Blueprint for fall 2020 at MIT

How are instructors planning for remote learning in the fall? Why do on-campus students have to be on a meal plan? What will happen if there is a Covid-19 breakout in a residence hall? These and many other questions were on the minds of undergraduate students and their families at the Fall Reopening Virtual Town Hall sponsored by the Office of the Chancellor and the MIT Parents Association.

Thousands of participants tuned in on July 15 as 16 members of MIT’s administration and faculty fielded crowdsourced questions from the audience, along with several from student leaders. More than 600 questions were submitted during the 75-minute event, which was moderated by Matthew Bauer, senior director of communications in the Division of Student Life.

The forum fleshed out the plans described in the July 7 fall decision letter to the community from President L. Rafael Reif. Panelists also offered a window into how MIT arrived at its decisions and the core principles that were considered, such as protecting the community’s health, enabling students to stay on track to their degrees, and, as a matter of equity, giving every student the opportunity to spend at least one semester on campus.

Living on campus

Several panelists addressed what life will be like in the residences. Vice President and Dean for Student Life Suzy Nelson noted that several issues related to policies and community expectations were still being ironed out, such as the common space usage and guest policies. Judy Robinson, senior associate dean in the Residential Education Office, explained that the goal of the policies is to ensure “students have a real clear understanding of not just what the expectations are, but the responsibility to each other to minimize the spread of the virus.”

Professor of architecture and head of house for Baker House John Fernandez fielded a question about communal gathering. “We do know that there is the need for seeking out and developing alternative ways to socialize,” he said. To that end, a group of students, faculty, and staff are exploring ways to use outdoor spaces as much as possible and are developing a process to form self-organized social “pods” made up of small groups of residents in each house.

Students will play a vital role in ensuring these policies succeed, Fernandez noted — even simple gestures such as one student reminding another to wear a mask. “We can talk about compliance, and we can try to figure out ways to monitor student behavior, but what we’re most interested in is developing a new culture in which students are partnering with us and doing the right thing,” he said.

MIT is well-positioned for a potential Covid-19 breakout in the residence halls, Nelson said. There will be only one student per room, so students could effectively shelter in place, if needed. MIT Medical can provide increased testing, and there are isolation spaces available for students who test positive. “We certainly feel prepared, from full-scale breakout to a single case, and hopefully zero cases,” added Shawn Ferullo, associate medical director and chief of student health at MIT Medical.

Chancellor Cynthia Barnhart addressed one of the most upvoted topics: how the Institute is helping seniors who have signed off-campus leases but have decided to break them, to be able to live in MIT housing and access the campus. In addition to guidance about subletting, reassigning, or canceling a lease, MIT is offering a $5,000 Covid-era grant. “We knew that students and their families are facing new situations this year, situations that we couldn’t even begin to imagine,” she said. “And this is one of those situations where the additional grant that we’re providing will be able to provide families with some financial flexibility.” Barnhart suggested that students who need additional help reach out to staff in Student Support Services or Student Financial Services, who will work with them to address their concerns.

Following the town hall, the Division of Student Life launched the Student Housing Assistance Review Process (SHARP) on July 17. SHARP is designed to assist two categories of students: rising sophomores and juniors who wish to request on-campus housing during the fall 2020 semester; and students, including seniors, who are experiencing significant hardship and who believe they absolutely cannot live at home and cannot live on campus.

New ways of teaching and learning

The audience had several questions related to academics, including plans for remote instruction and experiential learning. “There’s a lot of work happening across MIT to make it a very rich remote and, for those on campus, in-person learning experience,” said Ian A. Waitz, vice chancellor for undergraduate and graduate education. He cited several examples: developing hands-on kits to send to remote students; shifting the timing of recitations to cover multiple time zones; making iPads available for teaching assistants and all undergraduates to replace “pencil and paper” work; implementing a new learning management system, called Canvas; and focusing on balancing synchronous and asynchronous teaching and learning.

In a similar vein, much effort has gone into ensuring that students can access hands-on learning experiences, explained Associate Dean of Engineering Peko Hosoi. “There are tremendous resources online now under Project Manus to help guide the students through making processes, understanding what tools are accessible, what kinds of tools can you use where, and how to get in touch with mentors.”

Fernandez reminded viewers that all undergraduates are eligible to pursue research, teaching, or service opportunities and earn a stipend of up to $1,900. “That will allow undergraduates to take full advantage of this new reality to do work, whether they’re on campus or remote, through programs such as UROP, UTOP, MISTI, PKG, Open Learning, and Sandbox. There are many people thinking about this, because it’s a very high priority for us to continue the ethos of making as part of learning.”

Welcoming MIT’s newest class

Several questions pertained to plans for first-year students, who will begin their MIT careers from home this fall. Concerns about forming connections with classmates, collaborating on schoolwork, and becoming part of the MIT community were addressed by Kate Weishaar ’18, project coordinator in the first-year experience program. “As anyone will tell you, the best part of MIT is the people, and we’re really trying to make sure that our first-year students see that, even if it is virtual.”

This summer, the Office of the First Year is offering orientation programming throughout the summer, a Slack channel, and small-group virtual gatherings. Many programs are in the works for the fall semester, Weishaar said, including expanding a successful mentoring pilot offered last spring in 8.02 (Electricity and Magnetism). She noted that more details about fall would be provided during the First-Year Town Hall on July 21.

Senior Associate Dean for Student Support and Wellbeing David Randall reassured first-years that MIT is committed to supporting them as they acclimate. “No matter how different it’s going to be in the fall, MIT is still going to be MIT … challenging, and rigorous, and sometimes overwhelming. Our amazing faculty are very aware of the challenges that students are facing and are being responsive. But we’ve got a whole team of support resources that remain available,” including advisors, Student Support Services, and Student Mental Health and Counseling at MIT Medical. “Right now, we’re thinking about all sorts of creative ways that we can allow students to easily ask for help online,” Randall added.

Dean for Admissions Stu Schmill offered guidance to incoming students weighing whether to take a gap year: consider your motivation for taking a gap year, and keep in mind that, although this won’t be a typical year at MIT, many gap year experiences are not available. Although each student should make the choice that is best for them, he said, “we’re working very hard to make the MIT experience continue to be special, continue to be something that’s in line with MIT’s mission, ‘mind and hand.’” 

Striking the right balance

In addition to fielding specific questions, panelists had the opportunity to expand on the decision process and rationale behind MIT’s approach this year. “If you look at what’s happened over the last four months,” Barnhart said, “we have engaged across the Institute — faculty, students, staff, alumni — and we have had literally thousands of people involved. So the overall decision process is reflective of a lot of thought, it’s reflective of striking what we feel is the appropriate balance among the interests of the various stakeholders.”

MIT’s stance is intentionally conservative, Waitz said. “Our strategy is to start the fall in a way where we have a smaller number of students on campus, where they are all in our residential facilities, where we have the ability to do regular testing and really to learn what it takes to operate in the pandemic. The whole strategy is wrapped around this idea of succeeding in the fall — not being right on the edge where we may succeed or fail.”

This approach will allow MIT to adapt for the spring, whether Covid conditions improve or not. “We’ve thought a lot about this,” Barnhart said, noting that the default posture for spring is also conservative. There are two additional factors that may allow more students to return in the spring, though: new residence halls will be open by then, and MIT will have a better understanding about the disease and how to manage it within the community. However, Barnhart said, “we feel confident that if conditions do not get better, our spring plan can remain intact.”

Many of the panelists mentioned the integral role students have played on various task forces, working groups, and other teams as MIT has wrestled with difficult — and sometimes unpopular — decisions impacting every aspect of their education. Hosoi said that students have been deeply involved in housing policy discussions and, as a case in point, shared what she called a “very MIT” story.

“I was asked to take a look at ventilation in houses and probabilities of infections in different spaces. I’ve now handed that off to a team of students to do all those calculations for all of the dorms. I have to say, I teach fluid mechanics, and I have never had students more interested in ventilation than they are right now! So I think the partnership with students is really important in this.”

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Edward Allen, professor of architecture, dies at 81

Edward Allen, longtime professor of architecture, passed away from complications of Parkinson’s disease on July 7 in Wayland, Massachusetts. He was 81 years old.

An architect by training, Allen was the author of bestselling books for architecture students and practitioners. A faculty member in the MIT Department of Architecture from 1968 to 1983, his research and teaching focused on building materials and construction, as well as structural design.

Allen was particularly known for embracing technical constraints in architectural design, and many of his 10 published books are still used in teaching architecture around the country and world, including “Fundamentals of Building Construction” (with co-author Joseph Iano BSAD ’83), now in its seventh edition.

“Ed Allen’s legacy at SA+P runs deep, as an inspiring teacher, an influential writer, and a committed member of the community,” says Hashim Sarkis, dean of the School of Architecture and Planning (SA+P). “Scores of students and faculty became better designers and instructors through exposure to his ideas and approach.”

Allen received a BArch with high distinction from the University of Minnesota in 1962 and an MArch from the University of California at Berkeley in 1964. He was an associate in the architectural firm of Moore/Lyndon/Turnbull/Whittaker for two years and contributed to the design of several significant residential projects at Sea Ranch in California. He then received a Fulbright research grant to study traditional stone structures in southern Italy in 1966-67, during which he wrote his first book, “Stone Shelters” (MIT Press, 1969).

