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General question..

If homophobia was an instinct, why would it even exist? There was no threat that the homosexuals were going to stop the breeding heterosexuals from passing on their genetic material, and that IS what the following generations are based off of, right?

This is only theory, but I believe homophobia is an offset of "false memory" (Studies showed that people who were convinced enough that a fale event actually happened, start to believe, and often "remember" portions of that false event), and a need to belong within a group. I would deem homophobia very little chance, if any, of being inherited.