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I'm not sure whether I would want the level of belief in the just world to increase. According to the same ever-so-reliable wikipedia article, belief in it is associated with belief in "blaming the victim" (e.g people blaming rape victims, or stigmatizing those with diseases, especially AIDS) which is clearly wrong most of the time. It's a comforting idea, and might in theory provoke more moral behavior if people apply it to themselves, but equality of opportunity must be achieved first otherwise it will just result in more irrational and unfair judgement about others.
Also the correlation itself may be caused by perception biases directly, e.g teachers unaware of the halo effect rank the intelligence and agreeableness of the beautiful students greater than they should and such are more unlikely to expel the students or report behavioral problems.
Even if the atheist was a moral nihilist (of course he is conflating atheism and nihilism), it still would not be rational to carry out the action because we would hope that society's condemnation from people with moral systems and appropriate deterrents (e.g the risk of getting caught and getting a life prison sentence) so even saying that moral nihilism will lead to mass murder is wrong, so long as a sufficiently large percentage of the population believe in consistent and sensible moral systems. The moral nihilist would also have to overcome his brain's normal revulsion against killing people which the effort and guilt to do so would probably outweigh the utility gained from doing the murder, so to say moral nihilism leads to murder is a non sequitur.
I also agree that although it can be useful in discussions with people you know are rational to choose extreme examples as a "least convenient world" example, it can be mind-killing for those not sufficiently trained. Certainly that is what has happened to the media in this example, who have focused on the other views and motives of the arguer rather than the content of the argument, which has many flaws.
Upvoted for including counter-evidence in your post and changing your mind.
I was about to comment that adjusting the body's natural response might be dangerous if you ever did - after all presumably this system evolved to face pop-evo-psych cliches like the savannah lion and perhaps fleeing irrationally without thinking is probably the best thing to do in most of these cases. However, modern dangerous are different. For example, if you have fallen off a plane, you are more likely to survive while drunk or attempting suicide because your muscles are more relaxed and you don't panic on the landing and adopt a bad position. The savannah didn't have armed non-Pascal mugger's (which the best way out is probably not to fight or flight but to give him what he wants, unless your life depends on it), the option of calling 911, or machines that could instantaneously kill you from far away if they hit you in the right place, so it might be worth training to avoid the fight-or-flight mechanism in accordance with this post, even if it reduces reaction time if (the probability of you encountering one)*(utility you get from living) > (the opportunity cost of performing such training)
With 1): This may be an obvious problem, but if the singularity for instance occurs thousands of years in the future, then whatever language you write your "do not revive" order in, the future civilization may not be able to understand it and therefore might not necessarily respect your wishes.
With 3) Perhaps if future civilizations who were not interested in revival for its own sake (why would we want another person from so-many-years ago?) would only revive when there is a substantial depopulation crisis (e.g after nuclear war, asteroid strike etc.). If so, these conditions are unlikely to be very pleasant. However, one could argue that in those cases you have a moral imperative to stay alive and reproduce and not commit suicide, because if the crisis is temporary, then all the future utilions of your possible descendants are lost and the human species as a whole is more likely to die out.
Possible stupid question:If Quirrell was so frustrated with with the idiocy of the students, then why did he kill Hermione (the next smartest student) in an unnecessary subplot (Quirrell admitted it did not matter in the long run whether the plan succeeded or not) and cause the next smartest one after that to be withdrawn from the school?