MIT Research News' Journal

MIT’s entrepreneurial ecosystem steps up to the challenge of Covid-19

Innovation and entrepreneurship aren’t easy. New companies are forced to make due with minimal resources. Decisions must be made in the face of great uncertainty. Conditions change rapidly.

Perhaps unsurprisingly then, MIT’s I&E community has stepped up to the unforeseen challenges of the Covid-19 pandemic. Groups from many corners of the Institute are adapting to the myriad disruptions brought on by the emergency and spearheading efforts to help the people most affected.

At a time when most students would be on spring break, many were collaborating on projects and participating in hacking workshops to respond to Covid-19. And as faculty and staff develop new curricula and support structures, they’re focusing on the needs of their students with the same devotion entrepreneurs must focus on their customers.

Above all, members of the MIT community have treated the challenges presented by Covid-19 as opportunities to help. Perhaps nowhere is that more apparent than the Covid-19 Rapid Innovation Dashboard, which was just a rough idea as recently as March 16, but is now a bustling hub of MIT’s Covid-19-related activities. Projects on the dashboard include an initiative to help low-income K-12 students with school shutdowns, an effort leveraging behavioral science to reduce the spread of misinformation about the virus, and multiple projects aimed at improving access to ventilators.

People following those projects would hardly suspect the participants have been uprooted from their lives and forced to radically change the way they work.

“We never would’ve wished this on anybody, but I feel like we’re ready for it,” says Bill Aulet, the managing director of the Martin Trust Center for MIT Entrepreneurship and a professor of the practice at MIT’s Sloan School of Management. “Working in an environment of great change, if you’re a great entrepreneur, is playing to your strengths. I think the students will rise to the occasion, and that’s what we’re seeing now.”

The Rapid Innovation Dashboard

In the second week of March, as the global consequences of Covid-19’s spread were becoming apparent, members of the MIT Innovation Initiative began getting contacted by members of the MIT community looking for ways to help.

Most people wanted information on the various grassroots projects that had sprouted up around campus to address disruptions related to the spread of the virus. Some people were looking for ways to promote their projects and get support.

MITii’s team began brainstorming ways to help fill in those gaps, officially beginning work on the dashboard the week of March 16 — the same time staff members began working remotely.

“From ideation to whiteboarding, to concept, to iteration, to launch, we did it all in real time, and we went from idea to standing the dashboard up in four days,” MITii executive director Gene Keselman says. “It was beautiful for all of us innovation nerds.”

The site launched on March 19 with six projects. Today there are 50 live projects on the site and counting. Some of them deal with mechanical or scientific problems, like the aforementioned efforts to improve access to ventilators, while others are more data-focused, like an initiative to track the spread of the virus at the county level. Still others are oriented toward wellness, like a collection of MIT-related coloring pages for destressing.

“A lot of the things we’re seeing are data-driven, creative-driven projects to get people involved and get them feeling like they’re making an impact,” Keselman says.

The current dashboard is version 1.0 of an ongoing project that will continue to evolve based on the community’s needs. Down the line, the MITii team is considering ways to better connect the MIT community with investors looking to fund projects related to the virus.

“This is going to be a long term problem, and even when we go back to the office, issues will persist, we’ll be dealing with things that are the runoff from Covid-19,” Keselman says. “There will be an opportunity to keep this thing going to solve all kinds of second- or third-order problems.”

Overcoming adversity

The dashboard is just one example of how different entrepreneurial organizations on campus are stepping up to the challenges of Covid-19. The Trust Center is encouraging students to leverage its Orbit app, to get help from entrepreneurs in residence, engage with other members of MIT’s entrepreneurial community, and navigate MIT’s myriad entrepreneurial resources. And in response to Covid-19, the Trust Center launched the Antifragile Entrepreneurship Speaker Series to provide thought leadership to students.

“We’ve revitalized our speaker series,” Aulet says. “We used to fly people in, but now we can have anyone. They’re sitting at home, they’re bored, and we can have more interaction than we did before. We try to create antifragile humans, and antifragile humans excel in times like this.”

MIT D-Lab, where hands-on learning and common makerspaces are central to operations, is just one example of an area where faculty members are taking this opportunity to try new ways of managing projects and rethinking their curriculum.