He became a fellow of the American Institute of Architects in 2000, and was awarded the 2005 Topaz Medallion for Excellence in Architectural Education by the American Institute of Architects and the Association of Collegiate Schools of Architecture. The Topaz Medallion jury cited Allen’s role in developing project-driven courses for revolutionizing the teaching of technology in architecture schools. 

Allen taught and lectured widely at universities around the world and served as the Pietro Belluschi Distinguished Professor in Architectural Design at the University of Oregon in 1997. He returned to MIT as a lecturer in the Department of Architecture, teaching courses in building technology in 2003 and 2005.

Colleagues remember Allen as a brilliant teacher and designer who inspired students and professors alike with his deep rigor for the tectonics of architectural design and construction.

“Ed’s playful approach in linking architectural geometry with structural performance has galvanized generations of students and faculty to consider form and force as interacting drivers in creative design, and has certainly informed my own outlook and work in profound ways,” says Caitlin Mueller, associate professor of architecture and civil and environmental engineering.

Former SA+P Dean Adèle Santos says, “Ed’s books are on my bookshelves in my studio and are an essential source for any architectural practice. He was an inventive teacher with clarity of thinking that made students excited and passionate about the technical aspects of design. Ed was also a charming, thoughtful, and generous man. He was patient and calm with students, intellectually provocative and engaging with scholars, and a true friend to many. He will be greatly missed.”

Roger Goldstein BSAD ’74, MArch ’76, spoke for many former students in saying, “Ed’s thoughtful writings and teachings were an invaluable resource to me during school at MIT and later in my career as an architect. He was such a clear thinker and a great teacher — hence the dramatic success of his books on architecture.”

Allen is survived by his wife, Mary Allen, the Jean Glasscock Professor Emerita of Biological Sciences at Wellesley College. Together they established the Edward and Mary Allen Fund in Structural Design at MIT in 2012, to “support activities and teaching that will improve the ability of architects and engineers to design efficient, economical, and expressive structures.”

The endowed fund has brought leading designers to campus to give an annual lecture and work with students in the departments of Architecture and Civil and Environmental Engineering. Over the past nine years, the Allen Lecture has hosted prominent designers — including Jörg Schlaich, Janet Echelman, Les Robertson, and SawTeen See — who have continued to inspire MIT students and faculty in the fields of structural engineering and architectural geometry. 

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MIT-Wits Program continues to thrive

Now in its seventh year, the MIT-Wits Program is one of MIT’s most active in Africa. Whether through MIT International Science and Technology Initiatives (MISTI)-organized student opportunities and faculty seed funds, visiting professors, or its array of edX courses, the relationship is as strong as ever.

Known fondly known as Wits (and pronounced “Vits”), the University of the Witwatersrand in Johannesburg is one of South Africa’s oldest and most celebrated universities. Much like MIT, Wits has evolved alongside society — from a small technical institute focused on mining to a dynamic, diverse, and progressive research university with 40,000 students, 33 schools, and multiple Nobel Prizes under its belt.

“Generations of South African business and industrial leaders have been educated at Wits; so have many top politicians, trade unionists, and activists. Nelson Mandela is an alumnus of Wits,” says Professor Barry Dwolatzky, emeritus professor in the Wits School of Electrical and Information Engineering. “Our partnership with MIT over the past seven years has grown stronger and has found important synergies between our two important institutions. This has been achieved via the close collaborative engagement between Professor Hazel Sive and myself.”

“I set up this program as Wits is one of the very top research universities in Africa, and a good partner for MIT," says MIT biology professor and Wits alumna Hazel Sive, who established the MIT-Wits Program. “Wits has a student population representative of South African demographics, and serves as a clearinghouse for students from other African countries.”

Sive, who founded the MIT-Africa initiative, left MIT this June to become dean of the College of Science at Northeastern University in Boston. The momentum the collaboration has built will continue to grow unabated. Since 2012, MISTI has facilitated opportunities for more than 50 MIT students at Wits, both through research internships and in leading Global Startup Labs (GSL) at Wits’ Tshimologong Digital Innovation Precinct, which Dwolatzky founded.

"The GSL experience at Wits was a highlight of my graduate school experience,” says Ethan Poskanzer, PhD candidate in economics. “I met tons of interesting people and became a part of a South African community in a way that would have been difficult through other ways of traveling. The experience was also formative for my research interests as a social scientist."

Rising senior Andrea Orji worked as a researcher at the Wits University Centre of Excellence for Biomedical Tuberculosis Research during summer 2018. As a researcher, Orji went through the process of building a genomic DNA library to study a specific set of recurring genes in the DNA of mycobacteria, and improve understanding of their function. “I loved how open people were to answering my questions about the history and politics of the country,” she says. “They were not afraid to share their opinions or ask for mine. It made for really good conversations, as I waited through three-hour incubation periods for my E.coli transfections.”

In May 2020, Wits played a key role in the “Africa Takes on Covid19 Challenge.” The leadership of Tshimologong and several professors are committed to advising teams who participated in the challenge with the implementation of their ideas.

Beyond the MISTI opportunities for students, MISTI has been instrumental in creating research opportunities for faculty. The MISTI Global Seed Funds program has provided early-stage funding for several Wits-MIT research collaborations in both political science and physics.

Wits faculty have also had the opportunity to host their courses on edX. With over a dozen classes on the platform covering a range of topics from media studies to chemistry, learners from across the world have the opportunity to engage with the university. Wits is currently the only African university partner featured on edX and is a leader in establishing the African continent as an intellectual destination on the world stage. The availability of these courses is particularly relevant as the world grapples with the Covid-19 pandemic.

“We feel a strong affinity to MIT, that has similar origins amongst the great universities of the world,” says Dwolatzky. “Our university is a dominant influence on the South African educational landscape.”

"I am a proud Wits alum, having received my undergraduate degrees at Wits in chemistry and zoology. The familiar and vibrant Wits atmosphere made the MIT-Wits relationship a wonderful place to begin MIT-Africa," Sive says.

Professor Evan Lieberman, who is taking over as faculty director of MISTI’s MIT-Africa Program, has been working with colleagues at Wits since his first trip to the university in 1991 and looks forward to deepening the relationship in the years to come. "Wits is a remarkable institution for its research, its teaching, and its role in South Africa's future. I look forward to working closely with the faculty and administration to develop new collaborative opportunities with MIT."

In February 2020, the Wits’ newly appointed vice chancellor, Professor Zeblon Vilakazi, visited MIT to underscore the importance of the MIT-Wits relationship and lay the groundwork for more collaboration in the future. During his address to the MIT-Africa Forum, he discussed strides Wits was making to further its research activities across Africa. Wits played a leading role in the establishment of the African Research Universities Alliance (ARUA) – a network of universities across Africa enhancing research and post-graduate training on the continent.

“As a founding member of ARUA, Wits has played a leading role in supporting and growing world-class research in Africa,” says Vilakazi. “Working with Professor Hazel Sive and MIT-Africa, Wits and MIT has developed close collaborative partnerships with some ARUA members, which advances the positive narrative of “Africa Rising.’”

The MIT-Wits relationship is a critical piece of MIT’s overall Africa engagement strategy. Associate Provost for International Activities Richard Lester designated Africa, broadly, as a strategically important region.

“Frontier scientific research on major global challenges, and frontier applications of new technologies to address these challenges, will increasingly involve the African continent. Fostering stronger educational and research ties with African universities and collaborations of all kinds with our African alums will be an important priority for MIT in the coming years and decades,” says Lester.

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MindHandHeart announces a record 24 Community Innovation Fund projects

The MindHandHeart Innovation Fund has awarded a record 24 projects and has a new name. The newly titled MindHandHeart Community Innovation Fund seeks to leverage the creativity and problem-solving skills of MIT students, staff, and faculty to increase awareness about mental health, build communities of support, promote life skills, foster resiliency, and advance diversity, equity, inclusion, and racial justice at MIT.

Sponsored by the Office of the Chancellor, the fund has supported 162 projects to date. “The MindHandHeart Community Innovation Fund is helping to fuel grassroots projects that are bringing our community together during this challenging time,” says Chancellor Cynthia Barnhart. “It is heartening to see our community’s creativity, compassion, and hard work on full display in all of our Community Innovation Fund projects.”

The MindHandHeart Community Innovation Fund also launched a special summer edition. MIT staff, faculty, students, and students’ spouses are welcome to apply by Aug. 5 with ideas to build community and resilience in light of the Covid-19 pandemic; advance diversity, equity, inclusion, and racial justice at MIT; support mental and physical health; encourage healthy sleep, eating, and exercise; spread humor and joy; and welcome new members of the MIT community virtually. Grants of up to $10,000 are available.

This spring, nine of the newly funded 24 projects aim to build community and promote mental health. Sponsored by the Department of Athletics, Physical Education, and Recreation (DAPER), the 12-session “Fitness and Resiliency: The Power to Thrive” course is teaching the science and application of fitness and resiliency skills so students have the tools to manage life’s stressors and achieve their personal goals.

