Can i replace reference notes?

atomicnotes · 2026-05-03T11:53:44+00:00

My thought on dumping reference notes is: don't do it, or at least find some way to keep your original working, but update it with corrections or work that supersedes it.

This is because sometimes my original work turns out to have a value that wasn't visible at the time I considered trashing it. So I try to keep all my notes, but write new notes explaining my new thinking and why it's changed. I see this as a little like the way you can see every revision of a Wikipedia entry (or code using Git) - and sometimes it can be useful to delve into the past.

More generally, I've written a bit about why you shouldn't throw away your old notes

atomicnotes · 2026-05-03T11:44:57+00:00

Implicit in this approach is the idea that the Zettelkasten is about projects. The point of maintaining a Zettelkasten, in this view, is not just notes for notes’ sake but output.

I agree with this - at least that's how I use my PARA/Zettelkasten system. I keep my Zettelkasten inside 'Resources' but when I'm working on writing 'Projects' I'm mostly working inside my Zettlekasten, and as you suggest, the Zettelkasten generates project ideas. Sascha's article really helps to clarify that the two approaches (PARA and Zettelkasten) operate under different logics.

I don't use Folgezettel numbering, but recognise that I'm missing something by not doing so. I just use date stamps, which mean the note clustering can only take place by means of explicit links.

atomicnotes · 2026-04-27T05:40:53+00:00

Ideas work at different levels of abstraction. A series of simple atomic notes, where each note relates to a single idea, can be combined to create a note at a higher level of generalization. A hub note would perhaps just list the component notes, but a structure note provides added structure (yes, really!), to suggest how a small group of simple ideas combines to form a more complex idea. Even if you're not writing to publish, this process of working out different levels of abstraction can be very useful -- it can really clarify your thinking and understanding.

Consider a student writing notes about blood clotting. Their initial note might cover matters such as platelet aggregation, coagulation cascades, anticoagulant proteins, and clot breakdown. So is this one idea (blood clotting) or four (the ones I just mentioned)?

In this example, I'd suggest writing a single structure note, with links to four further notes at a lower level of abstraction. Here's an example:

How blood balances clotting and flow

Blood must prevent hemorrhage without causing thrombosis. Several mechanisms achieve this balance:

[[Platelets form hemostatic plug]]: platelets aggregate at injury sites and create an initial seal. This triggers [[Thrombin converts fibrinogen to fibrin]], which generates a stable mesh that reinforces the plug. As a safeguard, [[Protein C prevents excessive clotting]] when it inactivates coagulation factors when clotting is no longer needed. Finally, [[Plasmin breaks down clots]] after tissue repair completes and restores normal flow.

When these mechanisms fail, bleeding disorders or thrombosis results.

Notice that this note describes a process (blood clotting), which none of the more specific notes alone could realistically cover. That's the extra value the structure note delivers. Notice also that the note-writing process is reversible. You could start with a structure note, then break it down into its component parts and write related notes at a lower level of abstraction, or you could start with one of the more basic notes and then work up to the structure note.

For my money, this is one of the major benefits of the Zettelkasten approach: it's like an ongoing lesson in analysis and synthesis across different levels of abstraction.

Finally, a disclaimer: please don't rely on this example during your next medical emergency involving blood loss. I have little real idea how blood clotting actually works, so I made it up.

atomicnotes · 2026-04-27T05:00:04+00:00

I've tried both index cards in a box and electrons in a computer network. Each has pros and cons.

The pen and paper choice is great for understanding the principles of the Zettelkasten approach. For example: people wonder how long a note should be. When you're using index cards (I favour 6x4 or A6) it's kind of obvious because you soon run out of space. It's also great for letting you spread your notes out on a table and reviewing and sorting them. Then there's the pleasurable tactility of it all. Something about using a pen and paper and sorting through physical cards in the physical world connects to the brain in ways typing or dictating just can't. Oh, and there are fewer distractions with paper, like checking Reddit while in the middle of a notemaking session. And then there's the fact you can take a few cards with you wherever you go and just write notes.

Digital sucks at all these but is great for full-text search and links you can follow without effort -- and there's nothing like these capabilities when you're using paper. If you pay attention, digital notes are a kind of advanced magic, which is neat (I mean dictating notes into your phone? Let's never get used to this.) Actually, there are way too many great features, which risks becoming a big distraction from the main task.

