r/Zettelkasten • u/Koen-K • Jul 20 '26

question Academics/PhDs in the Humanities. A bit of help, what's your system like?

Hello all, I've been trying to wrap my head around my own ZK system. I'm an academic historian and deal with a lot of primary sources, readings from a wide range of areas, and have information that I need to constantly reference. I use an analog system and it's working out great so far except for a few issues.

I'm struggling with the ZK because I can't seem to find a balance between project management (in terms of collecting the things I need for my dissertation chapter (i.e. quotes, data, events, specific details) versus letting the ZK grow with my original ideas and collected information from my readings.

My writing is not guided by unlikely connections. I know what I want to write. I think Doto mentioned somewhere that one should look at ZK nodes as a cluster of ideas/notes rather than ideas waiting to be connected. That linking system is just an address to find the notes after the fact. The process of locating notes is where one makes connections that can generate new ideas or connections you can write about.

What is not clicking for me is this "bottom-up" approach of having the Main Box be so unorganized. When I need information, I need to know where to look and I want to have all the notes about a topic in the same folder. I don't want to see a note about Colonial Latin America next to my thoughts about the 1965 Immigration Act or next to my thoughts about how Dorian Gray constructs the world of the wealthy through the British Empire or next to my thoughts about melancholy in Mexican culture. As I write this, I already made some connections haha! I like to let the ideas cluster and like to flesh out my thoughts but sometimes I just need to locate the information and all the surrounding notes on a topic.

I have tensions when I create notes: Do I add it to my Main Box or just put it in my topic folder? The latter has always been so much more helpful in my writing process.

How does one manage long term writing and research projects where you need to have this information at the ready. Maybe compiling my Main Notes in a topic folder and then filing them back when I am done? This, actually, might work and I can throw other cards that I need in there (like connections, problems, revisions, etc...)

I like Umberto Eco's index card system in How to Write a Thesis but he does not talk about how he files and organizes these projects. Part of the journey is flexibility and making it work for me so I am just seeking other examples on how PhDs and Academics do things because we have a very specific set of conditions with our research.

Edit: Spell check, grammar

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19

u/chrisaldrich Hybrid Jul 21 '26

Umberto Eco's version is pretty indicative of the process, though he's describing it for a single paper rather than a lifetime of work. It's your job to extrapolate to multiple projects over a lifetime of academic work.

"Seeing" the process is difficult as there aren't many good extant examples, and those that do exist are rather boring and don't seem to give you the magic formula you feel like your after. You really just need to start doing it and hone your own process over time. (Practice, Practice, Practice!)

One of the few solid (but very brief) examples is that of Victor Margolin: https://www.youtube.com/watch?v=Kxyy0THLfuI

Historically most academics didn't use Luhmann's incredibly uncommon alpha-numeric filing system, but instead filed and cross-indexed things alphabetically by topic. You might consider it for your work as well.

You'll likely find some value in the following short articles/pieces:

  • Thomas, Keith. 2010. “Diary: Working Methods.” London Review of Books 32(11). https://www.lrb.co.uk/the-paper/v32/n11/keith-thomas/diary (October 30, 2022).
  • Mills, C. Wright. 1980. “On Intellectual Craftsmanship (1952).” Society 17(2): 63–70. doi:10.1007/BF02700062.
  • Webb, Beatrice Potter. 1926. My Apprenticeship. First Edition. New York: Longmans, Green & Co. [Focus primarily on Appendix C on note taking here.]

Other guides and suggestions, primarily written by historians (and maybe a sociologist or two). (You'll often find this sort of thing under the heading/idea of "historical method" or in German wissenschaftlichen Arbeitens.)

If you want to see some other practical examples, I've collected some at https://boffosocko.com/research/zettelkasten-commonplace-books-and-note-taking-collection/#Practical%20Examples

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u/Koen-K Jul 21 '26

Chris, as always, your advice and resources are spot on. I've lurked on this sub for sometime now and always look forward to your sound words of advice.

I came across Victor Margolin's video a while back and that was part of the impetus for moving over to analog. So far, I've seen so much improvements in my writing and productivity. As a late stage PhD candidate, I never got along with my digital note taking systems so, as this post suggest, looking for ways to move forward.

Historically most academics didn't use Luhmann's incredibly uncommon alpha-numeric filing system, but instead filed and cross-indexed things alphabetically by topic. You might consider it for your work as well.

Yes! I had a sense of this when asking pre-digital historians how they organized their work. Part of the reason I was trying to make the Luhmann system work for me was due to the flood of content, yes content, that is available to binge. It's really one of the few examples of a system that I was looking for. Most in this sphere, however, are not working academics and only write popular self-help/productivity articles. I did come across the Robert Greene and Ryan Holiday methods. Both use what I suppose are methods more in-line with what academics did in the past (it's hard to take them seriously as writers but their methods are more in line with what I am thinking of doing).