“Now, more than ever, the importance of maintaining and developing personal resiliency is paramount,” says Sarah Johnson, primary wellness instructor at DAPER and project lead for the course design. “This course is designed to teach resiliency concepts, such as the power of gratitude, growth mindset, identifying and leveraging one’s personal character strengths, and more. It will be an honor to teach and connect with students around these concepts, in addition to learning from and supporting each other, during this time of physical distancing.”

Organized by the Muslim Students' Association and the Office of Religious, Spiritual, and Ethical Life, “Muslim Mental Health Dialogues” is an event series sparking discussion about Muslim youth and mental health. PhD student and project lead Rabab Haider describes the event series, saying: “The goal of the Muslim Mental Health Dialogues Project is to facilitate honest conversations on mental health, wellness, and spirituality amongst the Muslims at MIT. We hope to create safe spaces within the community and promote meaningful and healthy dialog. Together, we're working to debunk myths and misconceptions that contribute to the perceived taboo of addressing mental health in our communities, answer questions and concerns, and provide resources to students seeking support or learning how to be better allies.”

Senior Fiona Chen’s “Loneliness and its Effect on Academic Performance” project consists of a research study designed to understand the effects of loneliness on academic outcomes. “The innovation fund has played an invaluable role in advancing my project,” says Chen. “Social science research projects often require substantial amounts of funding, but most funds only have grants available to PhD students or professors. I will be using the funding to recruit and compensate study participants — so without the innovation fund, the project would not be possible.”

This fall, the Department of Chemistry is launching their “Peer Mentoring Program” where current graduate students are matched with new graduate students in order to facilitate peer support and resource sharing. The Department of Biological Engineering (BE) is building out their “belong.mit.edu” website project with the aim of connecting the BE department during the Covid-19 pandemic and beyond. This summer, the Department of Earth, Atmospheric, and Planetary Sciences (EAPS) is bringing a conflict management training to their department as part of their “Conflict Management Training for the MIT-WHOI Joint Program and EAPS Community” project.

Sponsored by the Black Graduate Student Association, the “Self-Care in Community” initiative is sending a variety of care package kits to 50 of its members to support multiple dimensions of self-care, while supporting small Black-owned businesses during this time of economic crisis. “America’s Path Forward, Better Understanding Through Shared Experiences at MIT” is an inclusive civic technology that invites the entire MIT community to share questions and experiences they feel our nation must address, and participate in facilitated group discussions.“Voiceplace” is a student-driven interactive virtual environment where users can work, hold meetings, and connect.

Eight newly funded projects use art and storytelling to build community during the Covid-19 pandemic.

In partnership with the Alumni Association, juniors Emily Han and Amber Shen launched their “Sticker+Together” project to mail positive and affirming stickers to members of the MIT community. Organized by Active Minds, “Virtual Paint Bar” invites undergraduate students to paint images of campus together during a virtual paint night. The “Draw with Me” project consists of an informal weekly hangout for the MIT community to pause and refresh through drawing together online.

The “Calm Down with Coloring” project is bringing coloring books and pencils to the children and adults living in the Eastgate and Westgate residences. The “Happy Working from Home” project is engaging students in the Department of Electrical Engineering and Computer Science with virtual coloring events. The “Lumos” project consists of a series of workshops on making digital crafts.

Launching this summer, the “Staying Human Podcast” is a platform where MIT community members and prominent guests explore how to hold on to our collective humanity in this time of physical distancing. The “Stand-Up Comedy Class with Last Comic Standing’s Dan Crohn” is offering two classes in standup comedy to bring humor and joy to MIT.

Other projects include: “Asian Pacific Heritage Month,” a project to raise awareness of Asian American events and milestones through t-shirts and a digital campaign; “The Future is Latina,” a virtual event where a prominent Latina writer will speak to MIT’s Latina community; “Covid-19 Impact on Academic Well-being of Lab-based STEM Doctoral Students at their Research Midpoint,” an interview study that explores the disruption of the Covid-19 pandemic on the academic well-being of 30 lab-based STEM doctoral students; “Diaspora Recipe,” a website with recipes for healthy affordable meals that encourages students to stay connected to their heritages; “CovEd Continuing Education,” a virtual community connecting college students with low-income K-12 students in need of academic support during school shutdowns; “MIT Press Live! Virtual Author Talk Series,” a weekly virtual author talk series aimed at building vibrant online communities; and “Summer Yoga,” a weekly yoga classs for members of the Westgate and Eastgate residences.

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Bill Hanson, a founder of MIT Leaders for Global Operations, dies at 80

Bill Hanson, an inspirational founding figure of the MIT Leaders for Global Operations (LGO) program and a mentor to hundreds of its alumni, died on July 15 at the age of 80.

Hanson was senior vice president for manufacturing at the Digital Equipment Corporation, where he had a front-row seat to the challenges facing U.S. manufacturing in the 1980s, and brought this vision to his role helping found and develop LGO (then Leaders for Manufacturing, or LFM) in 1988 with MIT faculty including Kent Bowen, Thomas Magnanti, and the late Don Rosenfield.

Hanson moved full-time from the Digital Equiptment Corporation to MIT in 1996 to become LFM’s first industry co-director. He later helped found what is now the William C. Hanson, Don W. Davis and Janice Klein Leadership Fund to honor Davis (LFM’s first leadership instructor) and support leadership training within LGO. He retired in 2012 to Mashpee, Massachusetts, with his wife, Bette.

“Bill was an enlightened person with unusual warmth and a great passion for life, and he was a true friend to many of us,” says Magnanti, MIT Institute Professor. “He had a remarkable impact on manufacturing and industry, but also on education, especially at MIT. He was a beacon in bringing industry to the leadership of LFM. I had the privilege of working closely with him and benefited enormously from his wisdom, insight, and unfailing enthusiasm, as well as rooting with excitement with him for the Red Sox, Celtics, and Patriots.”

"Bill left an indelible legacy through his support of the LGO program and its graduates and industrial partners,” says Jeff Wilke LGO ’93, CEO of Global Consumer at Amazon. “He generously modeled ethical leadership by listening carefully and helping students and alums hone their individual styles.”

As a mentor to Leaders for Global Operations students, Hanson was known for asking questions that prompted students to look within themselves. “He asked what impact I wanted to have on the world, and how I would use the many opportunities I have been given to change lives for the better,” says Christina Simpson LGO ’11, senior manager for market development at Medtronic. “Bill inspired us all to be better and do more, and he will be greatly missed.”

During her LGO admission interview, “I immediately sensed Bill’s kindness, his earnestness and his belief in people’s potential,” says venture investor Rachel Sheinbein LGO '04. “He was a wonderful mentor during my time at LGO, and it didn’t stop there. When I was making a critical career decision, he asked his famous question: Was I looking for a job, a career, or an environment? He reminded me of my own passions and encouraged me to take a risk. It was the best decision of my life, and I wouldn’t have made the leap without Bill.”

SkipStone President A-P Hurd LGO ’04 had a similar experience during what seemed like a routine conversation, when Henson paused and asked, “What’s your legacy?”

“I was taken aback. ‘What do you mean? I'm 27, I don't have a legacy.’ Bill replied, ‘Well, you've been given a lot of opportunity. You better start figuring it out, because it's not just going to happen by itself.’ To this day, that is one of the best questions anyone has ever asked me.”

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An automated health care system that understands when to step in

In recent years, entire industries have popped up that rely on the delicate interplay between human workers and automated software. Companies like Facebook work to keep hateful and violent content off their platforms using a combination of automated filtering and human moderators. In the medical field, researchers at MIT and elsewhere have used machine learning to help radiologists better detect different forms of cancer. 

What can be tricky about these hybrid approaches is understanding when to rely on the expertise of people versus programs. This isn’t always merely a question of who does a task “better;” indeed, if a person has limited bandwidth, the system may have to be trained to minimize how often it asks for help.

To tackle this complex issue, researchers from MIT’s Computer Science and Artificial Intelligence Lab (CSAIL) have developed a machine learning system that can either make a prediction about a task, or defer the decision to an expert. Most importantly, it can adapt when and how often it defers to its human collaborator, based on factors such as its teammate’s availability and level of experience.

The team trained the system on multiple tasks, including looking at chest X-rays to diagnose specific conditions such as atelectasis (lung collapse) and cardiomegaly (an enlarged heart). In the case of cardiomegaly, they found that their human-AI hybrid model performed 8 percent better than either could on their own (based on AU-ROC scores).  

“In medical environments where doctors don’t have many extra cycles, it’s not the best use of their time to have them look at every single data point from a given patient’s file,” says PhD student Hussein Mozannar, lead author with David Sontag, the Von Helmholtz Associate Professor of Medical Engineering in the Department of Electrical Engineering and Computer Science, of a new paper about the system that was recently presented at the International Conference of Machine Learning. “In that sort of scenario, it’s important for the system to be especially sensitive to their time and only ask for their help when absolutely necessary.”

The system has two parts: a “classifier” that can predict a certain subset of tasks, and a “rejector” that decides whether a given task should be handled by either its own classifier or the human expert.

Through experiments on tasks in medical diagnosis and text/image classification, the team showed that their approach not only achieves better accuracy than baselines, but does so with a lower computational cost and with far fewer training data samples.

