Autonomous FAIR Digital Objects: From Passive Assertions to Active Knowledge

F(AI)2R is FAIR research with AI in the loop, twice: an AI-assisted authoring pass and a machine-readable audit pass over every artefact. AI systems now draft, refactor, and verify research artefacts, yet their contributions are rarely recorded in a form a later human or machine can audit. Building on the original F(AI)2R experiment, we generalize its provenance model beyond scholarly writing into aiprov, a PROV-O extension covering any AI-in-the-loop artefact, and we package the method as an executable skill that an AI agent operates itself: setup asks the human operator for their ORCID ID, resolves their identity from the public registry, and scaffolds continuous integration that gates every push on graph conformance and publishes the current build of this very paper. The paper is its own case study. Every activity, claim, and source in its production is recorded in the repository's provenance graph under two invariants: no parentless claim, and verification rungs that only humans may grant.

AI-assisted claims can appear authoritative when evidence, analysis, human authorization, presentation, and correction history refer to different states. Provenance, attestation, and transparency expose history but alone do not specify the publication transition examined here. We develop Publication Authority as an exact-state, non-transferable, single-use publication capability and instantiate it in PAC-2026 (Publication-Accountability Calculus), a machine-readable AIJIM Protocol candidate. We evaluate its fourth bounded semantic freeze (SF-4), a fixed-profile specification designed for replaceable bindings. Six obligations govern evidence, runs and artifacts, measurement disclosure, authorization, surface correspondence, and lifecycle continuity. Each yields a target-bound witness, localized counterexample, or localized unverifiability; none can compensate for another. Only a fresh, complete all-pass record derives the permit consumed by one atomic publication transition. We use identity vectors, adversarial cases, finite models, and historical implementations. Ten models explored 110,764 safe reachable states; 76 unsafe configurations produced the expected violation or observer countermodel. A reader surface passing its correspondence check cannot authorize publication unless the accepted record admits that surface. SF-4 separates evidence horizon from verification time and rejects an authentic but causally invalid authorization. A historical predecessor path reproduced 17 frozen authorization-successor outcomes. A later in-house, instance-blind test of known case classes matched all 183 scored expectations; same-host package execution reproduced its 240 archived observations. Results support internal coherence, bounded safety, fault sensitivity, and limited constructibility, but not factual truth, general refinement, blind interoperability, field efficacy, or standards status.

Multi-agent language systems often treat agreement as evidence, yet heterogeneous agents can jointly repeat an unsupported claim or omit a correct specialist fact. We introduce C-MoA, an agreement-based conformal filter that turns inter-agent semantic support into a claim-level nonconformity score and calibrates a retention threshold at the example level, giving distribution-free within-domain factuality control for heterogeneous Mixture-of-Agents. C-MoA is effective: it nearly doubles retained-claim precision on long-form generation (from 0.41 to 0.75), certifies a human-labelled medical set, and transfers across domains without recalibration; its one failure mode is short-form answering, where consensus is cheap and the score is left near chance. We then ask whether counterfactual falsifiability can push past consensus, and introduce CONTRA-MoA, which adds a blinded near-miss tournament, leave-one-agent-out stability, and availability-aware fusion. This extension helps only where the verifier holds domain knowledge, dropping half of the false medical claims at 0.940 precision, whereas with a memory-only judge the added signals are near chance (AUC 0.531 and 0.511) and naive max fusion degrades the working agreement signal from 0.687 to 0.652. The message is twofold: agreement-based conformal calibration delivers reliable, transferable factuality control, while moving beyond consensus requires a knowledgeable verifier, availability-aware signals, and robust fusion.