Unlike traditional engineering, breakthroughs in foundational AI research often feel binary. A model can be completely broken until a handful of key insights are discovered, at which point it suddenly works. This "all or nothing" dynamic makes it impossible to predict timelines, as you don't know if a solution is a week or two years away.

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.

Current AI can learn to predict complex patterns, like planetary orbits, from data. However, it struggles to abstract the underlying causal laws, such as Newtonian physics (F=MA). This leap to a higher level of abstraction remains a fundamental challenge beyond simple pattern recognition.

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.

With directed evolution, scientists find a mutated enzyme that works without knowing why. Even with the "answer"—the exact genetic changes—the complexity of protein interactions makes it incredibly difficult to reverse-engineer the underlying mechanism. The solution often precedes the understanding.

Despite AI's power, 90% of drugs fail in clinical trials. John Jumper argues the bottleneck isn't finding molecules that target proteins, but our fundamental lack of understanding of disease causality, like with Alzheimer's, which is a biology problem, not a technology one.

Current biosecurity screens for threats by matching DNA sequences to known pathogens. However, AI can design novel proteins that perform a harmful function without any sequence similarity to existing threats. This necessitates new security tools that can predict a protein's function, a concept termed "defensive acceleration."

While a world model can generate a physically plausible arch, it doesn't understand the underlying physics of force distribution. This gap between pattern matching and causal reasoning is a fundamental split between AI and human intelligence, making current models unsuitable for mission-critical applications like architecture.

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.