“Our algorithms allow you to optimize for whatever choice you want, whether that’s the specific prediction accuracy or the cost of the expert’s time and effort,” says Sontag, who is also a member of MIT’s Institute for Medical Engineering and Science. “Moreover, by interpreting the learned rejector, the system provides insights into how experts make decisions, and in which settings AI may be more appropriate, or vice-versa.”

The system’s particular ability to help detect offensive text and images could also have interesting implications for content moderation. Mozanner suggests that it could be used at companies like Facebook in conjunction with a team of human moderators. (He is hopeful that such systems could minimize the amount of hateful or traumatic posts that human moderators have to review every day.)

Sontag clarified that the team has not yet tested the system with human experts, but instead developed a series of “synthetic experts” so that they could tweak parameters such as experience and availability. In order to work with a new expert it’s never seen before, the system would need some minimal onboarding to get trained on the person’s particular strengths and weaknesses.

In future work, the team plans to test their approach with real human experts, such as radiologists for X-ray diagnosis. They will also explore how to develop systems that can learn from biased expert data, as well as systems that can work with — and defer to — several experts at once. For example, Sontag imagines a hospital scenario where the system could collaborate with different radiologists who are more experienced with different patient populations.

“There are many obstacles that understandably prohibit full automation in clinical settings, including issues of trust and accountability,” says Sontag. “We hope that our method will inspire machine learning practitioners to get more creative in integrating real-time human expertise into their algorithms.” 

Mozanner is affiliated with both CSAIL and the MIT Institute for Data, Systems and Society (IDSS). The team’s work was supported, in part, by the National Science Foundation.

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New design principle could prevent catheter failure in brain shunts

For medical professionals treating hydrocephalus — a chronic neurological condition caused by an abnormal accumulation of cerebrospinal fluid (CSF), resulting in pressure on the brain — there have been a limited range of treatment options. The most common is the surgical placement of a medical device called a shunt, a sort of flexible tube, which is placed in the ventricular system of the brain, diverting the flow of CSF from the brain to elsewhere in the body.

While effective, this surgery comes with risks (the procedure requires drilling a hole into the skull, after all), and the failure rate for these shunts, despite their lifesaving properties, is quite high. Whether congenital (present at birth, including spina bifida) or acquired (from a brain injury, for instance) — hydrocephalus affects more than 1 million Americans, ranging from infants and older children to seniors.

Now, MIT researchers have released a paper in the Journal of the Royal Society Interface that proposes and validates a new design principle for hydrocephalus catheters that seeks to overcome a central challenge in the design of these devices: that they regularly become clogged. A clogged catheter has life-threatening implications, especially for children, and usually leads to emergency surgery, the reopening of sealed scars and the possible need for resection of the implanted catheter from the brain before putting a new catheter in, followed by required additional healing time. This process carries with it the risk of damage to brain tissue and infection. For pediatric patients, catheters have a 60 percent chance of failure, often due to tissue that is clogs the catheters, eventually stopping the flow of CSF away from the brain.

The new research focuses on the potential redesign of the shunts, according to one of the authors of the paper, Thomas Heldt, an associate professor of electrical and biomedical engineering in the Department of Electrical Engineering and Computer Science and the Institute of Medical Engineering and Science (IMES). He points out that an important part of the research process was to conduct in vitro experiments exposing cell cultures to fluid shear stress, in addition to microfluidic flow imaging, and conducting fluid dynamic calculation and measurements.

“The point we are seeking to bring across is how to best design the catheter geometry to optimize the function of this medical device,” says Heldt. “These are design parameters that can change in such a way that a minimum force on the catheter walls is imposed to ensure minimal risk of cells adhesion in the first place.”

Lydia Bourouiba, the senior author of the paper and an associate professor in the departments of Civil and Environmental Engineering, Mechanical Engineering, and IMES, who directs The Fluid Dynamics of Disease Transmission Laboratory, says of the research: “The novelty is that we leveraged the coupling between mechanical (i.e., fluid dynamics here) principles and biological and cell response to enable novel pathways in design principles of these lifesaving medical devices.”

Along with Bourouiba and Heldt, the authors of the paper are Songkwon Lee, a PhD student in the Department of Mechanical Engineering; Nicholas Kwok, an MD student in the Harvard-MIT Program in Health Sciences and Technology; and James Holsapple, chief of neurosurgery at Boston Medical Center.

According to Heldt, the new research could lead to redesigned shunts that would “keep the minimum wall shear stress sufficiently high, above a threshold value we identified to be sufficient to minimize cell adhesion and proliferation. If  we prevent these cells from adhering in the first place, we undercut the key step responsible for long-term clogging and failure of brain catheters.”

Dwight Meglan, an engineer who is the chief technology officer of HeartLander Surgical, a medical device company, has a daughter, Emma, who has needed hydrocephalus catheters since birth. He says that due to his own background as an engineer, he has puzzled over how catheters could be more resistant to failure, and has sometimes conferred with Heldt on the challenge. He says that what he finds interesting about the new research, if it leads to a new catheter construction, is that “this is more foundational than some other research I’ve seen, because they are actually looking at this from the point of view that perhaps the problem is due to an underlying design failure.”

Bourouiba says that previously, research on preventing shunt failures has often focused on “surface engineering, with little translation into practice due to the sensitive location in which these catheters are used: the brain. A major concern is the durability and stability of chemical solutions in long-term usage in a patient’s brain, particularly when developing brains are involved.”

By contrast, she continues, “Our paper leveraged a novel combination of state-of-the-art flow visualization and quantification, fluid dynamics modeling, coupled with in-vitro experiments, to arrive at new design principles for these catheters, based on the concept of maximizing the minimal fluid shear stress so as to prevent cells from successfully adhering to and weakly proliferating onto the catheter in the first place.”

Kwok, a fourth-year medical student, said he was looking for a research project for his thesis when Heldt suggested the hydrocephalus catheter research idea, combining “engineering and medicine to develop new diagnostic and therapeutic technologies … and I was hooked.” He says he hopes to pursue basic science research during an internal medicine residency he will apply for in the fall, with the goal of “clinically oriented engineering research as a practicing physician, combining patient care with therapeutic innovation.”

For Edward Smith, the R. Michael Scott Chair in Neurosurgery at Boston Children’s Hospital, the potential for lifesaving advances that could mitigate the frequency of shunt malfunctions is encouraging. “The data presented in this manuscript are novel, and offer a different way of looking at a serious problem routinely faced by clinicians,” he adds.

Now that the researchers have demonstrated experimental validation to the design principles, prototypes would need to be produced and used in clinical trials. But whether the research advances and results in better functioning shunts somewhere down the line, Bourouiba says that the process has already proved rewarding. “It was very exciting to gain a fundamental understanding of the coupling between flow and particular brain cell behavior, and to leverage such understanding to develop fluid-dynamics-based and validated algorithms, guiding a novel design principle for hydrocephalus catheters, rooted in the inherent coupling between the physics and biology involved,” she says.

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Q&A: Peter Fisher discusses JASON report on reopening university laboratories

What will it take for research universities across the U.S. to safely open their labs? That’s the subject of a recently released report by JASON, an independent group of scientists who advise the U.S. government about science and technology, in association with the MITRE Corporation. The report was led by Peter Fisher, professor and head of MIT’s Department of Physics, who is a JASON member. (MIT has separately examined the question, and began a phased ramp-up of lab research in June; Fisher participated in MIT reopening efforts as well.) MIT News talked with Fisher about the JASON report.

Q: What are the main things the JASON report recommends to universities trying to reopen labs?

A: Probably the top-level things are just mask-wearing, handwashing, and social distancing. Those are three things that everybody can do. And people know this, but the report looks in exhaustive detail at why those things are important — from the physics of masks to a whole section on air handling and how the virus builds up in the air. The design of campuses, including MIT, is intended to bring people together as much as possible, so we are really fighting the physical nature of MIT.

The research is important because the people who work in the labs and come back to campuses have to buy into these rules. And I think they buy in much better if they understand the science behind the rules.

Q: One implication of the report is that details matter greatly. For instance, the report notes that, compared to breathing, the viral load people exhale from speaking is 20 times as great — so you recommend communicating via text, whiteboards, scratch pads, or other nonverbal means. And the report has a section on proper mask fitting. Won’t people have to get used to some distinctly new practices?

A: Yes. For example, really minimize the amount you speak. And you can whisper. The amount that comes out between breathing [on the one hand], and speaking, singing, and shouting [on the other] is just enormous. … [Regarding masks], if you are in a hospital wearing one, part of the standard operating procedure is there is a specialist who fits it onto your face. There’s a metal bar that goes across your nose and it’s all about how you press down that metal bar so it forms a good seal, going across your nose and your cheekbones.

Q: Beyond those things, the report suggests making aggregate health information available to community in a dashboard format. Why would that help?

 A: Because people are competitive. And sometimes if you want to get people to do something, you turn it into a game. Also, from some of the work the organization does with the military, there is what’s called situational awareness. That comes down to a few numbers that tell you how you’re doing. And for Covid-19, it would be how many tests have you administered; how many of them came back positive; how many people are coming onto campus every day; and how many of them are not complying with the rules, like wearing masks. It’s all anonymous, but it gives you a snapshot of how you’re doing.

