It's ironic because the same tools can be used to empower your thinking[0]. Instead of collecting notes, note taking utilities can be used as a sort of L2 cache when you're trying to think something through. E.g. most of my problem solving involves repeated sessions with a text file, in which I dump my stream of thought and refine it. Sometimes it means literally talking with myself via a text file, sometimes it's constructing an artifact (like a prioritized list of things to do). Same tool, slightly different approach.
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[0] - Or damage your brain. The fact that I can't think things through unless I'm writing thoughts down or drawing diagrams may be a sign of improved quality of thoughts, or a sign of me no longer being able to think without a crutch.
I think your [0] note points to a hard truth of life. You have to be aware of how you're used to thinking so you can challenge yourself to make your brain work in new ways. I don't think this is by any means essential but I think it can be immensely useful to not always default to the same habit. 80% of the time, it's ok to exploit what you know, but maybe that remaining 20% of the time try thinking in a new way. The hard part is finding those new ways and not being too lazy or rushed to skip it.
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[0] - Or damage your brain. The fact that I can't think things through unless I'm writing thoughts down or drawing diagrams may be a sign of improved quality of thoughts, or a sign of me no longer being able to think without a crutch.