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Isn't second order effects quite common and observable in software systems, in history, in economics and everything?

Yes. Zeynep isn't saying "second order effects don't exist". She's saying "don't overthink it".

Consider the public health nightmare we've been stuck in for the last three+ years. Instead of giving direct and useful guidance, people worry about how people will react to guidance and make second order arguments against the basic guidance that would actually help.

Yes, but those are still the exception. The rule is that higher order consequences are small or nonexistent.

The problem is that, there are so many of them that for any decision you will get many of those exceptions worth looking at.

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