire activity throughout the 2023 fire season. Fire susceptibility will continue to respond to changing weather conditions, and whether the U.S. is impacted will depend on the winds and how air is transported across those regions. So far, the fire season in the United States has been below average, but fire risk is expected to increase modestly through the summer, so we may see local smoke influences as well.

      Q: How has air pollution from wildfires affected human health in the U.S. this year so far?

      Selin: The pollutant of most concern in wildfire smoke is fine particulate matter (PM2.5) – fine particles in the atmosphere that can be inhaled deep into the lungs, causing health damages. Exposure to PM2.5 causes respiratory and cardiovascular damage, including heart attacks and premature deaths. It can also cause symptoms like coughing and difficulty breathing. In New England this week, people have been breathing much higher concentrations of PM2.5 than usual. People who are particularly vulnerable to the effects are likely experiencing more severe impacts, such as older people and people with underlying conditions. But PM2.5 affects everyone. While the number and impact of wildfires varies from year to year, the associated air pollution from them generally lead to tens of thousands of premature deaths in the U.S. overall annually. There is also some evidence that PM2.5 from fires could be particularly damaging to health.

      While we in New England usually have relatively lower levels of pollution, it’s important also to note that some cities around the globe experience very high PM2.5 on a regular basis, not only from wildfires, but other sources such as power plants and industry. So, while we’re feeling the effects over the past few days, we should remember the broader importance of reducing PM2.5 levels overall for human health everywhere.

      Q: While firefighters battle fires directly this wildfire season, what can we do to reduce the effects of associated air pollution? And what can we do in the long-term, to prevent or reduce wildfire impacts?

      Selin: In the short term, protecting yourself from the impacts of PM2.5 is important. Limiting time outdoors, avoiding outdoor exercise, and wearing a high-quality mask are some strategies that can minimize exposure. Air filters can help reduce the concentrations of particles in indoor air. Taking measures to avoid exposure is particularly important for vulnerable groups. It’s also important to note that these strategies aren’t equally possible for everyone (for example, people who work outside) — stressing the importance of developing new strategies to address the underlying causes of increasing wildfires.

      Over the long term, mitigating climate change is important — because warm and dry conditions lead to wildfires, warming increases fire risk. Preventing the fires that are ignited by people or human activities can help.  Another way that damages can be mitigated in the longer term is by exploring land management strategies that could help manage fire intensity. More

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      in Energy

      Tackling the MIT campus’s top energy consumers, building by building

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      When staff in MIT’s Department of Facilities would visualize energy use and carbon-associated emissions by campus buildings, Building 46 always stood out — attributed to its energy intensity, which accounted for 8 percent of MIT’s total campus energy use. This high energy draw was not surprising, as the building is home of the Brain and Cognitive Sciences Complex and a large amount of lab space, but it also made the building a perfect candidate for an energy performance audit to seek out potential energy saving opportunities.

      This audit revealed that several energy efficiency updates to the building mechanical systems infrastructure, including optimization of the room-by-room ventilation rates, could result in an estimated 35 percent reduction of energy use, which would in turn lower MIT’s total greenhouse gas emissions by an estimated 2 percent — driving toward the Institute’s 2026 goal of net-zero and 2050 goal of elimination of direct campus emissions.

      Building energy efficiency projects are not new for MIT. Since 2010, MIT has been engaged in a partnership agreement with utility company Eversource establishing the Efficiency Forward program, empowering MIT to invest in more than 300 energy conservation projects to date and lowering energy consumption on campus for a total calculated savings of approximately 70 million kilowatt hours and 4.2 million therms. But at 418,000 gross square feet, Building 46 is the first energy efficiency project of its size on the campus.

      “We’ve never tackled a whole building like this — it’s the first capital project that is technically an energy project,” explains Siobhan Carr, energy efficiency program manager, who was part of the team overseeing the energy audit and lab ventilation performance assessment in the building. “That gives you an idea of the magnitude and complexity of this.”

      The project started with the full building energy assessment and lab ventilation risk audit. “We had a team go through every corner of the building and look at every possible opportunity to save energy,” explains Jessica Parks, senior project manager for systems performance and turnover in campus construction. “One of the biggest issues we saw was that there’s a lot of dry lab spaces which are basically offices, but they’re all getting the same ventilation as if they were a high-intensity lab.” Higher ventilation and more frequent air exchange rates draw more energy. By optimizing for the required ventilation rates, there was an opportunity to save energy in nearly every space in the building.