When you design a system, you can’t just assume that compliance is going to be 100 percent. It’s going to be lower, and you have to account for that in your planning and thinking. That’s one [reason] we talked about the dashboard. Another thing [that helps] is really good modeling. At MIT, the senior researchers and faculty are very highly regarded and closely watched. And I think really the faculty and senior research staff have to model this behavior.

Q: The report also discusses whether university campuses can be “islands” apart from the pandemic, or part of larger community. What are some of the factors at play there?

A: It depends on what you’re willing to do and where you are. MIT is an urban campus and Cambridge is one of the most densely populated places around. Everybody on campus, before the Covid-19, relied on the surrounding community for something — food, entertainment, health services. And it’s hard to change that. Inevitably, how a university is doing is going to be closely coupled to the community it’s embedded in. It’s true of all the big Boston-area campuses.

In [rural cases], the college can separate itself pretty well from the city. … [For example], at Vassar they are having a strict rule: Nobody leaves campus, and they’re going to try to make it into a bubble. Some colleges, you can draw a line around campus, and it’s clear what is campus and what is not campus. But MIT leaks out all into the city.

Q: It seems apparent from all this that some universities might have midstream, midsemester decisions to make. There might be plans in place, but don’t institutions have to keep in mind that circumstances can change, this fall or further out in the future?

A: It’s really tough because the nature of this disease is that the people feeling symptoms now were infected five days ago. The people who are in the hospital now [were infected] 14 days ago. Knowing how many positive cases you’re getting today is not a great indicator of how many people are going to feel sick tomorrow. It’s an indicator of how many people are going to feel really sick in two weeks, and during that time, the virus can spread exponentially. So there are going to have to be some tough decisions to be made. You don’t want to have to suddenly make them when you have 400 sick students to contend with. I think MIT’s done smart things — including the single-room occupancy housing policy. The leadership at MIT is taking the long view.

One thing that everybody is only starting to struggle with is that the world just changed, in this really fundamental way. We’re all hoping it gets a lot better, but where that ends up is not going to be where we were at the start of 2020. We’re living through a remarkable moment in history. It’s quite daunting to think about, but what we always try to do with JASON [reports] is just detail the bedrock science.

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Rapid antibody development yields possible treatment for yellow fever

Yellow fever, a hemorrhagic disease that is common in South America and sub-Saharan Africa, infects about 200,000 people per year and causes an estimated 30,000 deaths. While there is a vaccine for yellow fever, it can’t be given to some people because of the risk of side effects, and there are no approved treatments for the disease. 

An international team of researchers, led by MIT Professor Ram Sasisekharan, has now developed a potential treatment for yellow fever. Their drug, an engineered monoclonal antibody that targets the virus, has shown success in early-stage clinical trials in Singapore. 

This class of antibodies holds promise for treating a variety of infectious diseases, but it usually takes several years to develop and test them. The MIT-led researchers demonstrated that they could design, produce, and begin clinical trials of their antibody drug within seven months.

Their approach, which condenses the timeline by performing many of the steps necessary for drug development in parallel, could also be applied to developing new treatments for Covid-19, says Sasisekharan, the Alfred H. Caspary Professor of Biological Engineering and Health Sciences and Technology. He adds that a potential Covid-19 antibody treatment, developed using this approach in a process that took just four months, has shown no adverse events in healthy volunteers in phase I clinical trials, and phase 3 trials are expected to start in early August in Singapore.

“Traditional drug development processes are very linear, and they take many years,” Sasisekharan says. “If you’re going to get something to humans fast, you can’t do it linearly, because then the best-case scenario for testing in humans is a year to 18 months. If you need to develop a drug in six months or less, then a lot of these things need to happen in parallel.”

Jenny Low, a senior consultant in infectious diseases at Singapore General Hospital, is the lead author of the study, which appears today in the New England Journal of Medicine. Researchers from the Singapore-MIT Alliance for Research and Technology (SMART), Duke-National University of Singapore Medical School, and the biotechnology company Tysana Pte also contributed to the study.

Speeding up the process

Several types of monoclonal antibodies have been approved to treat a variety of cancers. These engineered antibodies help to stimulate a patient’s immune system to attack tumors by binding to proteins found on cancerous cells.

Many researchers are also working on monoclonal antibodies to treat infectious diseases. In recent years, scientists have developed an experimental cocktail of three monoclonal antibodies that target the Ebola virus, which has shown some success in clinical trials in the Democratic Republic of Congo.

Sasisekharan began working on a “rapid response” to emerging infectious diseases after the Zika outbreak that started in 2015. Singapore, which experienced a small outbreak of the Zika virus in 2016, is home to the SMART antimicrobial resistance research group, where Sasisekharan is a principal investigator.

The Sasisekharan lab antibody design process uses computational methods to target functionally important, and evolutionarily stable, regions on the virus. Building blocks from a database of all known antibody elements are selected based on several criteria, including their functional importance, to build candidate antibodies to evaluate. Testing these candidates provides valuable feedback, and the design loop continues until an optimized antibody that fully neutralizes the target virus is identified.

The group also explored new approaches to compress the timeline by performing many of the necessary steps in parallel, using analytical techniques to address regulatory risks associated with drug safety, manufacturing, and clinical study design. 

Using this approach, the researchers developed a candidate Zika treatment within nine months. They performed phase 1a clinical trials to test for safety in March 2018, but by the time they were ready to test the drug’s effectiveness in patients, the outbreak had ended. However, the team hopes to eventually test it in areas where the disease is still present.

Sasisekharan and his colleagues then decided to see if they could apply the same approach to developing a potential treatment for yellow fever. Yellow fever, a mosquito-borne disease, tends to appear seasonally in tropical and subtropical regions of South America and Africa. A particularly severe outbreak began in January 2018 in Brazil and lasted for several months. 

The MIT/SMART team began working on developing a yellow fever antibody treatment in March 2018, in hopes of having it ready to counter an outbreak so that it could be made available for potential patients in late 2018 or early 2019, when another outbreak was expected. They identified promising antibody candidates based on their ability to bind to the viral envelope and neutralize the virus that causes yellow fever. 

The researchers narrowed their candidates down to one antibody, which they called TY014. They then developed production methods to create small, uniform batches that they could use to perform necessary testing phases in parallel. These tests include studying the drugs’ effectiveness in human cells, determining the most effective dosages, testing for potential toxicity, and analyzing how the drug behaves in animal models. As soon as they had results indicating that the treatment would be safe, they began clinical trials in December 2018.

“The mindset in the industry is that it’s like a relay race. You don’t start the next lap until you finish the previous lap,” Sasisekharan says. “In our case, we start each runner as soon as we can.”

Clinical trials

TY014 was clinically tested in parallel to address safety through dose escalation in healthy human volunteers. Once an appropriate dose was deemed safe, the researchers began a phase 1b trial, in which they measured the antibody’s ability to clear the virus. Even though the 1b trial had begun, the 1a trial continued until a maximum safe dose in humans was identified. 

Because there is a vaccine available for yellow fever, the researchers could perform a type of clinical trial known as a challenge test. They first vaccinated volunteers, then 24 hours later, they gave them either the experimental antibody drug or a placebo. Two days after that, they measured whether the drug cleared the weakened viruses that make up the vaccine.

The researchers found that following treatment, the virus was undetectable in blood samples from people who received the antibodies. The treatment also reduced inflammation following vaccination, compared to people who received the vaccine but not the antibody treatment. The phase 1b trial was completed in July 2019, and the researchers now hope to perform phase 2 clinical trials in patients infected with the disease. 

The research was funded by Tysana Pte. Tysana is also performing the clinical trials now underway for a Covid-19 treatment that was developed along with Singaporean government agencies including the Ministry of Defense, the Ministry of Health, and the Economic Development Board.

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Proteins — and labs — coming together to prevent Rett syndrome

New discoveries about the disruption of condensates in the neurodevelopmental disorder Rett syndrome provide insights into how cells compartmentalize chromosomes, as well as new potential paths for therapies.

Scientists have, for many years, conceptualized the cell as a relatively free-flowing space, where — apart from the organization provided by specific cellular structures — molecules float freely, somehow ultimately ending up in the right place at the right time. In recent years, however, scientists have discovered that cells have much more spatial organization than previously thought, thanks to a mechanism called phase separation, which occurs in cells when certain molecules form large droplet-like structures that separate what's inside of the droplet from the rest of the cell. The droplets, called condensates, help sequester and concentrate molecules in specific locations, and appear to increase the efficiency of certain cellular functions.

Whitehead Institute member and MIT professor of biology Richard Young has been exploring the previously unknown role that condensates play in gathering the molecules needed for gene transcription — the process by which DNA is read into RNA. In order to better understand when and how cells use phase separation, Charles Li, a graduate student in Young's lab, set out to identify more proteins that can form condensates. That search led him to MeCP2, a protein associated with the severe neurodevelopmental disorder Rett syndrome, studied by Young's colleague, Whitehead Institute founding member Rudolf Jaenisch, who is also a professor of biology at MIT. No cure for Rett syndrome currently exists, and Jaenisch's lab has been investigating the biology of the disorder in the hopes of discovering a medical therapy that can rescue neurons affected by Rett syndrome.

