Virus busting beats

An interview with MIT Professor Markus Buehler

  • 11 months ago

"We believe that the analysis of sound and music can help us understand the material world better. Artistic expression is just a model of the world within us and around us. And because of that, music is a great way to engage with science and learn about science. My work has opened the door for many people to understand what proteins are. It also offers a new way to see scientific data and concepts – such as proteins or singularities."

- Markus J. Buehler

We recently snatched up the opportunity to speak to Professor Markus J. Buehler, the McAfee Professor of Engineering at MIT. Buehler’s work in material sciences and proteins has recently been in the global spotlight, as he and his students attempt to find a cure for COVID-19 — using music.

JMI: How does an engineering and materials professor come to use music visualisation in his work?

MB: I have worked with music since I can remember — listening to it, creating it. I learned how to play several instruments. I became very interested in writing my own music around the time when I was a teenager, and to understand the “magic” by which music encodes emotion. The whole is more than the sum of its parts, it is a composite image with deep, intricate information levels. The creation of new sounds, and new music by composing a complex evolution of multiple sounds has fascinated me. I have also been very interested to understand how different styles of music are generated, and what the distinguishing and unifying principles are. Over the past decades I have written various original compositions, many of which are on SoundCloud and other music services like Spotify.

In recent years I have focused heavily on classical style compositions, but I also enjoy pushing the boundary and mixing genres — like in this fusion piece: Viral Protein Jam. I am also intrigued by experimental approaches, where we use non-traditional musical scales and instruments — like the vibrations of proteins and other molecules — as the origin of sound e.g. Orchestra of Amino acids.

Other work used a mix of spider webs and proteins. I also built musical models of intriguing physical phenomena such as singularities, or to represent the infection of a human cell by the coronavirus. Here you can hear some work that invokes fractures, proteins, piano and human voice.

Music has been a way to build models of really complex phenomena and use the ears with their direct connection to the human brain. 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.

Through my work as a material scientist and professor, I was able to apply the tools of computation, coding, understanding audio signals through a mathematical lens, algorithms such as AI, and our knowledge of the molecular structure to music. There is a direct connection to my work in music — as in music where I am keen to understand how music is created, in materials, my interest is how nature creates materials — such as spider silk, wood, sea shells, living materials in our body, and so on. In my research I discovered that the generation of music and materials is quite similar, and that there are unifying principles across these seeming distinct domains. So, I have been trying to connect these in my research — not only finding ways how to make new sounds from the motions of molecules, but also see what we can learn from music that was written without a sonification application. What can we discover through the amazing abstraction of structure in a composer’s mind about our body’s physical realization?

A lot of the recent work has been on proteins, which are the molecules encoded by DNA. They are a perfect way to connect information as a sequence (DNA letters) to a material. 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 sometimes have antimicrobial properties, so can be very versatile. In materials, the whole is more than the sum of its parts, just as in music!

JMI: Our perception is always that areas like the study of materials and data, by their very nature, are unemotional. Music on the contrary is all about emotion. Did you specifically set out with the aim of injecting emotion into your data sets?

MB: Emotions are innate in the structure of the data, the sort of internal details that aren’t obvious. I call these the residual components – the stuff that remains, which is the unseen that music can capture. My work has developed ways to realize those residues in music. I think the art is that emotions can bring the data to life through an understanding of how music composition works. In other words, we don’t just assign a pitch to each data, and let it play. We model, in music the complex structural relations in the data – like in a folded protein. These internal features are actually what carry the emotion in the data. However, there are artistic choices I make, as you can see in the examples above – like what instruments we pick, how we design the sound makeup, and so on. I am able to do this because I work on both conventional ways to generate music and data driven approaches. I also spend a lot of time discerning how existing music was generated, everything from the composition of the score to sound design, so I understand the intricacies.

JMI: I have to be honest, this track made me cry a little. (Okay, quite a lot.) It was as if the full weight of the impact of the virus hit me as I listened to the composition. If we were to make a movie of this time in history, I can picture this being the soundtrack. Was it a choice to make it haunting and ambient or was there a possibility of making it light and happy? Or perhaps, to give it a hip-hop beat?

MB: I believe you are referring to this piece.

Markus J. Buehler · Viral Counterpoint of the Coronavirus Spike Protein (2019-nCoV)

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. To do that 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 students at MIT. 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.