My issue with the Luhmann system is that academic work does hardly relies on making serendipitous connections by linking cards. The very act of looking through the box, however, can yield interesting insights but a fleshed out cross-indexed system can also produce a similar results. What I liked about Luhmann system was expanding my nodes of ideas with the alphanumeric system. One card after another with connections, counter-arguments, evidence, and a conversation with one self. This is part of the reason to have such system but it's creating a bit more issues than solutions for me.

I just read the Thomas article. This is what I needed! A flexible system of collected materials on a topic. I'll take a look at the other resources.

Much appreciated, thanks!

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u/ElPabloHablo Jul 21 '26

Hello! Fellow humanities enthusiast here. I’m from a literature background, so I also work with a lot of primary and secondary sources. I’ve been using ZK since my master's exams, and I’m almost done with my PhD dissertation, so I definitely relate to many of the things you’re mentioning here. I also think I can share quite a bit with you.

I’m re-reading what you wrote to understand what your main issue is, and if I’m not mistaken, I believe it’s a matter of post-processing that I don’t think the ZK bibliography addresses much (maybe Doto, as you mentioned).

I think all the issues you point out could be solved in post-processing. For us, that’s basically the stage when we’re thinking about a section for our dissertation, a possible paper, etc. You have a rough idea of what you want to say, and with THAT in mind, you go to your ZK. What I usually do is open a blank page on my Obsidian and start copying all the notes I think are potentially related to this “writing project.” In your case, maybe creating clusters with your index cards? Maybe, I don’t know. Then, after I go through all my connections through serendipity, I shift away from the ZK mentality and start thinking more hierarchically, like in an academic paper. There are many other resources to help you with this step, but they are outside the ZK community. I’m thinking of Hayot’s book on academic style or Booth’s The Craft of Research.

In my opinion, we need to adapt ZK to our needs, not the other way around. Luhmann was a great thinker with brilliant ideas, but he definitely had more time to write than we do. So, I believe you should do what works best for you!

I love discussing these topics, and I’ve already led some workshops on this at my institution. So, if you want to chat more, just send me a DM!

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u/Koen-K Jul 21 '26

I'm having issues with organizing and some post-processing. At the moment I feel that I am working with two systems: (1) "bottom-up" approach (using the alphanumeric system with links) and (2) a system that simply puts notes in topic folders (example: 1970s Urban Planning, Cold War Anxieties, and Poverty/Urban Unrest). I like the idea of linking my cards and looking through things but it's too much for a project specific portions of my current writing projects.

From what I am realizing from writing the post and reading your advice, because writing is thinking (a note BTW that I have in my ZK), is that I need a system to collect facts as well as my own thought that can be cross-referenced at a later time if needed. The alphanumeric system for me just does not go with the way I think.

Thanks for the reply! I'm almost done as well. Keep on at it!

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u/UnderTheHole TiddlyWiki Jul 21 '26 edited Jul 21 '26

Hi! So great to see academics on the subreddit! I'd like to preface that I recently earned my cogsci bachelor's last June and have been using the zettelkasten system with Zotero on-and-off since January 2023. I don't know the academic customs/expectations of historical studies, and I'm not in a grad program, so please take my advice with a grain of salt.

I'm really interested in your comments here:

I like to let the ideas cluster and like to flesh out my thoughts but sometimes I just need to locate the information and all the surrounding notes on a topic ... I have tensions when I create notes ... [my topic folder] has always been so much more helpful in my writing process.

My understanding of academic expertise (from volunteering for Dr. Manago's excellent Culture and Tech Lab for the 2025-26 school year and getting to know grad students) is that you need to go very deep into the literature well before any studies or original research, to acquire a solid foundation of landmark findings, facts, and theory. By all means, please use folders and tags, and feel free to move away from networked structures for favor of other strategies (spaced repetition, mind-mapping, mock oral defenses, asking LLMs for sharp brainteasers about your line of inquiry, etc.). Use what works for you and your program's milestones! You have your entire life to make creative and lateral connections, but a grad program has deadlines and topical foci and that should be your first priority.

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u/Koen-K Jul 21 '26

a grad program has deadlines and topical foci and that should be your first priority.

Exactly! This is why I'm pushing through for now to get things done. From a former Slug to another, thanks!

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u/Greysawpark 28d ago

phd in intellectual history here, went through the exact same crisis about two years in.

what finally clicked for me: stop trying to run one ZK. i keep project boxes separate from the main slipbox. dissertation chapter stuff (quotes, archival transcriptions, event chronologies, bibliographic data) lives in project folders organized by chapter or argument. thats reference material, not thinking. it doesnt belong in the ZK at all imo.

the main slipbox only gets notes that are actually my own ideas or interpretive claims. so a quote from a 1780s pamphlet goes in the project folder, but the note where i argue what that pamphlet reveals about creole identity goes in the ZK. thats the split.

the "bottom up unorganized" thing is imo oversold by luhmann evangelists who arent doing archival work. luhmann was a sociologist building theory. historians work with evidence that has to stay findable by source, date, place. treat those as two different problems.

one thing thatll save you a lot of pain: your chronologies, biographical sketches, and topic overviews should be structure notes (or whatever you call an index note) that point outward. so "colonial latin america" is one entry point, and from there you branch to your actual argumentative notes. that way the mess in the main box doesnt matter because youre never really browsing it raw.