      In addition to the optimized ventilation, the project team will convert fume hoods from constant volume to variable volume and install equipment to help the building systems run more efficiently. The team also identified opportunities to work with labs to implement programs such as fume hood hibernation and unoccupied setbacks for temperature and ventilation. As different spaces in the building have varying needs, the energy retrofit will touch all 1,254 spaces in the building — one by one — to implement the different energy measures to reach that estimated 35 percent reduction in energy use.

      Although time-consuming and complex, this room-by-room approach has a big benefit in that it has allowed research to continue in the space largely uninterrupted. With a few exceptions, the occupants of Building 46, which include the Department of Brain and Cognitive Sciences, The McGovern Institute for Brain Research, and The Picower Institute for Learning and Memory, have remained in place for the duration of the project. Partners in the MIT Environment, Health and Safety Office are instrumental to this balance of renovations and keeping the building operational during the optimization efforts and are one of several teams across MIT contributing to building efficiency efforts.

      The completion date of the building efficiency project is set for 2024, but Carr says that some of the impact of this ongoing work may soon be seen. “We should start to see savings as we move through the building, and we expect to fully realize all of our projected savings a year after completion,” she says, noting that the length of time is required for a year-over-year perspective to see the full reduction in energy use.

      The impact of the project goes far beyond the footprint of Building 46 as it offers insights and spurred actions for future projects — including buildings 76 and 68, the number two and three top energy users on campus. Both buildings recently underwent their own energy audits and lab ventilation performance assessments. The energy efficiency team is now crafting a plan for full-building approaches, much like Building 46. “To date, 46 has presented many learning opportunities, such as how to touch every space in a building while research continues, as well as how to overcome challenges encountered when working on existing systems,” explains Parks. “The good news is that we have developed solutions for those challenges and the teams have been proactively implementing those lessons in our other projects.”

      Communication has proven to be another key for these large projects where occupants see the work happening and often play a role in answering questions about their unique space. “People are really engaged, they ask questions about the work, and we ask them about the space they’re in every day,” says Parks. “The Building 46 occupants have been wonderful partners as we worked in all of their spaces, which is paving the way for a successful project.”

      The release of Fast Forward in 2021 has also made communications easier, notes Carr, who says the plan helps to frame these projects as part of the big picture — not just a construction interruption. “Fast Forward has brought a visibility into what we’re doing within [MIT] Facilities on these buildings,” she says. “It brings more eyes and ears, and people understand that these projects are happening throughout campus and not just in their own space — we’re all working to reduce energy and to reduce greenhouse gas across campus.”

      The Energy Efficiency team will continue to apply that big-picture approach as ongoing building efficiency projects on campus are assessed to reach toward a 10 to 15 percent reduction in energy use and corresponding emissions over the next several years. More

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      in Environment

      River erosion can shape fish evolution, study suggests

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      If we could rewind the tape of species evolution around the world and play it forward over hundreds of millions of years to the present day, we would see biodiversity clustering around regions of tectonic turmoil. Tectonically active regions such as the Himalayan and Andean mountains are especially rich in flora and fauna due to their shifting landscapes, which act to divide and diversify species over time.

      But biodiversity can also flourish in some geologically quieter regions, where tectonics hasn’t shaken up the land for millennia. The Appalachian Mountains are a prime example: The range has not seen much tectonic activity in hundreds of millions of years, and yet the region is a notable hotspot of freshwater biodiversity.

      Now, an MIT study identifies a geological process that may shape the diversity of species in tectonically inactive regions. In a paper appearing today in Science, the researchers report that river erosion can be a driver of biodiversity in these older, quieter environments.

      They make their case in the southern Appalachians, and specifically the Tennessee River Basin, a region known for its huge diversity of freshwater fishes. The team found that as rivers eroded through different rock types in the region, the changing landscape pushed a species of fish known as the greenfin darter into different tributaries of the river network. Over time, these separated populations developed into their own distinct lineages.

      The team speculates that erosion likely drove the greenfin darter to diversify. Although the separated populations appear outwardly similar, with the greenfin darter’s characteristic green-tinged fins, they differ substantially in their genetic makeup. For now, the separated populations are classified as one single species. 