With the discovery of MeCP2's condensate-forming ability, Young and Jaenisch saw the opportunity for a promising collaboration between their labs. Led by co-first authors Li and Eliot Coffey, another graduate student in Young's lab, the two labs investigated MeCP2 and whether the disruption of its condensate-forming ability contributes to Rett syndrome. During these investigations, the researchers also uncovered how cells may use condensates to help organize the active and inactive parts of chromosomes. Their findings, published in the journal Nature on June 22, report on these insights and suggest new paths for developing therapies for Rett syndrome.

Phase separation and Rett syndrome

Proteins that form condensates often contain intrinsically disordered regions (IDRs), long spaghetti-like strands that transiently stick together to form a dynamic mesh. Research has historically focused on the structured regions of proteins, which bind very specifically to other molecules, while IDRs have largely been overlooked. In this case, MeCP2's large IDRs were exactly what drew Li to it.

"What was striking to me was that this protein has been studied for decades, and so much function has been ascribed to the protein as a whole, yet it only has one structured domain with a recognized function, the DNA binding domain. Beyond that, the entire protein is disordered, and how its parts function was largely unknown," Li says.

The researchers found that MeCP2 used its IDRs to glom together and form condensates. Then they tested many of the mutations in the MECP2 gene that are associated with Rett syndrome and found that they all disrupt MeCP2's ability to form condensates. Their findings suggest that therapies targeting condensates associated with the protein, rather than the protein itself, may be promising in the hunt for a Rett syndrome treatment.

"MeCP2 and Rett syndrome have been studied intensely for many years in many labs, and yet not a single therapy has been developed. When the project began, I was immediately fascinated by the idea that we might find a new disease mechanism that could help us finally understand how Rett syndrome arises and how it could be treated," Coffey says.

"Rick [Young] has shown that condensates play key roles in maintaining normal cellular function, and our latest collaboration illuminates how their disruption may drive diseases such as Rett syndrome," Jaenisch says. "I hope the insights we have gained will prove useful both in our continued search for a treatment for Rett syndrome and, more broadly, in research on condensates and disease."

Compartmentalizing chromosomes

The researchers' investigation into MeCP2's condensate-forming behavior also shed light on how chromosomes are organized into regions of active and inactive genes. When MeCP2 is functioning normally, it helps to maintain heterochromatin, the roughly half of our chromosomes where genes are "turned off," unable to be read into RNA or further processed to make proteins. MeCP2 binds to sequences of DNA marked with a certain type of regulatory tag that is typically found in heterochromatin. This helps crowd MeCP2 to the threshold concentration needed to form heterochromatin condensates. These condensates, in turn, help to sequester the molecules needed to maintain it apart from euchromatin, the half of our chromosomes filled with active genes. Different proteins form condensates near euchromatin, concentrating the molecular machinery needed to transcribe active genes there.

Since condensates form when proteins with large spaghetti-like IDRs stick together, one might expect that any protein containing IDRs could interact with any other IDR-containing protein to form droplets, and that is what the researchers have often seen. However, what they observed with MeCP2, which is associated with heterochromatin, is that key condensate-forming proteins associated with euchromatin refused to mix.

It's important for the health of the cell that the genes in heterochromatin not be inadvertently turned on. The researchers reason that discrete euchromatin and heterochromatin condensates may play a key role in ensuring that transcriptional machinery localizes to euchromatin only, while repressive machinery — like MeCP2 — localizes to heterochromatin. The researchers are excited to turn their attention to how proteins are able to join condensates selectively, and when and where else in the cell they do so.

"There's a chemical grammar waiting to be deciphered that explains this difference in the ability of some proteins to move into one condensate versus another," Young says. "Discovering that grammar can help us understand how cells maintain the crucial balance between the active and silent halves of our genome, and it could help us understand how to treat disorders such as Rett syndrome."

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3 Questions: Jonathan King on the future of nuclear weapons testing

In an open letter published on July 16 in Science, four MIT professors and nearly 70 additional scientific leaders called upon fellow researchers to urge U.S. government officials to halt plans to restart nuclear weapons testing. Corresponding author and professor of biology Jonathan King sat down to discuss the history of nuclear testing, his personal ties to the issue, and his responsibilities as a scientist. He also co-chairs the Nuclear Disarmament Working Group of Massachusetts Peace Action, MIT’s annual Reducing the Threat of Nuclear War conference, and the editorial board of the MIT Faculty Newsletter.

Q: What events have made you passionate about the issue of nuclear weapons testing?

A: I grew up in the shadow of nuclear war, participating in drills at school where you would duck under your desk. During the Cold War, the world’s nations exploded hundreds of dangerous nuclear tests, releasing radioactivity into the atmosphere in order to develop these weapons. I was a college student during the Cuban Missile Crisis, and remember vividly the fear of a nuclear exchange.

Around that time, it became clear to our nation’s leaders that this was not the way to go. In his famous speech at American University, President Kennedy reversed direction. Professor of chemistry at Caltech Linus Pauling led an effort with his wife to back Kennedy and collect 9,000 signatures from scientists endorsing the president’s Partial Nuclear Test Ban Treaty. This was before the internet, so getting 9,000 signatures was not easy, and it had a national impact. I was actually a graduate student at Caltech, following up on Pauling’s work on proteins, when the treaty was ratified and he was awarded the Nobel peace prize for his work.

When I arrived at MIT as an assistant professor, Jerome Wiesner was the Institute president. He was also a key player in pushing the Partial Nuclear Test Ban Treaty, and Kennedy had previously named him chair of the President's Science Advisory Committee (PSAC). MIT was full of world leaders in nuclear disarmament, including physicists who had worked on the bomb and decided it was a mistake. I'm not a physicist, but I was among the generation at MIT that was very vocal about these issues.

Q: What is the current state of nuclear weapon testing and regulation in the United States, and what concerns do you have about renewed testing?

A: The U.S. hasn't tested a nuclear weapon since 1992. In that period of time, the Comprehensive Test Ban Treaty (CTBT) was developed by many nations, agreeing not to conduct a nuclear weapons test of any yield. The Senate hasn't ratified it, but in 2016 the U.S. did adopt UN Security Council Resolution 2310, agreeing to uphold the goal of the CTBT and withhold nuclear testing.

However, the current administration is proposing to modernize nuclear weapons and restart testing, which is both provocative and dangerous. Even if these tests are small, contained, and underground, they will still open the door for other nations to restart testing of their own, and possibly lead to a new nuclear weapons arms race.

When a nuclear weapon — either a conventional bomb or hydrogen bomb — explodes, many radioactive isotopes are produced. Some of them are short-lived and decay quickly, but others like strontium-90 are much longer-lived. These ones can make you sick very slowly, and some can mutate or damage DNA. Even underground tests can leak radioactivity into the atmosphere and environment.

Q: What spurred you and your colleagues to write an open letter to Science, and what was your goal in doing so?

A: Our letter was signed by 70 scientific leaders and Nobel Prize winners, and calls upon the scientific community to warn the nation that this is a dangerous way to go. We also urged the Senate to ratify the CTBT, and pass a new bill introduced by Senator Ed Markey called the Preserving Leadership Against Nuclear Explosives Testing (PLANET) Act — which would prevent spending money on the renewal of testing.

I come from a culture that views scientists as public servants. All my research has been funded by taxpayer dollars, and with that comes a responsibility to help address threats to the community. The very history of my department, the MIT Department of Biology, is tied to scientists taking a stand against social and political issues. I was just a young assistant professor when faculty members like David Baltimore and Ethan Signer led demonstrations to oppose the Vietnam War. It was a very open environment and we supported one another.

These days, science is simply a career. You do your work and you keep your eyes to the bench. But the world can be a better place if we take our eyes off the bench occasionally. So this letter is a reminder to our colleagues: Get involved, and consider it our contribution to the general public who support our research.

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School of Engineering first and second quarter 2020 awards

Members of the MIT engineering faculty receive many awards in recognition of their scholarship, service, and overall excellence. The School of Engineering periodically recognizes their achievements by highlighting the honors, prizes, and medals won by faculty working in our academic departments, labs, and centers.