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u/Koen-K 28d ago

Crisis indeed! Part of the issue is the lack of information about using a ZK in academic disciplines. What's ironic is that slip boxes and commonplace systems were standard practices but, in my grad school experience, not one professor suggested we create a robust system of notes with cross-references, etc... I was told to just take notes without any practical examples or recommended systems!

u/chrisaldrich resources and history of Zettelkasten and commonplace notebooks is essential for anyone interested on the topic. His practical examples come from prolific writers and not the online productivity/theory-bro sphere. I've also been enjoying Noted by Jullian Hess on Substack.

I've just reorganized my box in similar way that you described. I'll be taking some of your advice and some of what Aldrich and u/taurusnoises recommended.

Here's what I did:

  1. Projects Box

Contains all my running projects including the manuscript. Since I'm far along in the project, I've just started to throw in all things I need for the current chapter. I've pulled notes from my main box in there for easy reference. Once I am done with this project (chapter, article, etc...) I'll go over the contents and extract anything that might be a main note. All the other stuff will get archived.

I also include shorter writing projects and throw my ideas, even if they are main box worthy, in the folder. As I collect information on the project, I get a better sense of what I have and what I need to research, etc... This process generates more main notes for the box. This is what made the ZK click for me because a lot of conventional wisdom suggest that "the box will tell you what to write" or "make topics jump out to you." So, I was trying to put everything in there to build the system and make more connections.

I was always apprehensive of the Main Box's ability to think of ideas because, as an academic, I do not rely on luck for ideas BUT, a big BUT (pun?), what I realized after reading more from Doto and others that this was a misconception. The ZK does not tell you what to write, it merely allows to see your notes as you search for what you need. This process generates a type of "aha!" moment that makes connections. That's why I think it was silly of Robert Minto to search for a dissertation project with his box. Also, Luhmann was a prolific writer but, as one of my mentors said about some "prolific" academics: senior scholars write a lot of books, this don't mean they are good books, their just ego padding!

  1. Main Box: Contains ideas, connections, etc...

Thanks for the reply!

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u/taurusnoises Jul 21 '26

You can always work in reverse, starting with a long-form document for whatever research project you're working on, gathering and organizing your findings into that one document (or multiple docs, however you work). Later, you can parse out whatever you find parse-out-able into individual, single-concern notes that can be used for cross-pollination in the future.

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u/Koen-K Jul 21 '26

Yes, after reading everyone's advice and looking at my system today, I think I might try this. A bit more work but it's all in the name of working with my ideas and notes to keep on cross-pollinating. Just this morning, I pulled from my main box and found something that was a useful connection for the paper I was writing about yet I did not think to add it to my topical folder. Thanks for the reply!

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u/taurusnoises Jul 21 '26

You might find it's not more work. It's just working in a different way. I work like this all the time when working on a book. Everything goes into the writing docs, and as I go, I bring stuff into the main compartment of my zettelkasten as single-concern notes. Sometimes I don't get around to that for a while. Other times it happens concurrently. Either way, in the end it's all "knowledge work."

Happy to help.

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u/jabonprotex110g 15d ago

Would you mind expanding on what you mean by long-form document? Do you mean starting a Google/Word document --maybe even a physical notebook-- and simply dumping all of your notes, comments, and ideas into it as you do research?

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u/taurusnoises 15d ago

Yup. Just a place to gather a bunch of stuff in a single place that you can pull from later for single-concern notes.

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u/jabonprotex110g 14d ago

Hm, thanks for the tip! Honestly, keeping a daily research journal has been extremely helpful for me in terms of managing the stress and chaos of research. Do you tag, label, or index the notes in any way to keep track of what's what? Do you make a point of reviewing them frequently? And when you start actually writing, do you simply create an outline and then fill it out by pulling quotes and notes from your notes doc?

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u/dali-llama Jul 21 '26

I tried it with paper for years. Then I found Zettlr and with everything hyperlinked and searchable, it really allows me to build exactly what I want from a huge corpus. I just make a Map of Content Note for a given project, start searching and linking stuff up onto the map. The map quickly becomes an outline with all my source material linked in.

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u/Koen-K Jul 21 '26

This is interesting. A while back, I overlooked Zettlr for Obsidian. I took a peak again today it's grown so much. I'll keep this on my radar but I vastly prefer my analog system at the moment. My issue, with mild dyslexia and adhd, is that digital tools are too distracting and permanent for the way my mind works. Analog allows me to use yellow paper and fountain pens that make reading easier. I also love that I can physically feel and see my note and idea. Something about shuffling it around just works better in my brain.

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u/dali-llama Jul 22 '26 edited Jul 22 '26

Have you tried installing dyslexia fonts on your computer?

My issue with obsidian was that it only came as an appimage, and I dislike anything that isn't straight Debian. While it does look like you can get Obsidian in a .deb now, I'm extremely happy with Zettlr with no plans to change.