Sorry, but if you think people acting "like monkeys" must, by definition, be racist to black people, that says something disturbing about your attitude to black people.
Any chance you could ease up on the ad hominem attacks?
First I am only seeing racism because I'm hypersensitive and because I want to see racism. Then I am only seeing racism because I am secretly a racist.
I have assumed good faith on your part, answered the questions and criticisms made and accepted that you are perfectly justified to read the episode the way you want to read the episode.
However, the way that you want to read my argument is somewhat spurious. Nevertheless, I'll continue to assume good faith. So...
I do not think that any media featuring people acting "like monkeys" is inherently racist. Planet of the Apes is not racist. That argument would be absurd. In contrast, I think that any story which portrays a "primitive" and "less advanced" society in such light deserves scrutiny.
Similarly, arguing that anybody who has qualms about the portrayal of characters like Caliban in The Tempest must be secret racists seems equally absurd. (It's like an M. Night Shymalan twist! It turns out feminists are the biggest sexists of all!)
However, I think that there are a number of factors that contribute to make Extinction a staggeringly ill-judged and racist piece of television:
a.) the generally pulpy tone of the third season, down to the design of the Repitilian Xindi costumes and the emphasis on space pirates and other more broad space opera stylings; it works quite well elsewhere in the season, here it provides unfortunate context for some other terrible decisions;
b.) the fact that the world in question is portrayed as a tropic jungle that is home to a ruined civilisation; it doesn't matter that the whole world isn't tropical, what we see of it is;
c.) the episode's reliance of outdated colonial storytelling tropes that would not feel out of place in either a weird sci-fi magazine or even a late nineteenth-century pulp magazine;
d.) the portrayal of the indigenous population as "primitive" and "savage", unable of standing up straight and speaking with generic foreign accents while kidnapping the female white member of the primary cast;
e.) the idea that members of "advanced" civilisations will be seduced and corrupted by their exposure to these "primitives", essentially "going native";
f.) the idea that these savages need to be destroyed and controlled (or "cured") by members of more "advanced" civilisations, for their own good and for the greater good;
g.) the long and unfortunate associations between science-fiction storytelling, evolutionary biology and social darwinist subtext; there are entire books written on the subject, but Patrick B. Sharp provides a solid introduction in The Oxford Handbook of Science Fiction.
It seems hard to look at Extinction and not see its deep and unquestioning associations with colonial storytelling tropes.
(I should also clarify that these stereotypes are not exclusive to black indigenous populations. European explorers and settlers had a habit of defining most indigenous populations that way - whether the Native Americans or the Aborigines. Interestingly - and I'm wary about pointing this out because it might seem like a personal criticism - you were the one who jumped from "like monkeys" to "black." The link I was aiming for was "historical European portrayals of indigenous populations." I only cited the specific example from Transformers II in the context of "it is possible for science-fiction to be racist by analogy.")
(Edited to add: the "like monkeys" racist stereotype was not even specific to non-white indigenous populations; any casual browse through the Punch gallery or exploration of nineteenth-century British humour will offer countless examples of how the British portrayed the Irish as subhuman apes to justify their foreign policy. The fact that portraying an indigenous population "like monkeys" is a colonial attitude has nothing to do with skin colour.)
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