“We’re in a real brainstorming phase right now, in the best sense of the word — throwing out all the wild ideas that come to us, and entertaining anything as we decide how to move forward,” Libby Hsu, a lecturer and academic program manager at D-Lab, told MIT News the week before MIT classes resumed. “We’re getting ready to ship materials and tools to students at their homes. We’re studying how to use Zoom to facilitate project work student teams have already put in. We’re realistically re-assessing what deliverables we could ask of students to help D-Lab staff prototype things for them here on campus, perhaps later in the semester or over the summer.”

Other entrepreneurial groups on campus, like the Venture Mentoring Service, MIT Sandbox, and the Legatum Center, are similarly adopting virtualized support mechanisms.

On March 5, MIT Solve, which uses social impact challenges to tackle the world’s biggest problems, launched a new Global Challenge seeking innovations around the prevention, detection, and response of Covid-19. The winning team will receive a $10,000 grant to further develop their solution.

The students themselves, of course, are also organizing initiatives. In addition to many of the projects in the Rapid Innovation Dashboard, the MIT COVID-19 Challenge is a student-led initiative that held its first virtual “ideathon” this past weekend, with another major event April 3-5.

Indeed, Keselman could’ve been talking about any group on campus when he said of his team at MITii, “We feel like we lived an entire lifetime in just the last week.”

The early efforts may not have been the way many participants expected to spend their spring break, but in the entrepreneurial world, new challenges are par for the course.

“Being knocked out of your homeostasis is a good thing and a bad thing, and it’s an entrepreneur’s job to make it more of a good thing than a bad thing,” Aulet says. “I think we’ll come out of this utilizing technology to have more efficient, more effective, more inclusive engagements. Is this disrupting the entrepreneurial ecosystem? Absolutely. Should we come out of it stronger? Absolutely.”

Q&A: Markus Buehler on setting coronavirus and AI-inspired proteins to music

The proteins that make up all living things are alive with music. Just ask Markus Buehler: The musician and MIT professor develops artificial intelligence models to design new proteins, sometimes by translating them into sound. His goal is to create new biological materials for sustainable, non-toxic applications. In a project with the MIT-IBM Watson AI Lab, Buehler is searching for a protein to extend the shelf-life of perishable food. In a new study in Extreme Mechanics Letters, he and his colleagues offer a promising candidate: a silk protein made by honeybees for use in hive building.

In another recent study, in APL Bioengineering, he went a step further and used AI discover an entirely new protein. As both studies went to print, the Covid-19 outbreak was surging in the United States, and Buehler turned his attention to the spike protein of SARS-CoV-2, the appendage that makes the novel coronavirus so contagious. He and his colleagues are trying to unpack its vibrational properties through molecular-based sound spectra, which could hold one key to stopping the virus. Buehler recently sat down to discuss the art and science of his work.

Q: Your work focuses on the alpha helix proteins found in skin and hair. Why makes this protein so intriguing?

A: Proteins are the bricks and mortar that make up our cells, organs, and body. Alpha helix proteins are especially important. Their spring-like structure gives them elasticity and resilience, which is why skin, hair, feathers, hooves, and even cell membranes are so durable. But they’re not just tough mechanically, they have built-in antimicrobial properties. With IBM, we’re trying to harness this biochemical trait to create a protein coating that can slow the spoilage of quick-to-rot foods like strawberries.

Q: How did you enlist AI to produce this silk protein?

A: We trained a deep learning model on the Protein Data Bank, which contains the amino acid sequences and three-dimensional shapes of about 120,000 proteins. We then fed the model a snippet of an amino acid chain for honeybee silk and asked it to predict the protein’s shape, atom-by-atom. We validated our work by synthesizing the protein for the first time in a lab — a first step toward developing a thin antimicrobial, structurally-durable coating that can be applied to food. My colleague, Benedetto Marelli, specializes in this part of the process. We also used the platform to predict the structure of proteins that don’t yet exist in nature. That’s how we designed our entirely new protein in the APL Bioengineering study.

Q: How does your model improve on other protein prediction methods?

