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

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.
https://news.mit.edu/2020/qa-markus...avirus-and-ai-inspired-proteins-to-music-0402
 

luka

Moderator
I'm glad you're not dead too John. I wasn't really worried about you though, felt you'd be fine cos I knew Jah is watching over you.
 

IdleRich

IdleRich
So I guess we've all that seen that big report in the Times at the weekend about how they fucked everything up? Gotta say I'm finding it pretty fucking galling that a big part of it was cos they were spending all their time thinking about Brexit and that a lot of things were underfunded cos of Brexit and Tory austerity.
So the two worst things in the world turn out to be intimately connected.
 

IdleRich

IdleRich
It's fucking crazy... on the one hand all the right are banging on about re-opening the country cos they think it's more important to save the economy than people's lives, but on the other hand they are demanding we rush ahead to persist with the one thing that is most guaranteed to wreck that economy.
 

craner

Beast of Burden
So I guess we've all that seen that big report in the Times at the weekend about how they fucked everything up? Gotta say I'm finding it pretty fucking galling that a big part of it was cos they were spending all their time thinking about Brexit and that a lot of things were underfunded cos of Brexit and Tory austerity.
So the two worst things in the world turn out to be intimately connected.
The government has tried to fisk it:

https://healthmedia.blog.gov.uk/2020/04/19/response-to-sunday-times-insight-article/
 

Leo

Active member
seriously, the parts in that letter about flying out to a small airport in the midwest to check the quality of the shipment, wiring the money upon approval, loading it on to two trucks labeled as food service delivery vehicles and sending them on two different routes to minimize that chance of losing the entire buy...it's like a healthcare version of breaking bad.
 

IdleRich

IdleRich
It's very woolly, they are mainly contradicting opinions rather than facts. The point by point attempted rebuttal I mean.
With missing the Cobra meetings, I'm sure it's true that the PM doesn't absolutely have to attend every single one - but if there are FIVE on the same worldwide crisis and he doesn't go to one of them AND then the government's response is slower and less effective than almost every comparable country's despite having more warning - well it doesn't look good does it?
 

Mr. Tea

Shub-Niggurath, Please
seriously, the parts in that letter about flying out to a small airport in the midwest to check the quality of the shipment, wiring the money upon approval, loading it on to two trucks labeled as food service delivery vehicles and sending them on two different routes to minimize that chance of losing the entire buy...it's like a healthcare version of breaking bad.
The title (but nothing else, I think) of Blade Runner came from a little-known Burroughs novella, itself based on an earlier and apparently not very good sci-fi novel, about smugglers of medical equipment.

https://en.wikipedia.org/wiki/Blade_Runner_(a_movie)
 

IdleRich

IdleRich
In fact Johnson's whole response to the crisis has been a total shambles. Going from bragging about shaking hands with sick people and assuring everyone that there would be no big effect on their lives, to falling desperately ill and being saved by the very health service he hates, and as a result leaving the whole country leaderless for weeks on end during one of the worst crises it's faced. That sequence in itself is just embarrassing hubris and incompetence mixed together. Yet somehow, cos he almost died, people think he's a hero.
 

droid

Beast of Burden
Im leaning towards the conspiracists on his illness. The only thing this scum is good at is manipulating the soft, putrid and senile British national psyche and this is exactly the kind of stunt a bunch of lazy grifters would play.
 

IdleRich

IdleRich
I dunno though it makes him look like such a fucking dickhead based on his previous actions. I think it would be a gamble at the very least to try and manipulate the country that way - plus if it came out it would be awful.
 

droid

Beast of Burden
But it has been successful in managing to distract everyone from the appalling mismanagement and thousands of needless deaths, plus it gave him an excuse to take another couple of weeks off. If they're approaching this entire crisis as a PR problem (which they are) it is the kind of thing they'd consider doing.
 
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