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. There could be different ways to express the structure. A lot of the artistic choices were so that you can hear clearly the many interwoven melody lines that are due to the complex, large structure of the protein – I chose a koto harp due to its clarity of sound. The evolution of the piece does reflect the organization of this protein, and the innate emotive qualities are due to the actual sequence makeup.

JMI: As an organisation, JMI views music as a cultural bridge, connecting people across the globe. When it comes to music education, it is seen as a cultural practice and we see schools around the world stripping music from their curriculums. Your work reminds us again of the power of music as a bridge to the sciences.

Music is a universal language that connects people across the world! I think that is the case because it is ultimately a model of how our body, our brain, works structurally – sort of mirror images of the intricate structures of our own physical existence. And more, my work has explored to use the actual physical features of proteins that build our body and other forms of life to generate sound. I think this offers an even closer connection of music to build bridges between the physicality and the residue of the transitory. Hence, it is a model of our shared humanity. And we can cross scales and species – e.g., I love to explore distinct organisms like spiders and humans interact in musical space. Or here, how cows, bells, proteins, human voice, and waterfalls can communicate in the abstraction of musical space. Or here, a piece that is modeled after I visited an old mill, inspired by the novel “Krabat”, where I recorded the sounds of the mill running, then intersected it with the sounds of proteins in wheat (gliadin protein), and some classical analog synthesizers (I like to mix them with the protein sounds).

I 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 Artificial Intelligence to speak the language of protein design and let it imagine new structures — all through music! We believe that the analysis of sound and music can help us understand the material world better. Artistic expression is just a model of the world within us and around us. And because of that, music is a great way to engage with science and learn about science. My work has opened the door for many people to understand what proteins are. It also offers a new way to see scientific data and concepts — such as proteins or singularities.

JMI: Your work, of course, highlights the importance of music to society — how do you think we reimagine the relationship between music and society, as traditional music practice struggles in the time of COVID?

That is a significant challenge indeed, especially for music teachers who cannot share their gift, or at least not in person. I also see it with my own children (11, 8 and 5). All of them are learning to play the piano and have not been able to meet with their instructor in person since the start of the pandemic. The development of new ways of teaching — virtual, online, or with clever tools that allow students and teachers to interact virtually — may be important. Of course, nothing can substitute real in-person interaction, but perhaps we can augment these through some of these new approaches. It is also very difficult to perform together, remotely in real-time, due to the latency of tools like Zoom. So, still a long way to go.

JMI: Lastly, are their any pieces of advice that you can offer, or practical tools that you can recommend to young musicians who are interested in expanding their music practice beyond the expected?

MB: I would recommend to follow your passion. My own work has always tried to explore new ideas and new ways of making music — from when I was very young. This may be unconventional first, but keep at it! And learn to listen to others, network, and communicate your ideas. And be open to evolution as your skills and knowledge improves.

Don’t throw away your ideas, recordings, concepts! You will enjoy reviewing them you are older and you can build on them. I often work on musical compositions for many years, and the process often isn’t linear. You may be stuck and then it’s time to move on the revisit. Sometimes years later…

In all work I do, I try to have multiple projects ongoing, because I like to switch when I am stuck, and it works well especially in creative processes like music, or science. Recently I had a most amazing experience, where I went back to an old idea I recorded when I was around 16 years old. More than 25 years later, I was creatively engaging with, sort of communicating with my own, younger self – as I still recalled the details of where I wrote the music, how I did it, and where I got stuck. Music allowed me to do this time travel to solve a musical problem I was facing earlier, and it was mind blowing!

JMI: So there you have it. Time travel is possible with music!

We'd love to hear your thoughts on Prof. Buehler's work, music education, the virus and other things. Be sure to share them with us in the comments section below.

Markus J. Buehler is the McAfee Professor of Engineering at MIT material scientist, and a composer of experimental, classical and electronic music, with an interest in sonification. Using an approach termed "materiomusic", his work explores the creation of new forms of musical expression - such as those derived from the innate vibrations of biological materials and living systems - as a means to better understand the underlying science and mathematics. In recent work he has developed a new framework to compose music based on proteins – the basic molecules of all life, as well as other physical phenomena such as fracture singularities, to explore similarities and differences across species, scales and between philosophical and physical models. One of his goals is to use musical and sound design, aided by AI, as an abstract way to model, optimize and create new forms of matter from the bottom up – across scales (e.g., from nano to macro) and species (e.g., from humans to spiders). For example, he is researching whether J.S. Bach - one of the most influential composers - has inadvertently discovered fundamental physical and chemical principles of protein folding, through the use of counterpoint.