A First, AI Generates Bacteria-Killing Genome, Bringing Key Medical Breakthrough
For the first time in history, artificial intelligence (AI) has generated complete viral genomes that worked in the lab. The AI has written the full genetic code of viruses that can infect and kill bacteria, claim researchers in California.
16 of the AI-designed phages killed E. coli, including strains the natural phiX174 could not, and experts such as Jef Boeke, a genome scientist at NYU Langone Health in New York have opined that the AI’s output was impressive but still far from creating life.
The scientists at Stanford University and the Arc Institute tested hundreds of these AI-designed genomes in the lab, and found 16 of them produced working bacteriophages, viruses that attack bacteria, which replicated and wiped out Escherichia coli (E. Coli), a harmless bacterium often used in labs as a test system.
The development is being called the first generative design of complete genomes, as mentioned in the study published on bioRxiv, an online platform where scientists share research before it is formally reviewed.
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The project reportedly used an AI system called Evo, designed on the same principles as large language models. Evo was trained on about two million viral genomes so it could learn the “grammar” of DNA, the patterns of gene order and composition, instead of predicting words in a sentence. The trainers then guided the model to mimic phiX174, a small bacteriophage with just 11 genes and around 5,000 DNA letters that has long been a staple of molecular biology.
Evo eventually proposed complete, workable genome sequences, some with new or truncated genes, going beyond copying the existing phages as a result of training.
The research team selected 302 genomes to chemically synthesize, and these strands of DNA were introduced into bacterial systems to see if they would assemble into functioning phages. The test came when some of the designs produced plaques, clear spots in petri dishes where E. coli colonies had been wiped out by phages.
A total of 16 designs succeeded out of 302, producing viruses that replicated inside bacteria and burst them open.
