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A biological system was a system of related organs, glands, and other anatomy.

In 2375, following the destruction of a Borg sphere, The Doctor reported that although One's Borg implants were regenerating, his biological systems were severely damaged, necessitating immediate surgery. (VOY: "Drone")

In 2377, The Doctor questioned B'Elanna Torres' request that he remove the Klingon features of her and Tom Paris' unborn baby, asking why he ought to "tamper with biological systems that evolved over eons?" (VOY: "Lineage")

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