      “Give this process of erosion more time, and I think these separate lineages will become different species,” says Maya Stokes PhD ’21, who carried out part of the work as a graduate student in MIT’s Department of Earth, Atmospheric and Planetary Sciences (EAPS).

      The greenfin darter may not be the only species to diversify as a consequence of river erosion. The researchers suspect that erosion may have driven many other species to diversify throughout the basin, and possibly other tectonically inactive regions around the world.

      “If we can understand the geologic factors that contribute to biodiversity, we can do a better job of conserving it,” says Taylor Perron, the Cecil and Ida Green Professor of Earth, Atmospheric, and Planetary Sciences at MIT.

      The study’s co-authors include collaborators at Yale University, Colorado State University, the University of Tennessee, the University of Massachusetts at Amherst, and the Tennessee Valley Authority (TVA). Stokes is currently an assistant professor at Florida State University.

      Fish in trees

      The new study grew out of Stokes’ PhD work at MIT, where she and Perron were exploring connections between geomorphology (the study of how landscapes evolve) and biology. They came across work at Yale by Thomas Near, who studies lineages of North American freshwater fishes. Near uses DNA sequence data collected from freshwater fishes across various regions of North America to show how and when certain species evolved and diverged in relation to each other.

      Near brought a curious observation to the team: a habitat distribution map of the greenfin darter showing that the fish was found in the Tennessee River Basin — but only in the southern half. What’s more, Near had mitochondrial DNA sequence data showing that the fish’s populations appeared to be different in their genetic makeup depending on the tributary in which they were found.

      To investigate the reasons for this pattern, Stokes gathered greenfin darter tissue samples from Near’s extensive collection at Yale, as well as from the field with help from TVA colleagues. She then analyzed DNA sequences from across the entire genome, and compared the genes of each individual fish to every other fish in the dataset. The team then created a phylogenetic tree of the greenfin darter, based on the genetic similarity between fish.

      From this tree, they observed that fish within a tributary were more related to each other than to fish in other tributaries. What’s more, fish within neighboring tributaries were more similar to each other than fish from more distant tributaries.

      “Our question was, could there have been a geological mechanism that, over time, took this single species, and splintered it into different, genetically distinct groups?” Perron says.

      A changing landscape

      Stokes and Perron started to observe a “tight correlation” between greenfin darter habitats and the type of rock where they are found. In particular, much of the southern half of the Tennessee River Basin, where the species abounds, is made of metamorphic rock, whereas the northern half consists of sedimentary rock, where the fish are not found.

      They also observed that the rivers running through metamorphic rock are steeper and more narrow, which generally creates more turbulence, a characteristic greenfin darters seem to prefer. The team wondered: Could the distribution of greenfin darter habitat have been shaped by a changing landscape of rock type, as rivers eroded into the land over time?

      To check this idea, the researchers developed a model to simulate how a landscape evolves as rivers erode through various rock types. They fed the model information about the rock types in the Tennessee River Basin today, then ran the simulation back to see how the same region may have looked millions of years ago, when more metamorphic rock was exposed.

      They then ran the model forward and observed how the exposure of metamorphic rock shrank over time. They took special note of where and when connections between tributaries crossed into non-metamorphic rock, blocking fish from passing between those tributaries. They drew up a simple timeline of these blocking events and compared this to the phylogenetic tree of diverging greenfin darters. The two were remarkably similar: The fish seemed to form separate lineages in the same order as when their respective tributaries became separated from the others.

      “It means it’s plausible that erosion through different rock layers caused isolation between different populations of the greenfin darter and caused lineages to diversify,” Stokes says.

      “This study is highly compelling because it reveals a much more subtle but powerful mechanism for speciation in passive margins,” says Josh Roering, professor of Earth sciences at the University of Oregon, who was not involved in the study. “Stokes and Perron have revealed some of the intimate connections between aquatic species and geology that may be much more common than we realize.”

      This research was supported, in part, by the mTerra Catalyst Fund and the U.S. National Science Foundation through the AGeS Geochronology Program and the Graduate Research Fellowship Program. While at MIT, Stokes received support through the Martin Fellowship for Sustainability and the Hugh Hampton Young Fellowship. More

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      in Environment

      Civil discourse project to launch at MIT

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      A new project on civil discourse aims to promote open and civil discussion of difficult topics on the MIT campus.