• Jesús del Alamo of the Department of Electrical Engineering and Computer Science won the Indium Phosphide and Related Materials Award 2020 on May 18.
• Saman Amarasinghe of the Department of Electrical Engineering and Computer Science was named an Association for Computing Machinery Fellow on Dec. 12, 2019.
• Brian Anthony of the Department of Mechanical Engineering won the Google Faculty Research Award 2019-2020 on Feb. 17.
• Robert C. Armstrong of the Department of Chemical Engineering was made member of the American Academy of Arts and Sciences on April 23.
• Guy Bresler of the Department of Electrical Engineering and Computer Science won a National Science Foundation CAREER Award on Jan. 24.
• Michael Carbin of the Department of Electrical Engineering and Computer Science was awarded a Sloan Research Fellowship in Computer Science on Feb. 12.
• Joel Emer of the Department of Electrical Engineering and Computer Science was elected to the National Academy of Engineering on Feb. 6, and won the IEEE/ACM International Symposium on Microarchitecture Best Paper Award in October 2019.
• William Freeman of the Department of Electrical Engineering and Computer Science was named a Fellow of the Association for the Advancement of Artificial Intelligence on Feb. 9.
• Daniel Frey of the Department of Mechanical Engineering was awarded the Charles M. Manly Memorial Medal on March 20.
• Robert Gallager of the Department of Electrical Engineering and Computer Science was named a Japan Prize Laureate by the Japan Prize Foundation on Feb. 7.
• Ming Guo of the Department of Mechanical Engineering was named the 2020 Sloan Research Fellow in Physics on Feb. 17.
• Song Han of the Department of Electrical Engineering and Computer Science won a National Science Foundation CAREER Award on Jan. 24.
• David Hardt of the Department of Mechanical Engineering was nominated to the 2020 Society of Manufacturing Engineers College of Fellows on June 9.
• Neville Hogan of the Department of Mechanical Engineering was awarded the Science Foundation Ireland’s St. Patrick’s Day Medal for Academia 2020 on March 20.
• Roger Kamm of the Department of Mechanical Engineering won the Shu Chien Achievement Award on Jan. 20.
• James LeBeau of the Department of Materials Science and Engineering was awarded the Burton Medal on March 27.
• Heather Lechtman of the Department of Materials Science and Engineering won the Pomerance Award for Scientific Contributions to Archaeology on Jan. 20.  
• Jae Lim of the Department of Electrical Engineering and Computer Science was named a 2020 Ho-Am Prize laureate on April 8.
• Muriel Médard of the Department of Electrical Engineering and Computer Science received an Honorary Doctorate from the Technical University of Munich on Jan. 17, and she became a member of the National Academy of Engineering on Feb. 6.
• Stefanie Mueller of the Department of Electrical Engineering and Computer Science won the Sloan Research Fellowship in Computer Science on Feb. 12, and was named a Microsoft Research Faculty Fellow on April 17.
• Yury Polyanskiy of the Department of Electrical Engineering and Computer Science won the 2020 James L. Massey Award on June 29.
• Wim van Rees of the Department of Mechanical Engineering was named principal investigator for the U.S. Department of Energy's Office of Science Early Career Research Program on June 23.
• Alberto Rodriguez of the Department of Mechanical Engineering won the IEEE Early Academic Career Award in Robotics and Automation on Feb. 5, and the Google Faculty Research Award 2019-2020 on Feb. 20.  
• Jeffrey H. Shapiro of the Department of Electrical Engineering and Computer Science won the IEEE Signal Processing Society Best Paper Award on May 5.
• Collin Stultz of the Department of Electrical Engineering and Computer Science was named a Fellow of the American Institute for Medical and Biological Engineering on March 24.
• Vivienne Sze of the Department of Electrical Engineering and Computer Science won the inaugural Rising Star Award from the Association for Computing Machinery Council on Women in Computing on May 29.
• Dick K.P. Yue of the Department of Mechanical Engineering was elected to the National Academy of Engineering on Feb. 6.

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“Giant atoms” enable quantum processing and communication in one

MIT researchers have introduced a quantum computing architecture thatcan perform low-error quantum computations while also rapidly sharing quantum information between processors. The work represents a key advance toward a complete quantum computing platform.

Previous to this discovery, small-scale quantum processors have successfully performed tasks at a rate exponentially faster than that of classical computers. However, it has been difficult to controllably communicate quantum information between distant parts of a processor. In classical computers, wired interconnects are used to route information back and forth throughout a processor during the course of a computation. In a quantum computer, however, the information itself is quantum mechanical and fragile, requiring fundamentally new strategies to simultaneously process and communicate quantum information on a chip.

“One of the main challenges in scaling quantum computers is to enable quantum bits to interact with each other when they are not co-located,” says William Oliver, an associate professor of electrical engineering and computer science, MIT Lincoln Laboratory fellow, and associate director of the Research Laboratory for Electronics. “For example, nearest-neighbor qubits can easily interact, but how do I make ‘quantum interconnects’ that connect qubits at distant locations?”

The answer lies in going beyond conventional light-matter interactions.

While natural atoms are small and point-like with respect to the wavelength of light they interact with, in a paper published today in the journal Nature, the researchers show that this need not be the case for superconducting “artificial atoms.” Instead, they have constructed “giant atoms” from superconducting quantum bits, or qubits, connected in a tunable configuration to a microwave transmission line, or waveguide.

This allows the researchers to adjust the strength of the qubit-waveguide interactions so the fragile qubits can be protected from decoherence, or a kind of natural decay that would otherwise be hastened by the waveguide, while they perform high-fidelity operations. Once those computations are carried out, the strength of the qubit-waveguide couplings is readjusted, and the qubits are able to release quantum data into the waveguide in the form of photons, or light particles.

“Coupling a qubit to a waveguide is usually quite bad for qubit operations, since doing so can significantly reduce the lifetime of the qubit,” says Bharath Kannan, MIT graduate fellow and first author of the paper. “However, the waveguide is necessary in order to release and route quantum information throughout the processor. Here, we’ve shown that it’s possible to preserve the coherence of the qubit even though it’s strongly coupled to a waveguide. We then have the ability to determine when we want to release the information stored in the qubit. We have shown how giant atoms can be used to turn the interaction with the waveguide on and off.”

The system realized by the researchers represents a new regime of light-matter interactions, the researchers say. Unlike models that treat atoms as point-like objects smaller than the wavelength of the light they interact with, the superconducting qubits, or artificial atoms, are essentially large electrical circuits. When coupled with the waveguide, they create a structure as large as the wavelength of the microwave light with which they interact.

The giant atom emits its information as microwave photons at multiple locations along the waveguide, such that the photons interfere with each other. This process can be tuned to complete destructive interference, meaning the information in the qubit is protected. Furthermore, even when no photons are actually released from the giant atom, multiple qubits along the waveguide are still able to interact with each other to perform operations. Throughout, the qubits remain strongly coupled to the waveguide, but because of this type of quantum interference, they can remain unaffected by it and be protected from decoherence, while single- and two-qubit operations are performed with high fidelity.

“We use the quantum interference effects enabled by the giant atoms to prevent the qubits from emitting their quantum information to the waveguide until we need it.” says Oliver.

“This allows us to experimentally probe a novel regime of physics that is difficult to access with natural atoms,” says Kannan. “The effects of the giant atom are extremely clean and easy to observe and understand.”

The work appears to have much potential for further research, Kannan adds.

“I think one of the surprises is actually the relative ease by which superconducting qubits are able to enter this giant atom regime.” he says. “The tricks we employed are relatively simple and, as such, one can imagine using this for further applications without a great deal of additional overhead.”

Andreas Wallraff, professor of solid-state physics at ETH Zurich, says the research "investigates a piece of quantum physics that is hard or even impossible to fathom for microscopic objects such as electrons or atoms, but that can be studied with macroscopic engineered superconducting quantum circuits. With these circuits, using a clever trick, they are able both to protect their giant atom from decay and simultaneously to allow for coupling two of them coherently. This is very nice work exploring waveguide quantum electrodynamics."

The coherence time of the qubits incorporated into the giant atoms, meaning the time they remained in a quantum state, was approximately 30 microseconds, nearly the same for qubits not coupled to a waveguide, which have a range of between 10 and 100 microseconds, according to the researchers.

Additionally, the research demonstrates two-qubit entangling operations with 94 percent fidelity. This represents the first time researchers have quoted a two-qubit fidelity for qubits that were strongly coupled to a waveguide, because the fidelity of such operations using conventional small atoms is often low in such an architecture. With more calibration, operation tune-up procedures and optimized hardware design, Kannan says, the fidelity can be further improved.

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Bringing RNA into genomics

The human genome contains about 20,000 protein-coding genes, but the coding parts of our genes account for only about 2 percent of the entire genome. For the past two decades, scientists have been trying to find out what the other 98 percent is doing.

A research consortium known as ENCODE (Encyclopedia of DNA Elements) has made significant progress toward that goal, identifying many genome locations that bind to regulatory proteins, helping to control which genes get turned on or off. In a new study that is also part of ENCODE, researchers have now identified many additional sites that code for RNA molecules that are likely to influence gene expression.

These RNA sequences do not get translated into proteins, but act in a variety of ways to control how much protein is made from protein-coding genes. The research team, which includes scientists from MIT and several other institutions, made use of RNA-binding proteins to help them locate and assign possible functions to tens of thousands of sequences of the genome.

“This is the first large-scale functional genomic analysis of RNA-binding proteins with multiple different techniques,” says Christopher Burge, an MIT professor of biology. “With the technologies for studying RNA-binding proteins now approaching the level of those that have been available for studying DNA-binding proteins, we hope to bring RNA function more fully into the genomic world.”

Burge is one of the senior authors of the study, along with Xiang-Dong Fu and Gene Yeo of the University of California at San Diego, Eric Lecuyer of the University of Montreal, and Brenton Graveley of UConn Health.

The lead authors of the study, which appears today in Nature, are Peter Freese, a recent MIT PhD recipient in Computational and Systems Biology; Eric Van Nostrand, Gabriel Pratt, and Rui Xiao of UCSD; Xiaofeng Wang of the University of Montreal; and Xintao Wei of UConn Health.

