The answer is going ultimately be a restatement of the question: high levels of carbon dioxide cause discomfort or pain because our bodies have mechanisms for detecting it, whereas we don’t have comparable mechanisms for detecting low levels of oxygen. (High levels of nitrogen *are* toxic, but only under conditions that never existed until the late 19th century and the advent of pressurized caissons and, eventually, saturation diving.)
The best further elaboration is that situations with elevated carbon dioxide levels *do* happen in nature, and it’s a good idea to get out of them. But low-oxygen conditions are rare in the environment where humans evolved.
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