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Too many go too deep into the idea of "atomic notes" without either questioning or realizing their use case. What is your purpose in having atomic notes? Most writing about them online talk about the theoretical without addressing the underlying "why".

They're great for capturing things on the go and having the ability to re-arrange and reuse them into much larger works. Often once you've used them a few times, they're less useful, specially for the average person. (Of course it's another matter if you're an academic researcher, they're probably your bread and butter.) For the beekeepers of the world who need some quick tidbits which they use frequently, then keeping them in a larger outlined document or file is really more than enough. Of course, if you're creating some longer book-length treatise on beekeeping, then it can be incredibly helpful to have them at atomic length.

There's a spectrum from the small atomic note to the longer length file (or even book). Ask yourself, "what's your goal in having one or the other, or something in between?" They're tools, choose the best one for your needs.

Indices are certainly an old construct. One of the oldest structured examples in the note taking space is that of John Locke who detailed it in Méthode nouvelle de dresser des recueils (1685), later translated into English as A New Method of Organizing Common Place Books (1706).

Previously commonplace books had been structured with headwords done alphabetically. This meant starting with a preconceived structure and leaving blank or empty space ahead of time without prior knowledge of what would fill it or how long that might take. By turning that system on its head, one could fill a notebook from front to back with a specific index of the headwords at the end. Then one didn't need to do the same amount of pre-planning or gymnastics over time with respect to where to put their notes.

This idea combined with that of Konrad Gessner's design for being able to re-arrange slips of paper (which later became index cards based on an idea by Carl Linnaeus), gives us an awful lot of freedom and flexibility in almost any note taking system.

Building blocks of the note taking system

• atomic ideas
• written on (re-arrangeable) slips, cards, or hypertext spaces
• cross linked with each other
• cross linked with an index
• cross linked with references

are there others? should they be broken up differently?

Godfathers of Notetaking

• Aristotle, Cicero (commonplaces)
• Seneca the Younger (collecting and reusing)
• Raymond Llull (combinatorial rearrangements)
• Konrad Gessner (storage for re-arrangeable slips)
• John Locke (indices)
• Carl Linnaeus (index cards)