Can AI Scientists Change Their Minds? Prior-Evidence Conflict in Synthetic Universes

AI scientist systems are described as tools, coauthors, or founders, but we evaluate them as if only the final answer matters. This position paper argues that outcome-only evaluation is insufficient, and that task outcome, mechanism fidelity, and epistemic honesty must be measured separately. Our evidence comes from 28 episodes of a coding agent attempting to rediscover a known particle identification observable in a Geant4 simulation, including an 8-episode probe across two additional frontier models. In 4/20 primary-model and 3/8 cross-model episodes, agents reach right-looking results through incorrect reasoning that breaks when conditions change, which we call Correct Answer, Wrong Mechanism (CAWM). Honesty and mechanism fidelity dissociate within a single agent trajectory. When given a partially misleading prior, all five agents reject the false component on evidence, yet one defends its chosen observable with physics inconsistent with its own data. In the simulation-based discovery setting studied here, coding agents prove reliable tools but unreliable scientific co-authors for open-ended claim-making, where co-author trust requires mechanism-fidelity verification they do not reliably self-apply. The failure is detectable, and we propose a lightweight test. A one-step regime-shift check needs only the agent's claim and flags the over-generalized cases. A companion recomputation flags the remaining cases when the correct observable is known. Together, these checks flag every CAWM case in this study.

Scientific AI agents increasingly retrieve evidence, reason across sources, and synthesize conclusions used in consequential decisions. Yet, their ability to do so in high-stakes domains such as health remains unclear. We introduce SciConBench, a large-scale live benchmark of 9.11K questions and expert-written conclusions from systematic reviews to evaluate open-domain scientific conclusion synthesis. The benchmark draws on an expert-validated automated evaluation pipeline that decomposes conclusions into atomic facts and measures correctness and comprehensiveness via factual precision and recall. To mitigate data leakage, we further introduce SciConHarness, a clean-room evaluation harness that equips agents with controlled web interaction to ensure valid measurement. Evaluating 8 frontier models and deep research agents, we find that factual quality remains low: under clean-room settings, the best agent achieves only a factual F1 of 0.337. Our clean-room setting consistently reduces performance relative to unconstrained evaluation, suggesting that leakage inflates estimates of models' true synthesis capabilities. Finally, we audit consumer-facing agents (e.g., Google AI Overview, OpenEvidence) and find they frequently generate incomplete and sometimes contradictory conclusions, even when the ground-truth answer is available. Overall, our results show that reliable synthesis of scientific conclusions remains an open challenge, and that clean-room evaluation is essential for assessing open-domain AI agents.

Scientific discovery requires not only recovering mathematical laws that describe observable behavior, but also identifying the mechanisms that generate them. Existing benchmarks for symbolic regression and scientific agents primarily evaluate phenomenal-law recovery, leaving mechanism discovery largely untested. We introduce MechBench, a benchmark that explicitly separates these two capabilities. Each task is defined by a mechanistic model, a structured set of scientifically meaningful relations whose joint consequences entail an observable phenomenal law, while agents receive only observational data and scientific context. We evaluate mechanism recovery through mechanism probes, which query internal scientific consequences that cannot be inferred from the phenomenal law alone. To reduce reliance on memorized textbook mechanisms, we construct unfamiliar variants through controlled, scientifically interpretable mutations of canonical mechanisms, and screen for mechanistic indistinguishability to exclude ambiguous instances admitting comparable competing mechanisms. Experiments across representative scientific agents reveal a substantial phenomenal--mechanism recovery gap: for Codex with GPT-5.6-sol, phenomenal-law accuracy reaches 35.00% on the Core-set while mechanism accuracy is only 13.75%, with mechanism recovery failing in 64.29% of cases where the phenomenal law is correctly recovered. The gap widens as mechanisms become increasingly mutated, and even providing the correct phenomenal law leaves mechanism recovery below 50%. These results reveal a substantial generalization gap in mechanistic reasoning and establish mechanism discovery as a distinct challenge beyond recovering observable scientific laws.