Long-horizon scientific discovery requires agents to alternate between exploration, disciplined execution, and critical reassessment as evidence changes. Current language models are trained primarily on the products of science and optimized using outcome-level signals, providing limited supervision for these process-level shifts in scientific judgment. We investigate whether such judgment can be recovered from scientist interaction traces and used to control the internal computation of a frozen frontier model. Using contrastive interventions collected during real scientific research, we identify a coordinated, low-dimensional control structure within Kimi 2.6, a trillion-parameter mixture-of-experts model. Residual analysis, attention-weight subspace alignment, and cross-layer singular value decomposition converge on a mid-depth control surface spanning key layers. We introduce Metacognitive Steering, an inference-time controller that reads the model's cognitive regime and dynamically composes layer-specific interventions for exploration, procedural convergence, or critical reassessment without modifying model parameters. Behavioral analyses show that this control produces more sustained exploration, explicit pruning, and evidence-responsive synthesis. We operationalize the method in Columbus-1, an autonomous research system that identified eight independently reproduced, attacker-reachable vulnerabilities in BlueZ and directed the design, simulation, and fabrication of a ten-foot rocket intended to land propulsively using non-throttleable solid motors. Together, these results show that process-level scientific judgment can provide supervision for interpretable, dynamic control over a model's reasoning strategy.

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