gwern comments on A "Failure to Evaluate Return-on-Time" Fallacy - Less Wrong
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Your post includes a "silly" and a business-scale example, but not a personal one. In order to answer the questions about causes that you ask, it seems necessary to look at specific situations. Is there a real-life situation that you can talk about where you have two options, one almost certainly hundreds of times as good as the other, and you choose the option that is worse?
I used to be pretty cavalier about messing with Windows, and would lose my files on an annual or bi-annual basis. I spent a heck of a lot of time tracking down files and restoring from my sporadic backups, not to mention the virus scan time or defragging.
Then the 4th or 5th time I realized that this was crazy, switched to Linux, and learned how to use DVCSes. I'm not sure that this has yet amounted to a 300x improvement in wasted time, but I'm pretty confident that by the time I die it will have.