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Lokai had once heard that people on some Federation planets believed that they were descended from apes. Spock clarified to him that "the actual theory is that all lifeforms evolved from the lower levels to the more advanced stages." (TOS: "Let That Be Your Last Battlefield")
In 2151, Doctor Phlox advocated denying treatment to the Valakians for their genetic disease to Captain Jonathan Archer. He believed that the Menk, who coinhabited Valakis, were on the verge of an "evolutionary awakening", and that they would be interfering with an natural process if they saved the Valakians. (ENT: "Dear Doctor")
In late 2369, when Vedek Winn Adami demanded that Keiko O'Brien stop teaching the Bajoran wormhole as a scientific phenomenon, Keiko asked what would happen when it came time to teach evolution or the creation of the universe. Winn replied that those "issues" would be dealt with when they arose. (DS9: "In the Hands of the Prophets")
In 2370, Lieutenant Commander Data speculated that the strange contagion that had overtaken the USS Enterprise-D was "de-evolving" the crew, by activating introns that reverted them to earlier evolutionary forms. (TNG: "Genesis")
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Ronald D. Moore commented: "Trek [...] accepts evolution as a believable and valid theory. Gene himself felt this very strongly and although we do try to embrace many points of view and many beliefs, there are some matters on which we do make our feelings known. That said, I also think that anyone within the Trek universe who espoused a "creationist" or similar view as to the origins of life would find their beliefs respected -- "respected" being fundamentally different than "believed." (AOL chat, 1997)