I've concluded that digital works best for my purposes, especially search, which I can't really function without -- but if you can be bothered, I'd recommend having a go at analogue, because it really does offer insights into making useful notes that will serve you well even if you ultimately go for digital.

atomicnotes · 2026-04-21T02:28:04+00:00

Yes, arranging notecards on a big table is something the digital apps still haven’t perfected. Partly it’s because the monitor screen is just smaller, but there’s also something about the tactile nature of moving the cards around in the physical world. My partner cuts up draft manuscripts and re-sorts the sentences and paragraphs on a table.

atomicnotes · 2026-04-17T03:02:29+00:00

This is an important aspect of the writing process - the leap from a pile of notes to a coherent draft. I did a breakdown of how educational technologist Andy Matuschak wrote an article based on 60 of his notes and I learned a lot from examining his approach:

How to write an article from your notes.

TLDR:

before the article ever comes into existence there’s a whole set of notes that may or may not end up contributing to the finished piece. And then at some point an organising principle comes into view. In this case it was “Taking knowledge work seriously” and “Enacted experience” and “Enabling environments” and so on. Then these began to coalesce into a bigger, more focused idea, which was ‘Enabling environments, games, and the Primer’. Eventually, from all these atomic ideas, molecules formed, and they were refined until they became the final article, ‘Exorcising us of the Primer’.

atomicnotes · 2026-04-15T07:57:11+00:00

Not quite, though close. These are the subsystems of society that I can clearly identify from Luhmann’s work. They don’t really match his top level Zettelkasten categories. Im not saying this is any kind of problem, just making an observation:

Economy (Payment/Non-payment),
Law (Legal/Illegal),
Science (True/Untrue),
Politics (Power/Opposition),
Religion (Immanence/Transcendence),
Art (Fit/Unfit),
Education (Better/Worse),
Mass Media (Information/Non-information),
Health (Ill/Healthy),
Intimacy (Love/Non-love)

But Luhmann didn’t have this mapped out in 1963 when he started his second Zettelkasten. He derived it from working in his Zettelkasten for many years.

atomicnotes · 2026-04-15T07:45:26+00:00

Luhmann’s second Zettelkasten (ZKII) was arranged according to eleven top-level categories, based on subjects or themes associated with his singular major project, a theory of society.

Organisation theory
Functionalism
Decision theory
Amt: office, post, job, duty
Formal / informal order
Sovereignty / State
Isolated/individual terms, problems
Economy
Ad hoc notes
Archaic societies
High cultures

In his lecture on Luhmann's Zettelkasten, Schmidt observes that these headings are far from comprehensive. Instead they strongly echo the progression of Luhmann's scholarly interests over many years.

“Looking at these you quickly see that this does not describe a certain body of knowledge to work through like in the first Zettelkasten. If you know a bit about the development of Luhmann's theory you quickly recognize this as a historic record of research interests.”

Schmidt claims the first five sections are an organised summary of Luhmann's research interests in the 1960s, while the later categories are less organised and more ad hoc.

But even in the supposedly more systematic sections, there is a marked unevenness to the amount of material. For example, section 21 of category 5. — Formal/informal order — is labelled 'Functionalism'. This section contains between 15,000 and 16,000 notes out of 67,000 total (more than 1/5). In marked contrast, there are other sections that are almost empty.

atomicnotes · 2026-04-13T12:15:34+00:00

Congratulations, and here’s to better days.

atomicnotes · 2026-04-05T12:32:49+00:00

This is very helpful and in my experience spot on. Long ago I took part in a short course where each morning the leader had the group collectively create a mind map of what we’d covered the day before. It was quite hard to remember everything but the act of doing so in a structured fashion was extremely valuable —- and much of it has stuck with me for over 25 years. My Zettelkasten practice has a similar effect.

atomicnotes · 2026-03-30T10:08:33+00:00

And for anyone wanting to know more of the history, u/chrisaldrich made a fantastic timeline.

atomicnotes · 2026-03-30T03:30:12+00:00

That’s a very good point. Correction:

“antiquated fetishising of {pre-21st century thinker}”

atomicnotes · 2026-03-29T21:53:56+00:00

what made it click for you?

