The word ‘app’ is horrendous. It makes me think of Angry Birds and Candy Crush. It feels utterly inadequate to describe the majesty of things like and
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Alan Kay argued that "medium" is often a more powerful frame than "tool." doubles down, suggests "environment" is better still—includes cultural context, social interaction, ecology, etc. Notion/Roam have some environment-like properties, so "tool" feels wrong.
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(I've found the phrase "enabling environment" to be quite generative as an aspiration… some rough notes along those lines here: notes.andymatuschak.org/z3DaBP4vN1dutj)
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I think the analogies that make the most sense feel architectural—making spaces, environments, contexts, places
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You might enjoy "Design Unbound," which attempts to create a philosophy of system design around architectural practice: desunbound.com
I found many sections quite helpful, though I don't understand enough about architecture to grasp it all.