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

An experimental agent can succeed for the wrong reasons. Evaluations, however, often focus on the outcome, not the experiments, evidence, and inferences that produced it. We introduce LUCA, a configurable synthetic world for evaluating this process under fully known ground truth. Agents learn unknown regulatory systems through budgeted experimentation, then predict unseen interventions, diagnose hidden faults, and attempt rescues. This setup allows us to evaluate experiment selection, prediction, diagnosis, and intervention separately. Across seven frontier LLMs and three baselines, these capabilities dissociate sharply. Agents frequently rescue malfunctioning systems while diagnosing the wrong fault; diagnosis varies 7x across models while prediction varies only 1.4x. Models also adopt surprisingly different experimental strategies, and greater exploration does not reliably yield better performance. In one failure mode, agents often perform the experiment needed to distinguish competing causes, but still fail to use the resulting evidence. LUCA turns these hidden failures into measurable behaviours, providing a controlled environment to study where experimental agents succeed and fail. Code: https://github.com/RelationRx/luca.

Large language model (LLM)-based systems are increasingly deployed to conduct scientific research autonomously, yet whether their reasoning adheres to the epistemic norms that make scientific inquiry self-correcting is poorly understood. Here, we evaluate LLM-based scientific agents across eight domains, spanning workflow execution to hypothesis-driven inquiry, through more than 25,000 agent runs and two complementary lenses: (i) a systematic performance analysis that decomposes the contributions of the base model and the agent scaffold, and (ii) a behavioral analysis of the epistemological structure of agent reasoning. We observe that the base model is the primary determinant of both performance and behavior, accounting for 41.4% of explained variance versus 1.5% for the scaffold. Across all configurations, evidence is ignored in 68% of traces, refutation-driven belief revision occurs in 26%, and convergent multi-test evidence is rare. The same reasoning pattern appears whether the agent executes a computational workflow or conducts hypothesis-driven inquiry. They persist even when agents receive near-complete successful reasoning trajectories as context, and the resulting unreliability compounds across repeated trials in epistemically demanding domains. Thus, current LLM-based agents execute scientific workflows but do not exhibit the epistemic patterns that characterize scientific reasoning. Outcome-based evaluation cannot detect these failures, and scaffold engineering alone cannot repair them. Until reasoning itself becomes a training target, the scientific knowledge produced by such agents cannot be justified by the process that generated it.

We introduce CausaLab, a scalable environment for evaluating interactive causal discovery by LLM agents. Unlike prior evaluations, CausaLab evaluates both whether an agent can solve a problem using causal evidence and whether its answer is grounded in a faithful recovered causal mechanism. Each episode places an agent in a synthetic laboratory: it receives prior measurement records, intervenes on a manipulator crystal, and predicts the resonance frequency of a held-out reactor crystal governed by the same mechanism. The hidden data-generating process is a randomly sampled structural causal model (SCM), so success requires recovering both a causal graph and structural equations rather than recalling prior knowledge. Experiments show a persistent gap between prediction and mechanism recovery: in the purely observational 6-node setting, GPT-5.2-high reaches 92% task accuracy but only 0.471 all-edge $F_1$. Mixed observation-intervention strategies improve structural fidelity, while pure intervention remains difficult even for strong agents. We identify premature stopping as a major weakness and show that consistency verification mitigates it. CausaLab therefore separates predictive success from causal understanding and exposes current LLM agents' limits as experimental causal reasoners.