      The project, which will launch this fall, includes a speaker series and curricular activities in MIT’s Concourse program for first-year students. MIT philosophers Alex Byrne and Brad Skow from the Department of Linguistics and Philosophy lead the project, in close coordination with Anne McCants, professor of history and director of Concourse, and Linda Rabieh, a Concourse lecturer. 

      The Arthur Vining Davis Foundations provided a substantial grant to help fund the project. Promoting civil discourse on college campuses is an area of focus for AVDF — they sponsor related projects at many schools, including Duke University and Davidson College.

      The first event in the speaker series is planned for the evening of Oct. 24, on the question of how we should respond to climate change. The two speakers are Professor Steven Koonin (New York University, ex-provost of Caltech, and an MIT alum) and MIT Professor Kerry Emanuel from the Department of Earth, Atmospheric, and Planetary Sciences. Eight such events are planned over two years. Each will feature speakers discussing difficult or controversial topics, and will aim to model civil debate and dialogue involving experts from inside and outside the MIT community. 

      Byrne and Skow said that the project is meant to counterbalance a growing unwillingness to listen to others or to tolerate the expression of certain ideas. But the goal, says Byrne, “is not to platform heterodox views for their own sake, or to needlessly provoke. Rather, we want to platform collegial, informed conversations on important matters about which there is reasonable disagreement.” 

      Faculty at MIT voted last fall to adopt a statement on free expression, following a report written by an MIT working group. The project organizers want to build on that vote and the report. “The free expression statement says that discussion of controversial topics should not be prohibited or punished,” Skow says, “but the longer working-group report goes farther, urging MIT to promote free expression. This project is an attempt to do that — to show that open discussion and open inquiry are valuable.” 

      “It has the potential to generate lively, constructive, respectful discussion on campus and to show by example both that controversial views are not suppressed at MIT and that we learn by engaging with them openly,” says Kieran Setiya, the head of MIT Philosophy. Agustín Rayo, dean of the School of Humanities and Social Sciences, thinks that the project can “play a critical role in demonstrating — to faculty, students, staff, alumni, and friends — the Institute’s commitment to free speech and civil discourse.”

      Apart from climate change, topics for the first series of events include feminism and progress (Nov. 9, with Mary Harrington, author of “Feminism against Progress”), and Covid public health policy (Feb. 26, with Vinay Prasad, professor of epidemiology and biostatistics at the University of California at San Francisco). Organizers say they hope the speaker series becomes a permanent part of MIT’s intellectual life after the grant period. To amplify the work to an audience beyond MIT, the project organizers have partnered with the Johns Hopkins University political scientist Yascha Mounk and his team at Persuasion to produce podcast episodes around the speaker events. They will air as special episodes of Mounk’s podcast “The Good Fight.” 

      The Concourse component of the project will take advantage of the small learning community setting to develop the tools and experience for productive disagreement. 

      “The core mission of Concourse depends on both the principle of free expression and the practice of civil discourse,” says McCants, “making it a natural springboard for promoting both across the intellectual culture of MIT.”  

      Concourse will experiment with, among other things, seminars discussing the history and practice of freedom of expression, roundtable discussions, and student-led debates. Braver Angels, an organization with the mission of reducing political polarization, is another partner, along with Persuasion. 

      “Our goal,” says Rabieh, “is to facilitate, in collaboration with Braver Angels, the probing, intense, and often difficult conversations that lie at the heart of the Concourse program and that are the hallmark of education.” More

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      Exploring the links between diet and cancer

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      Every three to five days, all of the cells lining the human intestine are replaced. That constant replenishment of cells helps the intestinal lining withstand the damage caused by food passing through the digestive tract.

      This rapid turnover of cells relies on intestinal stem cells, which give rise to all of the other types of cells found in the intestine. Recent research has shown that those stem cells are heavily influenced by diet, which can help keep them healthy or stimulate them to become cancerous.

      “Low-calorie diets such as fasting and caloric restriction can have antiaging effects and antitumor effects, and we want to understand why that is. On the other hand, diets that lead to obesity can promote diseases of aging, such as cancer,” says Omer Yilmaz, the Eisen and Chang Career Development Associate Professor of Biology at MIT.

      For the past decade, Yilmaz has been studying how different diets and environmental conditions affect intestinal stem cells, and how those factors can increase the risk of cancer and other diseases. This work could help researchers develop new ways to improve gastrointestinal health, either through dietary interventions or drugs that mimic the beneficial effects of certain diets, he says. 

