Treating the Symptom, Missing the Cause: Anatomy of a Scientific Reasoning Failure

Anna Gogleva, Thomas Charman, Martin Balla, Karl Gemayel

Scientific agents can find interventions that work without understanding why they do. We study this failure mode in controlled synthetic regulatory systems, where agents must experimentally identify a hidden fault and rescue the resulting phenotype. Across seven LLMs, every model restores the healthy phenotypes more often than it identifies the fault. Claude Opus 4.6 and Sonnet 4.6 rescue every organism while diagnosing only 55% and 35% of them. This failure is not simply due to insufficient exploration or unavailable evidence. In most cases, the cause is experimentally identifiable, and agents encounter evidence that distinguishes competing causes in 91% of relevant sessions, and still frequently misdiagnose the system. Targeted probes reveal where experimental reasoning breaks down. Models reliably interpret decisive evidence and revise hypotheses when the causal comparison is explicit, and can locate that evidence within a full experimental record. However, they struggle to predict the outcome of the experiment under each competing cause, a necessary step in using the observed result to distinguish between them. Agents can therefore gather the right evidence and still infer…