DE Shaw Research (DESRES) invested heavily in custom silicon for molecular dynamics (MD) to solve protein folding. In contrast, DeepMind's AlphaFold, using ML on experimental data, solved it on commodity hardware. This demonstrates data-driven approaches can be vastly more effective than brute-force simulation for complex scientific problems.
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The AI industry is hitting data limits for training massive, general-purpose models. The next wave of progress will likely come from creating highly specialized models for specific domains, similar to DeepMind's AlphaFold, which can achieve superhuman performance on narrow tasks.
Unlike traditional methods that simulate physical interactions like a key in a lock, ProPhet's AI learns the fundamental patterns governing why certain molecules and proteins interact. This allows for prediction without needing slow, expensive, and often impossible physical or computational simulations.
A classical, bottom-up simulation of a cell is infeasible, according to John Jumper. He sees the more practical path forward as fusing specialized models like AlphaFold with the broad reasoning of LLMs to create hybrid systems that understand biology.
The DeepMind team was surprised that their specific software became a ubiquitous tool. They expected to solve a grand challenge and then have others build useful systems based on the concepts, not use the original artifact directly.
Early AI models advanced by scraping web text and code. The next revolution, especially in "AI for science," requires overcoming a major hurdle: consolidating and formatting the world's vast but fragmented scientific data across disciplines like chemistry and materials science for model training.
AlphaFold's success in identifying a key protein for human fertilization (out of 2,000 possibilities) showcases AI's power. It acts as a hypothesis generator, dramatically reducing the search space for expensive and time-consuming real-world experiments.
Counterintuitively, Nobel laureate John Jumper's path to AI began not with abundant resources, but as a way to use sophisticated algorithms to compensate for a lack of computational power for protein simulations during his PhD.
The ultimate goal isn't just modeling specific systems (like protein folding), but automating the entire scientific method. This involves AI generating hypotheses, choosing experiments, analyzing results, and updating a 'world model' of a domain, creating a continuous loop of discovery.
Following the success of AlphaFold in predicting protein structures, Demis Hassabis says DeepMind's next grand challenge is creating a full AI simulation of a working cell. This 'virtual cell' would allow researchers to test hypotheses about drugs and diseases millions of times faster than in a physical lab.
Traditional science failed to create equations for complex biological systems because biology is too "bespoke." AI succeeds by discerning patterns from vast datasets, effectively serving as the "language" for modeling biology, much like mathematics is the language of physics.