      “Our findings have raised the possibility that fasting interventions, or small molecules that mimic the effects of fasting, might have a role in improving intestinal regeneration,” says Yilmaz, who is also a member of MIT’s Koch Institute for Integrative Cancer Research.

      A clinical approach

      Yilmaz’s interest in disease and medicine arose at an early age. His father practiced internal medicine, and Yilmaz spent a great deal of time at his father’s office after school, or tagging along at the hospital where his father saw patients.

      “I was very interested in medicines and how medicines were used to treat diseases,” Yilmaz recalls. “He’d ask me questions, and many times I wouldn’t know the answer, but he would encourage me to figure out the answers to his questions. That really stimulated my interest in biology and in wanting to become a doctor.”

      Knowing that he wanted to go into medicine, Yilmaz applied and was accepted to an eight-year, combined bachelor’s and MD program at the University of Michigan. As an undergraduate, this gave him the freedom to explore areas of interest without worrying about applying to medical school. While majoring in biochemistry and physics, he did undergraduate research in the field of protein folding.

      During his first year of medical school, Yilmaz realized that he missed doing research, so he decided to apply to the MD/PhD program at the University of Michigan. For his PhD research, he studied blood-forming stem cells and identified new markers that allowed such cells to be more easily isolated from the bone marrow.

      “This was important because there’s a lot of interest in understanding what makes a stem cell a stem cell, and how much of it is an internal program versus signals from the microenvironment,” Yilmaz says.

      After finishing his PhD and MD, he thought about going straight into research and skipping a medical residency, but ended up doing a residency in pathology at Massachusetts General Hospital. During that time, he decided to switch his research focus from blood-forming stem cells to stem cells found in the gastrointestinal tract.

      “The GI tract seemed very interesting because in contrast to the bone marrow, we knew very little about the identity of GI stem cells,” Yilmaz says. “I knew that once GI stem cells were identified, there’d be a lot of interesting questions about how they respond to diet and how they respond to other environmental stimuli.”

      Dietary questions

      To delve into those questions, Yilmaz did postdoctoral research at the Whitehead Institute, where he began investigating the connections between stem cells, metabolism, diet, and cancer.

      Because intestinal stem cells are so long-lived, they are more likely to accumulate genetic mutations that make them susceptible to becoming cancerous. At the Whitehead Institute, Yilmaz began studying how different diets might influence this vulnerability to cancer, a topic that he carried into his lab at MIT when he joined the faculty in 2014.

      One question his lab has been exploring is why low-calorie diets often have protective effects, including a boost in longevity — a phenomenon that has been seen in many studies in animals and humans.

      In a 2018 study, his lab found that a 24-hour fast dramatically improves stem cells’ ability to regenerate. This effect was seen in both young and aged mice, suggesting that even in old age, fasting or drugs that mimic the effects of fasting could have a beneficial effect.

      On the flip side, Yilmaz is also interested in why a high-fat diet appears to promote the development of cancer, especially colorectal cancer. In a 2016 study, he found that when mice consume a high-fat diet, it triggers a significant increase in the number of intestinal stem cells. Also, some non-stem-cell populations begin to resemble stem cells in their behavior. “The upshot of these changes is that both stem cells and non-stem-cells can give rise to tumors in a high-fat diet state,” Yilmaz says.

      To help with these studies, Yilmaz’s lab has developed a way to use mouse or human intestinal stem cells to generate miniature intestines or colons in cell culture. These “organoids” can then be exposed to different nutrients in a very controlled setting, allowing researchers to analyze how different diets affect the system.

      Recently, his lab adapted the system to allow them to expand their studies to include the role of immune cells, fibroblasts, and other supportive cells found in the microenvironment of stem cells. “It would be remiss of us to focus on just one cell type,” Yilmaz says. “We’re looking at how these different dietary interventions impact the entire stem cell neighborhood.”

      While Yilmaz spends most of his time running his lab at MIT, he also devotes six to eight weeks per year to his work at MGH, where he is an associate pathologist focusing on gastrointestinal pathology.

      “I enjoy my clinical work, and it always reminds me about the importance of the research we do,” he says. “Seeing colon cancer and other GI cancers under the microscope, and seeing their complexity, reminds me of the importance of our mission to figure out how we can prevent these cancers from forming.” More