NO, IT'S NOT BIGOTED!! Sorry, but people's anti-racism trigger is now set so delicately and sensitively that people will cry "racism" before thinking it through. Any statement relating to skin color in any way can fall victim to this.
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One of the interesting things about this story is the baffling question of how these people came to be this way, with a sudden, jarring change in coloring, right down the middle of their faces, vertically. I like the fact that they expect the audience to be smart and perhaps science oriented, and question askers. They didn't feel the need to spell out completely what's so bizarre about the coloring, but it is this: How could any environment produce this sharp, opposite pigmentation? I think they wonder aloud if it's a tattoo, something man-made. It's not. How could natural selection produce something like this? Or mutation? The environment? We are supposed to be wondering this, along with Kirk, Spock, and McCoy.
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Whatever the cause, it's pretty certain that there was a cause, of some kind. Life isn't just going to spring up on some planet with faces split into exactly even black and white halves. That's what Spock's saying. He's not expressing some racist bias for "monochromes". Pause and remember who we're talking about, what show this is, and the fact that this is their big anti-racism episode...
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"Bigoted" is an extreme charge.