Coherent Without Grounding, Grounded Without Success: Observability and Epistemic Failure

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.

Large Language Models (LLMs) can generate natural language explanations that rationalize their own decisions, a phenomenon commonly referred to as self-explanations. Such explanations have emerged as a promising direction for explainable artificial intelligence (XAI), particularly for interpreting LLM behavior. However, while self-explanations often appear plausible, whether they faithfully reflect a model's underlying reasoning process remains an open question. In this opinion paper, we argue that self-explanations can be highly plausible, questionably faithful, and yet highly actionable. From a traditional XAI perspective, we identify the limitations of standard evaluation protocols for LLM-generated self-explanations and propose practical guidelines for assessing their plausibility and faithfulness. Moreover, we argue that evaluation should extend beyond these criteria to actionability, highlighting applications of LLM rationalization capabilities that support informed decision-making and appropriate action across diverse stakeholders.

Large Language Models (LLMs) are increasingly proposed as cognitive components for robotic systems, yet their opaque decision processes make it difficult to explain success or failure in closed-loop embodied tasks. Following an empirical AI methodology, we study an embodied LLM agent behaviorally by varying the available information and measuring the resulting changes in behavior. Using the Lockbox, a sequential mechanical puzzle with hidden interdependencies, we evaluate LLMs across RGB, RGB-D, and ground-truth symbolic observations in a physical robotic setup and use simulation to probe the resulting behavior. Counterintuitively, agents perform best under raw RGB input and worst under perfect ground-truth observations. In simulation, we probe this effect by randomly flipping perceived action outcomes and find that moderate noise improves performance, peaking at a 40% flip probability with a 2.85-fold success rate increase over the noise-free baseline. Further analysis links this gain to a reduction in repetitive action loops. These findings suggest that success rates alone are insufficient for evaluating LLMs, as measured performance may reflect the interaction between perceptual errors and reasoning failures rather than robust problem solving.