xamdam comments on Best career models for doing research? - Less Wrong
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You are compartmentalizing. What you should be asking yourself is whether the decision is correct (has better expected consequences than the available alternatives), not whether it conflicts with freedom of speech. That the decision conflicts with freedom of speech doesn't necessarily mean that it's incorrect, and if the correct decision conflicts with freedom of speech, or has you kill a thousand children (estimation of its correctness must of course take this consequence into account), it's still correct and should be taken.
(There is only one proper criterion to anyone's actions, goodness of consequences, and if any normally useful heuristic stays in the way, it has to be put down, not because one is opposed to that heuristic, but because in a given situation, it doesn't yield the correct decision. )
(This is a note about a problem in your argument, not an argument for correctness of EY's decision. My argument for correctness of EY's decision is here and here.)
Sounds like a good argument for WikiLeaks dilemma (which is of course confused by the possibility the government is lying their asses off about potential harm)
The question with WikiLeaks is about long-term consequences. As I understand it, the (sane) arguments in favor can be summarized as stating that expected long-term good outweighs expected short-term harm. It's difficult (for me) to estimate whether it's so.
I suspect it's also difficult for Julian (or pretty much anybody) to estimate these things; I guess intelligent people will just have to make best guesses about this type of stuff. In this specific case a rationalist would be very cautious of "having an agenda", as there is significant opportunity to do harm either way.