#deep mind

Going for Fold

For generations, scientists have struggled to follow the steps that shape life. Alphafold, a project that recently won the 2024 Nobel Prize in Chemistry, may be a giant leap ahead. Researchers use artificial intelligence to predict how proteins – the tiny machines with specific shapes set to tasks inside our cells – take shape from their amino acid building blocks. Similar perhaps to predicting a castle, pirate ship or bunch of flowers from a pile of Lego bricks (although ~100 million times smaller), at least the algorithms have some rules to guide them. Here they simulate the natural steps of protein synthesis – taking a virtual chain of amino acids and folding it up based on how different amino acids interact chemically. Researchers believe this predicted protein protects the malaria-carrying parasite Plasmodium falciparum from our immune defences. The next step is to scour the 3D structure for weaknesses, while Alphafold continues its predictions.

Written by John Ankers

Image from the AlphaFold Protein Structure Database

EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire and Google DeepMind, London, UK

Image originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)

Research referenced published in Nature Communications, May 2024

Last night I had this dream where the planets realigned and it caused the world to cease to exist as we know it. I’m talking like the oceans became dried, hollowed, carcasses of what once was. Once a bottomless yet enigmatic graveyard for dreams that couldn’t come true. So, they were submerged so that no one could ever find them unless they carried a likeness of that in their own head. In the beginning, I searched for safety with an admirer who I thought understood the burdensome weight that I held inside me. The seismic sea wave came pummeling down on us, almost drowning us both. I laid them on top of a withered old greenhouse untamed on the inside. It had an assortment of things growing unseen by the mortal eye— harsh, uncontrollable, too abundant for the small room it was given, but somehow bound to just that space because it had no other choice. I turned my back to him because I felt like my work wasn’t done and needed to search further. As I looked to where he once was I saw him no more, because then it dawned on me that he was never there in the first place. I wept on the rusted yet opaque glass as I tried to decipher the containments of it, yet realized it was the sheer piece of my heart that still hopes and dreams unfoundedly. I left there and tried to find a sense of safety that didn’t feel like upchucking gallons upon gallons of salty water that would swallow me whole. I visited friends on my journey upon this now desolate place of what we called Earth. I settled and gave them parts of myself that I loved, so they would know some comfort in a world that seemed like it didn’t have any anymore. I rested and made myself a space in upper floors of libraries that held water damaged books, and top carts of ferris wheels that overlooked the sunset. As soon as I felt like I could breathe again, the water would always come back or adjust without reverence forcing me up uproot and continue on. I passed by celebrated structures that once held thousands of memories inside its walls, that were now only just those memories and nothing more. I ventured in all the spots I used to call favorites and now saw them as places of hollowed ground where I could seek sanctuary for a bit. I made my way in the houses I grew up in and reveled at the girl I was before. She didn’t hold onto as much as the Me that is now. I was stricken with sadness knowing that those lost pieces of me were suffocated long ago, and that they could never come back because the sea inside me demanded for more room. I finally reached my loved ones and embraced their tear stained faces. Time had surely worn me and I was not the same girl they had last seen. They could not stay as I had discovered a way to ensure their welfare for good, and that was by distancing them from me. Because seconds before leaping to them, I had realized I controlled the water all along. That the water was merely following itself to where it belonged—that was within me.