One of the more common and insidious failure modes when it comes to writing notes1 is to think of the goal as building up a database rather than as scaffolding for your current thought and writing (that may also be useful in the future). I have seen many questions from note-taking neophytes on places such as the Zettelkasten Forum that assume this confusion, and I myself have often been tempted this way. There is a certain allure to creating a vast network of interconnected notes, perfectly indexed in the perfect system.
But several grave errors follow from this line of thinking. Zeroth, before even putting down one word, is thinking of what you are writing as “notes.” The word has a static flavor. It gives a sense of artificiality and impassibility. It is better to think of them as ideas. Ideas may change with time, and more importantly, they are a part of you, not a self-sufficient external system. Probably the only audience for your notes is yourself. They should augment your understanding, not serve as some fossilized hippocampal relic future historians will study.
First, having too high a threshold for including something as a note. If you are creating a monolithic database, you will only want to admit the best and most complete ideas. This will prevent you from writing down and fully considering countless ideas. True, you cannot write everything down, so you must have some filter. But having some indefinite standard of “good enough” will only make your notes vacant and inutile.
Second, confusion over what kind of content should be turned into a note, and in what form. This is closely related to the first issue. If you are writing notes to make the perfect graph, what do you put in it? This is a classic case of Goodhart’s Law: mistaking the means for the end, the means becomes less than worthless. Rather than focusing on the network of notes, we must get clear on our goal. Aimless general note-taking will not produce anything of value. You probably have something you are interested in or investigating, so select and format your notes in alignment with that. In my experience, projects are the best way to direct your efforts and produce good work. Likewise, the solution to both this error and the first is to ask yourself, “is this relevant to the project I am working on right now?”2 Not only does this solve the problem of selection, it also immediately makes clear how you should connect this note with that, and provides a context you will likely remember in which you can place the note to find it when and where you will want to.
Third, trying to collect ideas from the ground up, only adding new notes if they are already justified by previous ones. One of the core ideas of the American Pragmatists such as Charles Peirce was that you can only start in media res: the only conceivable place to start is where you are now. A priori thinking, trying to get to some solid Cartesian ground, is empty and fruitless. Reality is much too complex to derive from first principles. More fundamentally, where you are right now (and all that has lead up to that) ineluctably influences how you determine what those first principles are. The supposed starting point would be a function of the present end point. In our case, this means to just start taking notes on what you are working on right now. Don’t try to support every claim with perfect context: your notes are for you, and the context is in your mind.3 Write now and expand where you find lacking as you go.
Fourth, proliferating metadata and taxonomies. This unduly increases the friction required to actually write something. This makes sense if you are writing a database that needs to be searchable across 20 different dimensions with built-in redundancy. It makes no sense writing functional notes for yourself. You really just need to group things together in contexts you will want to find them in later. You don’t need tags. You don’t even need a global dashboard or index. If you merely have a project or focus you are working on, you will remember that as long as it is important. Then, all you need to do is put notes in that context (this could be as simple as a file full of links to related notes). Repeat for all other projects, and leave some breadcrumbs/links between them where relevant. If you really need to find something in the future outside of one of those contexts, full-text search will probably be enough.4
Fifth, and perhaps the most damnable, not actually using your notes. This flows from all the above errors, which introduce uncertainty and friction. It is bad on two levels: firstly, because, well, notes are no use if you don’t use them; secondly, because notes are, as I mentioned in error zero, better thought of ideas, and ideas live in a particular point in time, now. Even if you use your notes later, they will feel strange and alien. You will have lost the momentum and the throughline. Stephen King remarks in his book On Writing that he tries to get the first draft of his novels finished within three months. Any longer, and it starts to take on a stale and unfamiliar character. You cannot live a deferred life. If you do not deal with the thoughts that are important now, you probably never will.
The true purpose of taking notes is not merely to collect, but to produce. The notes are not the end product, but one of the tools with which we can create something new. They are building blocks for something greater.
A few practical asides. I think of notes primarily as mini-essays explaining one thing. That thing could be a relation, a concept, or a data point—anything, as long as it is my own writing and it relates to whatever I am working on now. You cannot hope to fit all the important details in one such mini-essay, but that is precisely the point. Writing in small chunks is much more approachable and fun than summoning forth all your thoughts on a subject a few days (or hours) before a deadline, in the case of assignments. Moreoever, writing in small chunks lets you actually think through and develop each idea as you go.5 When you do want to cover the missing pieces, you can just link to more notes. Links function as semantic zoom, allowing you to look (or write) further into any particular area or concept you are concerned with, without cluttering your writing or expanding the scope of a particular note beyond one thing.
When you really get the hang of note-taking—and the primary obstacle to this is frequently our own over-complication—it is wonderfully liberating. Once you start writing things down and connecting them as they come, directed to some end (an essay, a presentation, an answer to a particular question, etc.), writing becomes easy. It’s the thinking part that’s hard.

Notes
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I am chiefly speaking of idea- or concept-focused notes rather than reference or how-to style notes. However, I think the ideas I set out here can also be applied to those, perhaps with some modification. The main difference is in the purpose: the former for developing ideas and producing writings; the latter for looking up how to do something or where or what something is. ↩︎
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If you don’t have a clearly-defined project, substitute question, idea, area of focus, etc.. ↩︎
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This is not to say you should neglect to make your notes intelligible. Shorthand is for the short-term. Your future self is in a sense a different person than you are now. What I am saying is that the language of your notes lives in the context you are in now, and, if subordinated to a project as in the previous point, you will likely have enough information to understand what you were getting at earlier if it was actually important and developed enough. Of course, this assumes you actually write stuff down, link things, and clump ideas into more substantial threads. If you don’t (probably because of the next two errors), nothing can help you. ↩︎
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As long as I put my notes in one place (a directory or file), I can’t think of a time I have used full-text search (fuzzy with live-update is best) and not found what I was looking for. The only times I have failed were when I didn’t actually write it down or wrote it down in an unusual place (a scrap of paper or a text message or whatever else is not connected to the rest of my notes). ↩︎
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This includes connections between ideas/notes. You can write notes whose “one thing” is explaining how two or more things relate. You can group these into larger notes that chain ideas in to fully-fledged arguments, filling in the gaps with connective text. These function as local indexes, and are how I have written many of my academic papers. ↩︎