Artificial Intelligence in Computational Biology
Artificial intelligence is significantly advancing in the field of computational biology, marked by the recent creation of the world's first entirely AI-generated genome by researchers at Stanford and the Arc Institute.
Breakthrough in AI-Generated Genomes
- Researchers developed a new virus using AI that can infect and kill bacteria.
- Unlike prior achievements like designing individual proteins, creating an entire genome involves complex interactions between genes and regulatory switches necessary for growth and survival.
- The achievement addresses the challenge of orchestrating multiple interacting genes while maintaining a balance for replication and evolutionary fitness.
Case Study: Bacteriophage ΦX174
- The bacteriophage ΦX174 was chosen for this project due to its intricate genome structure consisting of 5,386 DNA letters and 11 overlapping genes.
- This virus was the first genome ever fully sequenced in 1977, synthesized in 2003, and now, the first designed by AI.
AI Training and Genome Creation Process
- The AI was trained using a genomic language model named Evo, fine-tuned on thousands of genomes from the virus's family.
- AI generated thousands of candidate genomes, followed by quality checks and lab tests using custom software to ensure all key genes and essential proteins were present.
- 16 new functional viruses emerged from AI-designed genomes, carrying numerous mutations never seen in nature.
- Notably, one design borrowed a protein from a distant relative, successfully fitting into the virus shell as confirmed by cryo-electron microscopy.
Significance of AI-Generated Viruses
- The AI was trained on 2 million viruses, producing 16 functional viruses from 302 attempts.
- AI viruses exhibited 392 unique mutations, including previously unsuccessful combinations.
- When bacteria developed resistance to natural viruses, AI-designed viruses were able to overcome defenses rapidly.
- This achievement signifies a new phase in biotechnology, transitioning from DNA sequencing and synthesis to designing genomes.
The advancements in AI emphasize its potential in accelerating scientific discoveries and breakthroughs, showcasing the expansive capabilities of AI in biotechnology.