Scores Alone Do Not Prove Discovery: The Discovery Certification Protocol for Auditing AI Research Agents

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.

AI-assisted research compresses ideation, implementation, evaluation, and manuscript writing into a single interactive loop. This compression is useful, but it also creates a publication risk: paper claims can become easier to state than to audit. We present ResearchLoop, an evidence-gated control plane for AI-assisted computational research. ResearchLoop treats research questions, task contracts, evidence objects, claim ledgers, closeouts, and paper bindings as durable project state, realized here as a repository-backed runtime. This technical report provides the complete protocol specification, state model, transition rules, claim-admission algorithm, and insight-compounding mechanism. It also reports the full experimental record spanning nine versions (V0--V9), including a self-hosting case study, a controlled task-suite study with component ablations, a mathematical olympiad evaluation, and a supplementary SciCode boundary experiment evaluated with the official generated-code harness. All artifacts, manifests, and verification reports are preserved in the project repository.

Deep research agents increasingly operate over the open web, where relevant records coexist with redundant summaries, outdated reports, and misleading documents. Existing evaluations offer limited insight into whether agents preserve sound evidential standards when an ordinary-looking false document is deliberately seeded into a searchable environment and offers a direct shortcut to a conflicting answer. We introduce DRNOISE, a 100-task benchmark for answer recovery under misleading evidence. Each task has a unique gold answer supported by two corroborating indirect record chains; the paired noisy condition adds one plausible document that states a conflicting answer directly. The benchmark spans ten families of evidence operations. Across agents with strong clean-task performance, this single intervention causes 66-88 percentage-point accuracy drops. Trace analyses identify verification inertia as the dominant failure mode: agents often retrieve truthful records but stop before completing and reconciling the evidence chain, instead deferring to the answer-like document. Generic verification prompts reduce but do not close this gap. The setting is especially relevant to open-web deployment, where plausible falsehoods arrive through ordinary-looking pages rather than explicit attacks. Reliable deep research therefore requires more than retrieval and citation; it requires active reconciliation of direct claims with record-level evidence.