The challenge of aligning artificial intelligence (AI) with human values persists due to the abstract and often conflicting nature of moral principles and the opacity of existing approaches. This paper introduces CogniAlign, a multi-agent deliberation framework based on naturalistic moral realism, that grounds moral reasoning in survivability, defined across individual and collective dimensions, and operationalizes it through structured deliberations among discipline-specific scientist agents. Each agent, representing neuroscience, psychology, sociology, and evolutionary biology, provides arguments and rebuttals that are synthesized by an arbiter into transparent and empirically anchored judgments. As a proof-of-concept study, we evaluate CogniAlign on classic and novel moral questions and compare its outputs against GPT-4o using a five-part ethical audit framework with the help of three experts. Results show that CogniAlign consistently outperforms the baseline across more than sixty moral questions, with average performance gains of 12.2 points in analytic quality, 31.2 points in decisiveness, and 15 points in depth of explanation. In the Heinz dilemma, for example, CogniAlign achieved an overall score of 79 compared to GPT-4o's 65.8, demonstrating a decisive advantage in handling moral reasoning. Through transparent and structured reasoning, CogniAlign demonstrates the feasibility of an auditable approach to AI alignment, though certain challenges still remain.

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