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lavalamp comments on Don't Build Fallout Shelters - Less Wrong
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Post-infection versions of yourself experience generally the same versions of worlds as pre-infection versions of you. Post-apocalypse yous find themselves inhabiting drastically difference worlds from your present self.
If you had an extremely large negative term for "having ever been infected" in your utility function or the infection was one that left you in horrible pain, then this reasoning applies equally well. Although with the caveat that not getting immunized makes you partly responsible for the infection of many others, so it's still not exactly the same.
Then that's good enough as a reductio.
Not being vaccinated makes you just a little responsible for other deaths. Not building a fallout shelter big enough for five people makes you totally responsible for five deaths. It seems commensurable.
Hm. My intuition says it doesn't balance, but of course this will depend on the specifics of the disease, so you could be right. We can also assume you can construct some disease such that the possibility of surviving it without the vaccine is similar to the possibility of surviving the apocalypse without a bunker.
But that's besides the point. I think this argument doesn't really work because to be consistent, you have to prefer suicide to living in a post-(apocalypse, infection) world. Or rather, it does work, but only for really extreme situations. Vaccines are typically much less expensive than bunkers, so the cost of deferring your suicide decision is much less (although you may not want to if e.g. the disease leaves people paralyzed).