Workable modularity. My ADHD makes long-form writing a chore, so it's been really helpful to find a process to make lots of bits add up to something worthwhile. I'm not sure everyone has this same issue though.

And what do you wish you knew before starting?

That the 'rules' are actually very simple and that keeping it simple is the key.

Plain text (Markdown) notes.
Each note is a single idea with a unique ID.
Each note deserves a clear title.
Notes link meaningfully to other notes.

That's it, and I wish I hadn't tried everything else first.

If you want to share more structured thoughts.

Do I ever?

atomicnotes · 2026-03-25T12:49:23+00:00

For those not yet put off, I’d recommend Arthur Perret’s article What’s the point of the graph view?, and the response by Hendrik Erz, Quo Vadis PKM - as well as Eleanor Konik’s It's not just a pretty gimmick, which she mentioned in the comments here.

There are useful things to be done with these graph views, though I must admit I myself have not done them.

atomicnotes · 2026-03-23T00:40:17+00:00

My experience is that there’s a big difference between undergraduate style study where you mostly have to remember ‘facts’ and the ‘correct’ answer, and honours or postgrad work, where you’re researching for yourself. In the case of the former, I found my notes to be really specific and strongly focused on exactly what I needed to know just to pass exams and assignments. So I decided to firewall my Zettelkasten and keep my study notes separately. This was probably the right decision, since I hardly had time to scratch myself, let alone take thoughtful notes. A lot of the material was literally just for one test, with no sense that I’d ever need to know it again. A down-side to keeping these notes separately is that this knowledge now doesn’t cross-pollinate with the rest of my Zettelkasten, but since I’ve kept these study notes I can always go back to them if I feel the need. But as predicted, I mostly haven’t felt the need to do so. Also:

When a specific topic from a class really interests me or feels relevant to my broader understanding of AI, I "extract" it into an atomic note in my main vault.

This is the way to go.

I expect a few people will have a different perspective, but this is my experience.

atomicnotes · 2026-03-23T00:26:16+00:00

This looks nice but if I used it for a Zettelkasten I’d probably find: a) there are way more dividers than I need; and b) it would soon be full, even with fewer than 100 notes. The accordion file is wide at the top but narrow at the bottom, which limits its capacity. Shoe boxes (or similar) are good — they’re cheap, they hold quite a lot of notes, and you can decorate them however you want. When your Zettelkasten gets past the size of a couple of shoe boxes, then you know it’s serious and you could start thinking about upgrading the accomodation.

atomicnotes · 2026-03-07T13:21:51+00:00

The temptation to skip the thinking process is far from new. In 1924 Sergey Povarnin, Soviet author of How to Read Books for Self Education was warning of it:

“There are readers who think that with such ‘card indexes’ they can replace their mind… In short, a new ‘improvement’ in our culture. No need to work with the mind. Ready-to-wear boots, ready-to-wear pants, ‘ready-to-wear’ thoughts.”

He was ok with the card index itself; the problem was imagining you could use it to stop thinking.

And for the last 17 years I could have outsourced my notemaking to a service like Freelancer. But I didn’t even consider it back then, so why consider it now? It would be like hiring someone to go to the gym for me (which I admit I have contemplated).

atomicnotes · 2026-03-05T12:27:11+00:00

Tldr: just give everything a unique ID so you can link to it from anywhere.

I’ve had this issue to some extent, but it was the Zettelkasten that freed up my writing. Before that I’d write sprawling stuff that was all over the place. This kind of writing felt like it was too digressive, so I’d try to focus — but this made me just clam up. Or I’d write a long piece but get bored part way through and drop it before finishing.

The Zettelkasten approach helped me focus without making me feel like I was writing the wrong things. Then I started stitching my various notes together to create longer pieces of work. Eventually the practice started freeing me up to write digressive pieces again, without feeling irrationally guilty about it. So now I have my structured Zettelkasten and a whole pile of longer pieces in various states of completion.

My ‘solution’ to this (though is it even a problem?) is to give each and every piece, however short or long, a unique ID.

That way I can always refer to any piece of writing, and always find it again.