A: We use end-to-end prediction. The model builds the protein’s structure directly from its sequence, translating amino acid patterns into three-dimensional geometries. It’s like translating a set of IKEA instructions into a built bookshelf, minus the frustration. Through this approach, the model effectively learns how to build a protein from the protein itself, via the language of its amino acids. Remarkably, our method can accurately predict protein structure without a template. It outperforms other folding methods and is significantly faster than physics-based modeling. Because the Protein Data Bank is limited to proteins found in nature, we needed a way to visualize new structures to make new proteins from scratch.

Q: How could the model be used to design an actual protein?

A: We can build atom-by-atom models for sequences found in nature that haven’t yet been studied, as we did in the APL Bioengineering study using a different method. We can visualize the protein’s structure and use other computational methods to assess its function by analyzing its stablity and the other proteins it binds to in cells. Our model could be used in drug design or to interfere with protein-mediated biochemical pathways in infectious disease.

Q: What’s the benefit of translating proteins into sound?

A: Our brains are great at processing sound! In one sweep, our ears pick up all of its hierarchical features: pitch, timbre, volume, melody, rhythm, and chords. We would need a high-powered microscope to see the equivalent detail in an image, and we could never see it all at once. Sound is such an elegant way to access the information stored in a protein.

Typically, sound is made from vibrating a material, like a guitar string, and music is made by arranging sounds in hierarchical patterns. With AI we can combine these concepts, and use molecular vibrations and neural networks to construct new musical forms. We’ve been working on methods to turn protein structures into audible representations, and translate these representations into new materials.

Q: What can the sonification of SARS-CoV-2's "spike" protein tell us?

A: Its protein spike contains three protein chains folded into an intriguing pattern. These structures are too small for the eye to see, but they can be heard. We represented the physical protein structure, with its entangled chains, as interwoven melodies that form a multi-layered composition. The spike protein’s amino acid sequence, its secondary structure patterns, and its intricate three-dimensional folds are all featured. The resulting piece is a form of counterpoint music, in which notes are played against notes. Like a symphony, the musical patterns reflect the protein’s intersecting geometry realized by materializing its DNA code.

Q: What did you learn?

A: The virus has an uncanny ability to deceive and exploit the host for its own multiplication. Its genome hijacks the host cell’s protein manufacturing machinery, and forces it to replicate the viral genome and produce viral proteins to make new viruses. As you listen, you may be surprised by the pleasant, even relaxing, tone of the music. But it tricks our ear in the same way the virus tricks our cells. It’s an invader disguised as a friendly visitor. Through music, we can see the SARS-CoV-2 spike from a new angle, and appreciate the urgent need to learn the language of proteins.

Q: Can any of this address Covid-19, and the virus that causes it?

A: In the longer term, yes. Translating proteins into sound gives scientists another tool to understand and design proteins. Even a small mutation can limit or enhance the pathogenic power of SARS-CoV-2. Through sonification, we can also compare the biochemical processes of its spike protein with previous coronaviruses, like SARS or MERS.

In the music we created, we analyzed the vibrational structure of the spike protein that infects the host. Understanding these vibrational patterns is critical for drug design and much more. Vibrations may change as temperatures warm, for example, and they may also tell us why the SARS-CoV-2 spike gravitates toward human cells more than other viruses. We’re exploring these questions in current, ongoing research with my graduate students.

We might also use a compositional approach to design drugs to attack the virus. We could search for a new protein that matches the melody and rhythm of an antibody capable of binding to the spike protein, interfering with its ability to infect.

Q: How can music aid protein design?

A: You can think of music as an algorithmic reflection of structure. Bach’s Goldberg Variations, for example, are a brilliant realization of counterpoint, a principle we’ve also found in proteins. We can now hear this concept as nature composed it, and compare it to ideas in our imagination, or use AI to speak the language of protein design and let it imagine new structures. We believe that the analysis of sound and music can help us understand the material world better. Artistic expression is, after all, just a model of the world within us and around us.

Co-authors of the study in Extreme Mechanics Letters are: Zhao Qin, Hui Sun, Eugene Lim and Benedetto Marelli at MIT; and Lingfei Wu, Siyu Huo, Tengfei Ma and Pin-Yu Chen at IBM Research. Co-author of the study in APL Bioengineering is Chi-Hua Yu. Buehler’s sonification work is supported by MIT’s Center for Art, Science and Technology (CAST) and the Mellon Foundation.