RNA regulation

Much of the ENCODE project has thus far relied on detecting regulatory sequences of DNA using a technique called ChIP-seq. This technique allows researchers to identify DNA sites that are bound to DNA-binding proteins such as transcription factors, helping to determine the functions of those DNA sequences.

However, Burge points out, this technique won’t detect genomic elements that must be copied into RNA before getting involved in gene regulation. Instead, the RNA team relied on a technique known as eCLIP, which uses ultraviolet light to cross-link RNA molecules with RNA-binding proteins (RBPs) inside cells. Researchers then isolate specific RBPs using antibodies and sequence the RNAs they were bound to.

RBPs have many different functions — some are splicing factors, which help to cut out sections of protein-coding messenger RNA, while others terminate transcription, enhance protein translation, break down RNA after translation, or guide RNA to a specific location in the cell. Determining the RNA sequences that are bound to RBPs can help to reveal information about the function of those RNA molecules.

“RBP binding sites are candidate functional elements in the transcriptome,” Burge says. “However, not all sites of binding have a function, so then you need to complement that with other types of assays to assess function.”

The researchers performed eCLIP on about 150 RBPs and integrated those results with data from another set of experiments in which they knocked down the expression of about 260 RBPs, one at a time, in human cells. They then measured the effects of this knockdown on the RNA molecules that interact with the protein.

Using a technique developed by Burge’s lab, the researchers were also able to narrow down more precisely where the RBPs bind to RNA. This technique, known as RNA Bind-N-Seq, reveals very short sequences, sometimes containing structural motifs such as bulges or hairpins, that RBPs bind to.

Overall, the researchers were able to study about 350 of the 1,500 known human RBPs, using one or more of these techniques per protein. RNA splicing factors often have different activity depending on where they bind in a transcript, for example activating splicing when they bind at one end of an intron and repressing it when they bind the other end. Combining the data from these techniques allowed the researchers to produce an “atlas” of maps describing how each RBP’s activity depends on its binding location.

“Why they activate in one location and repress when they bind to another location is a longstanding puzzle,” Burge says. “But having this set of maps may help researchers to figure out what protein features are associated with each pattern of activity.”

Additionally, Lecuyer’s group at the University of Montreal used green fluorescent protein to tag more than 300 RBPs and pinpoint their locations within cells, such as the nucleus, the cytoplasm, or the mitochondria. This location information can also help scientists to learn more about the functions of each RBP and the RNA it binds to.

“The strength of this manuscript is in the generation of a comprehensive and multilayered dataset that can be used by the biomedical community to develop therapies targeted to specific sites on the genome using genome-editing strategies, or on the transcriptome using antisense oligonucleotides or agents that mediate RNA interference,” says Gil Ast, a professor of human molecular genetics and biochemistry at Tel Aviv University, who was not involved in the research.

Linking RNA and disease

Many research labs around the world are now using these data in an effort to uncover links between some of the RNA sequences identified and human diseases. For many diseases, researchers have identified genetic variants called single nucleotide polymorphisms (SNPs) that are more common in people with a particular disease.

“If those occur in a protein-coding region, you can predict the effects on protein structure and function, which is done all the time. But if they occur in a noncoding region, it’s harder to figure out what they may be doing,” Burge says. “If they hit a noncoding region that we identified as binding to an RBP, and disrupt the RBP’s motif, then we could predict that the SNP may alter the splicing or stability of the gene.”

Burge and his colleagues now plan to use their RNA-based techniques to generate data on additional RNA-binding proteins.

“This work provides a resource that the human genetics community can use to help identify genetic variants that function at the RNA level,” he says.

The research was funded by the National Human Genome Research Institute ENCODE Project, as well as a grant from the Fonds de Recherche de Québec-Santé.

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Algorithm finds hidden connections between paintings at the Met

Art is often heralded as the greatest journey into the past, solidifying a moment in time and space; the beautiful vehicle that lets us momentarily escape the present. 

With the boundless treasure trove of paintings that exist, the connections between these works of art from different periods of time and space can often go overlooked. It’s impossible for even the most knowledgeable of art critics to take in millions of paintings across thousands of years and be able to find unexpected parallels in themes, motifs, and visual styles. 

To streamline this process, a group of researchers from MIT’s Computer Science and Artificial Intelligence Laboratory (CSAIL) and Microsoft created an algorithm to discover hidden connections between paintings at the Metropolitan Museum of Art (the Met) and Amsterdam’s Rijksmuseum. 

Inspired by a special exhibit “Rembrandt and Velazquez” in the Rijksmuseum, the new “MosAIc” system finds paired or “analogous” works from different cultures, artists, and media by using deep networks to understand how “close” two images are. In that exhibit, the researchers were inspired by an unlikely, yet similar pairing: Francisco de Zurbarán’s “The Martyrdom of Saint Serapion” and Jan Asselijn’s “The Threatened Swan,” two works that portray scenes of profound altruism with an eerie visual resemblance.

“These two artists did not have a correspondence or meet each other during their lives, yet their paintings hinted at a rich, latent structure that underlies both of their works,” says CSAIL PhD student Mark Hamilton, the lead author on a paper about “MosAIc.” 

To find two similar paintings, the team used a new algorithm for image search to unearth the closest match by a particular artist or culture. For example, in response to a query about “which musical instrument is closest to this painting of a blue-and-white dress,” the algorithm retrieves an image of a blue-and-white porcelain violin. These works are not only similar in pattern and form, but also draw their roots from a broader cultural exchange of porcelain between the Dutch and Chinese. 

“Image retrieval systems let users find images that are semantically similar to a query image, serving as the backbone of reverse image search engines and many product recommendation engines,” says Hamilton. “Restricting an image retrieval system to particular subsets of images can yield new insights into relationships in the visual world. We aim to encourage a new level of engagement with creative artifacts.” 

How it works 

For many, art and science are irreconcilable: one grounded in logic, reasoning, and proven truths, and the other motivated by emotion, aesthetics, and beauty. But recently, AI and art took on a new flirtation that, over the past 10 years, developed into something more serious. 

A large branch of this work, for example, has previously focused on generating new art using AI. There was the GauGAN project developed by researchers at MIT, NVIDIA, and the University of California at Berkeley; Hamilton and others’ previous GenStudio project; and even an AI-generated artwork that sold at Sotheby’s for $51,000. 

MosAIc, however, doesn’t aim to create new art so much as help explore existing art. One similar tool, Google’s “X Degrees of Separation,” finds paths of art that connect two works of art, but MosAIc differs in that it only requires a single image. Instead of finding paths, it uncovers connections in whatever culture or media the user is interested in, such as finding the shared artistic form of “Anthropoides paradisea” and “Seth Slaying a Serpent, Temple of Amun at Hibis.” 

Hamilton notes that building out their algorithm was a tricky endeavor, because they wanted to find images that were similar not just in color or style, but in meaning and theme. In other words, they’d want dogs to be close to other dogs, people to be close to other people, and so forth. To achieve this, they probe a deep network’s inner “activations” for each image in the combined open access collections of the Met and the Rijksmuseum. Distance between the “activations” of this deep network, which are commonly called “features,” was how they judged image similarity.

To find analogous images between different cultures, the team used a new image-search data structure called a “conditional KNN tree” that groups similar images together in a tree-like structure. To find a close match, they start at the tree’s “trunk” and follow the most promising “branch” until they are sure they’ve found the closest image. The data structure improves on its predecessors by allowing the tree to quickly “prune” itself to a particular culture, artist, or collection, quickly yielding answers to new types of queries.

What Hamilton and his colleagues found surprising was that this approach could also be applied to helping find problems with existing deep networks, related to the surge of “deepfakes” that have recently cropped up. They applied this data structure to find areas where probabilistic models, such as the generative adversarial networks (GANs) that are often used to create deepfakes, break down. They coined these problematic areas “blind spots,” and note that they give us insight into how GANs can be biased. Such blind spots further show that GANs struggle to represent particular areas of a dataset, even if most of their fakes can fool a human. 

Testing MosAIc 

The team evaluated MosAIc’s speed, and how closely it aligned with our human intuition about visual analogies.

For the speed tests, they wanted to make sure that their data structure provided value over simply searching through the collection with quick, brute-force search. 

To understand how well the system aligned with human intuitions, they made and released two new datasets for evaluating conditional image retrieval systems. One dataset challenged algorithms to find images with the same content even after they had been “stylized” with a neural style transfer method. The second dataset challenged algorithms to recover English letters across different fonts. A bit less than two-thirds of the time, MosAIc was able to recover the correct image in a single guess from a “haystack” of 5,000 images.

“Going forward, we hope this work inspires others to think about how tools from information retrieval can help other fields like the arts, humanities, social science, and medicine,” says Hamilton. “These fields are rich with information that has never been processed with these techniques and can be a source for great inspiration for both computer scientists and domain experts. This work can be expanded in terms of new datasets, new types of queries, and new ways to understand the connections between works.” 

Hamilton wrote the paper on MosAIc alongside Professor Bill Freeman and MIT undergraduates Stefanie Fu and Mindren Lu. The MosAIc website was built by MIT, Fu, Lu, Zhenbang Chen, Felix Tran, Darius Bopp, Margaret Wang, Marina Rogers, and Johnny Bui, at the Microsoft Garage winter externship program.

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