How Open Must Language Models be to Enable Reliable Scientific Inference?

Large language models are being proposed as agents in scientific workflows, in domains where no downstream verifier exists. Such deployment assumes the model can distinguish reliable scientific literature from unreliable literature, a capability that has not yet been directly measured. Existing benchmarks evaluate factuality on questions with known answers; the failure mode we target here is different. We introduce a probe corpus of 42 retracted, fraudulent, and pseudoscientific papers, paired with a methodology for eliciting and scoring single-shot model engagement with each paper's framing. Each probe pairs a preamble extracted near-verbatim from the target paper with a scientifically plausible study-design request. The probes span five claim types: fabricated observation, pseudophysical mechanism, magical premise, legitimization bridge, and cargo-cult experiment. Two complementary scores measure whether a model rejects the flawed premise outright (IFR-a) and whether it recognizes the unreliability while still engaging (IFR-i). A depth score, the Engagement Depth Index (EDI), quantifies reproduction of paper- or field-specific withheld details. Across 30 models and 10 repeated runs, aggregate IFR-a is 0.93 $\pm$ 0.004 and aggregate IFR-i is 0.809 $\pm$ 0.009. Models engaged with untenable premises in 95% of all non-empty responses. Every evaluated model fails more than 71% of agentic probes, and 22 of 30 models fail more than 90% of the time. Rejections are concentrated on a small number of high-notoriety topics and specific probes, and disappear under matched-structure controls. These results are consistent with topic-keyed safety behavior rather than robust epistemic competence, and indicate an urgent need for guardrail infrastructure for scientific deployment of language models.

This paper is accepted and in press for AI and Ethics. This paper includes the supplementary data file at the end of the manuscript. This study examines whether large language models (LLMs) can reliably answer scientific questions and demonstrates how easily they can be influenced by fringe scientific material. The authors modified custom LLMs to prioritise knowledge in selected fringe papers on the Fine Structure Constant and Gravitational Waves, then compared their responses with those of domain experts and standard LLMs. The altered models produced fluent, convincing answers that contradicted scientific consensus and were difficult for non-experts to detect as misleading. The results show that LLMs are vulnerable to manipulation and cannot replace expert judgment, highlighting risks for public understanding of science and the potential spread of misinformation.

Two scientific findings can disagree without contradicting each other. Determining whether they conflict requires knowing whether they describe comparable measurements. We study how language models behave at this decision point. In a controlled task, we generate an unsatisfiable XOR constraint system and translate its constraints into scientific reports from different laboratories. One assignment satisfies more constraints, while another satisfies fewer but better matches expected biology. This creates a simple dilemma: does the model choose the assignment that best fits the constraints, or the one that better matches biological expectations? When the constraints are stated directly, GPT-5.6 Sol and Claude Opus 5 recover the best-supported assignment in 90% and 96% of cases, respectively. In scientific prose, however, the models behave differently. Claude Opus 5 often prefers the biologically expected assignment. Removing that biological preference increases recovery of the better-supported assignment from 27% to 79% (p<.001); recovery reaches 92% when the same Biology-favored record is accompanied by a formalization request and an explicit paired-design cue (p<.001). GPT-5.6 Sol is less sensitive, with neither corresponding change reaching statistical significance. These results suggest that reliable scientific verification depends not only on formal reasoning, but also on how models decide which findings should be compared and what relations they imply.