Content warning: fictional illness, mentions of COVID-19

“Aegar has the spots again,” Iyashi groans, slumping next to Sanna at the cafeteria table. Sanna continues to stare at her screen, her glasses reflecting the display cramped with code.

Iyashi grumbles, “If I have to file one more medical report starting with ‘Aegar: infected with virus Manchadi morado causing purple spots’, I might die.” She buries her head in her hands. 

“No one said living on a spaceship would be easy Iya, let alone the Dromaius which visits planets with unknown environments on a regular basis.” Sanna speaks softly.

“That’s easy for you to say Sanna! You’re human so at least you have some resistance to these viruses, but Aegar doesn’t seem to have any, and then it’s up to me to look after him every single time.”

Sanna glances up, watching the fins on Iyashi’s head wave erratically. As a Mizu, Iyashi has features like those of underwater creatures on Sanna’s home planet. Iyashi also happens to be especially resistant to viruses herself. Sanna sighs, “If only there was some way to see it up close and figure out exactly how it works, just like with my code…”

Iyashi’s eyes spark to life, her head snapping towards Sanna so quickly, Sanna flinches.

“That is a genius idea Sanna, thank you!” Iyashi hastily scoots out of her chair and beelines for the cafeteria door. Sanna stares blankly after her. A few passing crew members glance over, then realising the cause of the disturbance was Iyashi, turn back to their conversations.

***

In the med bay, the Dromaius’ hub for all things medical-related, Iyashi types harshly on a holographic keyboard. The screen displays the virus’ genetic code. Iyashi and a group of other juniors had been working on a computer program to do just what Sanna had been talking about: seeing the virus up close, in 3D. The program wasn’t perfect just yet, but desperate times call for sanity-saving measures.

“Now if I just do this…” With the press of a button, the virus appears in front of Iyashi as a slowly spinning hologram. The fins on Iyashi’s head flutter in excitement. Iyashi scours the virus for its key parts, investigating them closely. She spins the virus in all directions, searches through different layers and even steps inside the hologram to see the virus from the inside out. But she still can’t figure out how to stop Aegar from being infected.

“This feels impossible.” Iyashi plops to the floor, exhausted. She pulls her phone out of the pocket of her lab coat, scrolling through the latest news from Synthetic. The science journal could be a great source for inspiration.

She lands on an article, eyes zeroing in on the title ‘Deep Network Hallucinations’.

“That’s an idea.”

***

Iyashi awakens to the sound of someone worriedly calling out her name. Groggily she sits up, discovering it’s Sanna supporting her back.

“Iya, what happened? You were meant to report in ages ago.” Sanna questions anxiously.

Iyashi blinks, then jumps to her feet in excitement. “It worked!” Sanna stares at her, brows furrowing.

“I read recently that hallucinations can connect ideas in ways your consciousness can’tcan’t, and it worked! I put myself in a self-induced fever and now I have an idea for a treatment for the spots! Aegar won’t have to worry about catching them and I won’t have to see him in my med bay every other week!”

As Iyashi rushes to her screen, Sanna stares in dumbfounded silence.

Luckily, in our world we don’t have to go to quite the lengths Iyashi did to find possible treatments for diseases.

For the past few years, it’s felt like we’ve been living in real-life Contagion. The 2011 film was right about a lot of things regarding a global pandemic (panic-buying, social distancing, everything just feeling like an unending sequence of unfortunate events). But the film doesn’t go into much depth about how a vaccine was finally developed. Our own COVID-19 vaccine required an immeasurable amount of expertise to bring to life. Here, I’ll be unpacking the crucial role of proteins in making our COVID-19 vaccine a reality.

Proteins are small molecules which exist everywhere. In you, in me, the environment, everywhere. They’re made of building blocks called amino acids which are like beads on a string. The beads interact with each other and fold the string into different shapes. This 3D shape allows proteins to function in certain ways, so if we can predict this structure, we can use proteins to our advantage.

Viruses rely on proteins to survive and infect cells. You’ve probably seen diagrams of the COVID-19 virus on TV; it’s generally shaped like a ball with spikes jutting out of it. These spikes are appropriately called spike proteins. They are essential for allowing the virus to enter human cells and begin infection. By studying the 3D shape and structure of the spike protein, researchers could determine how it works and develop vaccines against COVID-19. So, why don’t we do this for all proteins? Well, the number of proteins is huge–in the billions–and determining their structure by making them in a lab costs an enormous amount of time and resources.

However, a shiny new artificial intelligence (AI) program developed by Deepmind called AlphaFold has revolutionised how we predict protein structures.2,3 With it, we can use computers to make predictions about a protein’s structure before creating it in the lab, speeding up the whole process. The program is not unlike J.A.R.V.I.S., the late Tony Stark’s AI companion from the Marvel Cinematic Universe. While J.A.R.V.I.S. could digitally model and test Stark’s Iron Man suit, AlphaFold can digitally model proteins and assess how accurate the model is based on what we know about amino acids (the beads) and other proteins (similar strings). AlphaFold provides the fancy virtual blueprint which researchers use to create and manipulate real-life proteins.

Some exciting work developed by the Baker Lab at the Institute for Protein Design explores what they call “deep network hallucination”. While Iyashi falls into a self-induced fever to hallucinate a treatment for ‘the spots’, the Baker Lab has invented a method to cause computers to create ‘hallucinations’ which are essentially imaginary proteins. They start with a totally random sequence of amino acids and run it through programs like AlphaFold which use information–based on amino acids and other proteins as I mentioned earlier–to design new proteins. This could allow us to develop new treatments for diseases, but AlphaFold’s possible applications extend a lot further than just developing new vaccines or discovering treatments for diseases.

If you’d like to see some of AlphaFold’s structures for yourself, you can explore its online, open-access database full of 3D protein structures. You’ll have the first taste of how it may feel for us to be able to design our own destiny.