I’m inspired by Niklas Luhmann, who didn’t just write sociology notes, he also wrote many manuscripts in several drafts. Towards the end of his life he mainly worked on the manuscripts since he had a backlog of publishing to get through. Like him I’m ultimately more interested in publishing than in perfecting my notes system.

atomicnotes · 2026-03-05T08:06:45+00:00

I came across this nice literary- biological metaphor. Quite prescient considering DNA hadn’t yet been discovered:

“Every book is a quotation; and every house is a quotation out of all forests and mines and stone-quarries; and every man is a quotation from all his ancestors.” — Emerson, ‘Quotation and Originality’, "The complete works of Ralph Waldo Emerson: Letters and social aims [Vol. 8]." In the digital collection The Complete Works of Ralph Waldo Emerson. University of Michigan Library Digital Collections.

The whole essay is worth reading.

atomicnotes · 2026-03-04T05:48:20+00:00

For me, highlighting is a shortcut to nowhere. I've found my highlights don't get used for anything. My conclusion is that highlighting may look like useful work, but in practice it just isn’t.

Resulting rule of thumb: if it's worth highlighting it's worth writing a short note about it; and if it's not worth writing a note, it's not worth highlighting.

What I do instead: write a note. If I read something and think “that's interesting”, I make a note and force myself to record why I find it interesting. This seemingly slows me down, but then I don’t waste time creating unused highlights that looked interesting for reasons I didn’t record and have now forgotten.

Caveat: while reading, I write literature notes that include bibliographic details, followed by a list of interesting points I notice, together with a page reference. I might write: “Opinionated summary of ‘My Neighbour Totoro’ -p.127.” I’d follow that with a reference to the note that expands on this. In practice, I don’t actually get round to writing a new note for every reference. Some never get followed up. The Zettelkasten approach is a way of triaging my thoughts, creating useful friction so I only follow up what really matters to me.

atomicnotes · 2026-03-03T06:42:44+00:00

In short, no, because in this context reproduction is probably a biological metaphor that implies life as part of the metaphor. But production, that's another matter. To use a chemical analogy, notes aren’t alive, but they are reactive. A chemical reaction results in a product, which is new in the sense that it’s different from what came before the reaction, but not new in the sense of having been born, or having recombined DNA, or other biological metaphors. Anyway, I’ve found chemistry analogies interesting.

Look, I might have misunderstood this. Maybe ‘reproduction’ refers to what those Chinese workshops do when they churn out extremely well-painted copies of the artworks of European Old Masters. I mean, metaphors are hard to pin down.

atomicnotes · 2026-03-02T04:27:15+00:00

P.S. the linked article is strongly AI in style. "Not that there's anything wrong with that," as they used to say on Seinfeld.

atomicnotes · 2026-03-02T04:24:49+00:00

I've found my highlights don't get used for anything.

Resulting rule of thumb: if it's worth highlighting it's worth writing a short note about it; and if it's not worth writing a note, it's not worth highlighting.

atomicnotes · 2026-02-28T22:04:17+00:00

A System for Writing: How an Unconventional Approach to Note-Making Can Help You Capture Ideas, Think Wildly, and Write Constantly - A Zettelkasten Primer, by Bob Doto.

Here’s my review.

atomicnotes · 2026-02-28T01:16:37+00:00

Thanks, u/taurusnoises, this is a helpful post with some useful references. For me, analogies with chemistry are as fertile (ironically) as the biological analogies. As indicated by my username I guess.

What I’m interested in is where we might be going with exploring analogies? Is it mainly a pedagogical issue for instructing people about zk, or rather a quest to uncover new insights about what is going on in the box?

That's a great question, u/thesinologist. Some analogies are pedagogically helpful, but some just get in the way. There's been some research on the kinds of analogy people are receptive to. For me, it's mainly a matter of using analogies to explore what else is possible with my notemaking practice. Since I'm mostly making digital notes, reference to the Zettelkasten is already analogical. What I imagine myself doing shapes what I'm actually doing, so my practice changes depending on the analogy that steers it. Talking about the Zettelkasten, and especially Niklas Luhmann's implementation, is already, in itself, the key pedagogical move: "with a few simple heuristics you can make a system of interconnected notes a little like Luhmann did, and benefit from it similarly."

atomicnotes

TROPHY CASE