The traditional method of engineering enzymes by making precise, knowledge-based changes (“rational design”) is largely ineffective. Publication bias hides the vast number of failures, creating a false impression of success while cruder, high-volume methods like directed evolution prove superior.

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Caltech professor Frances Arnold developed her Nobel-winning "directed evolution" method out of desperation. Realizing her biochemistry knowledge was limited compared to peers using "rational design," she embraced a high-volume, random approach that let the experiment, not her intellect, find the solution.

Wet lab experiments are slow and expensive, forcing scientists to pursue safer, incremental hypotheses. AI models can computationally test riskier, 'home run' ideas before committing lab resources. This de-risking makes scientists less hesitant to explore breakthrough concepts that could accelerate the field.

The success of iterative design processes hinges entirely on the metric being measured. An enzyme evolved for temperature stability won't necessarily remove clothing stains unless stain removal is the specific property being screened for. This highlights the critical importance of defining the right success metric from the start.

The "bitter lesson" in AI research posits that methods leveraging massive computation scale better and ultimately win out over approaches that rely on human-designed domain knowledge or clever shortcuts, favoring scale over ingenuity.

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.

Frances Arnold, an engineer by training, reframed biological evolution as a powerful optimization algorithm. Instead of a purely biological concept, she saw it as a process for iterative design that could be harnessed in the lab to build new enzymes far more effectively than traditional methods.

Faced with China's superior speed and cost in executing known science, the U.S. biotech industry cannot compete by simply iterating faster. Its strategic advantage lies in

Physicist Brian Cox's most-cited paper explored what physics would look like without the Higgs boson. The subsequent discovery of the Higgs proved the paper's premise wrong, yet it remains highly cited for the novel detection techniques it developed. This illustrates that the value of scientific work often lies in its methodology and exploratory rigor, not just its ultimate conclusion.

Afeyan distinguishes risk (known probabilities) from uncertainty (unknown probabilities). Since breakthrough innovation deals with the unknown, traditional risk/reward models fail. The correct strategy is not to mitigate risk but to pursue multiple, diverse options to navigate uncertainty.

Beyond optimizing existing biological functions, Frances Arnold's lab uses directed evolution to create enzymes for entirely new chemical reactions, like forming carbon-silicon bonds. This demonstrates that life's chemical toolkit is a small subset of what's possible, opening up a vast "non-natural" chemical universe.

“Rational” Scientific Design Fails More Often Than Published Results Suggest | RiffOn