This is my rephrasing of (Ahrens, 2017, How to Take Smart Notes). I added some personal comments.

The amazing note-taking method of Luhmann

To be more productive, it's necessary to have a good system and workflow. The Getting Things Done system (collect everything that needs to be taken care of in one place and process it in a standardised way) doesn't work well for academic thinking and writing, because GTD requires clearly defined objectives, whereas in doing science and creative work, the objective is unclear until you've actually got there. It'd be pretty hard to "innovate on demand". Something that can be done on demand, in a predetermined schedule, must be uncreative.

Enter Niklas Luhmann. He was an insanely productive sociologist who did his work using the method of "slip-box" (in German, "Zettelkasten").

Making a slip-box is very simple, with many benefits. The slip-box will become a research partner who could "converse" with you, surprise you, lead you down surprising lines of thoughts. It would nudge you to (number in parenthesis denote the section in the book that talks about the item):

Find dissenting views (10.2, 12.3)

Really understand what you learned (10.4, 11.2, 11.3, 12.6)

Think across contexts (12.5)

Remember what you learned (11.3, 12.4)

Be creative (12.5, 12.6, 12.7, 13.2)

Get the gist, not stuck on details (12.6)

Be motivated (13.3)

Implement short feedback loops, which allows rapid improvements (12.6, 13.5)

Four kinds of notes

Fleeting notes

These are purely for remembering your thoughts. They can be: fleeting ideas, notes you would have written in the margin of a book, quotes you would have underlined in a book.

They have no value except as stepping stones towards making literature and permanent notes. They should be thrown away as soon as their contents have been transferred to literature/permanent notes (if worthy) or not (if unworthy).

Examples:

Jellyfish might be ethically vegan, since they have such a simple neural system, they probably can't feel pain.

Ch. 9 How to attention attend: One thing at a time. No multitasking When writing, attend to idea flow. Meaning, not wording. ...

Literature notes

These summarize the content of some text, and give the citation.

Example:

(Kahneman & Tversky, 1973) shows that people often do not take into account the prior when doing a Bayesian probability problem. In particular, when no evidence is given, the prior probabilities are used; when worthless evidence is given, prior probabilities are ignored. Kahneman, Daniel, and Amos Tversky. “On the Psychology of Prediction.” Psychological Review (1973)

Such notes could be made in Zotero, which is how I do it. You might make them separately in some other notebook software, or just in plain text files.

Permanent notes

Each permanent note contains one idea, explained fully, in complete sentences, as if part of a published paper.

There are many tools available for storing the permanent notes, see Tools • Zettelkasten Method. I personally recommend TiddlyWiki.

Project notes

These are notes made only for a project, such as a note that collects all the notes that you'd want to assemble into a paper. They can be thrown away after the project is finished.

Four principles

Writing is the only thing that matters.

Don't just read. Make reading notes. Don't just learn. Make blog posts or something to share what you learned.

Also, hand-written notes has some advantage. In (Mueller & Oppenheimer, The Pen Is Mightier Than the Keyboard: Advantages of Longhand Over Laptop Note Taking, 2014), it's shown that students who take notes by laptop understood lectures less, due to their tendency to transcribe verbatim without understanding. From mouth to ears to fingers, bypassing the brains completely.

The way I see it, this is not an argument against using the computer, but an argument for repharsing instead of copy-pasting/direct quoting/mere transcribing.

Be simple

Don't underline, highlight, write in the margins, or use several complicated systems for annotation. It'd make it really hard for you to retrieve these scattered ideas later. You would be forced to remember with your biological brain to keep track of what information is put where.

Put all these ideas in the same simple system of your slip-box, and you will be set free to use your biological brain to think about these ideas.

Your simple slip-box system would be like an external brain that interfaces seamlessly with your biological brain.

Papers are linear, but writing is nonlinear

This is why advice on "how to write" in the form of a list of "do this then that" is bound to do badly.

Instead, you should write a lot of permanent notes in your slip-box. Then when the time comes for you to write a paper, just select a linear path out of the network of notes, then rephrase and polish that into a paper.

Calculate productivity not by how many pages of paper you've written, but by how many permanent notes you've written per day. This is because some pages of a paper can take months to write, others can take hours. In contrast, each permanent note takes roughly the same amount of time to write.

Short feedback loops

Feedback loops should be short. It makes you learn fast, fail fast, succeed fast. According to (Kahneman & Klein, Conditions for Intuitive Expertise: A Failure to Disagree, 2009), this is how intuitive expertise is made: a lot of practice in an environment with rapid and unambiguous feedback.

The traditional way of writing a paper takes months before you get a feedback in the form of reviewers' comments. Instead, you should make notes, which you could make several per day, allowing fast feedback loops. If you really understood something, you'd see it in the form of a well-written note. If not, then you know you haven't really understood it. You can experiment with other ways to make the notes and you will see immediately what works and what doesn't.

Six methods

How to pay attention

Don't multitask. Pay attention to one task at a time.

When writing, pay attention to the idea flow, what you want the words to mean. Don't pay attention to what the words actually mean.

When proofreading, pay attention to what the words are saying, and not what you think they mean.

Pay attention only to what you must and don't pay attention to anything else, because attention is very precious.

Routinize things that can be routinized, such as food, water, clothes... Wear only one outfit ever, like Steve Jobs. Eat only one meal plan, buy exactly the same kind of groceries, or better, always eat the first vegan meal plan at the canteen.

Use the Zeigarnik effect to your advantage. If you want something to stop intruding your mind, write it down and promise yourself that you'll "deal with it later". If you want to keep pondering something (perhaps a problem you want to solve), don't write it down, and go for a walk with that problem on your mind.

How to make literature notes

As mentioned before, each literature note contains exactly two parts: the content of a text, and the bibliographical location of the text. If you do the note in a bibliography software like Zotero, you can attach the note directly to the text, and there's no need for the bibliography information.

The most important thing is to capture your understanding of the text, so don't quote. Quoting can easily lead to out-of-context quoting. Preseve the context as much as possible by paraphrasing.

Prepare the literature notes so that when you make permanent notes, you can elaborate on the texts, that is, describe the context, find connections and contrasts and contradictions with other texts.

How to make permanent notes

Recontexutalize ideas in your thought. Write down why you would care about an idea. For example (from section 11.2), if the idea is an observation from (Mullainathan and Shafir, 2013, Scarcity: Why having too little means so much):

people with almost no time or money sometimes do things that don’t seem to make any sense... People facing deadlines sometimes switch frantically between all kinds of tasks. People with little money sometimes spend it on seeming luxuries like take-away food.

Then

As someone with a sociological perspective on political questions and an interest in the project of a theory of society, my first note reads plainly: Any comprehensive analysis of social inequality must include the cognitive effects of scarcity. Cf. Mullainathan and Shafir 2013.

How to link between notes

There are three kinds of links between notes:

Index -> Entry point note

Note -> Note

Note <-> Note

At the top level, there is one note called "Index". The index note is just a list of tags/keywords with links. Each tag/keyword is a topic that you care about, and is linked to a few notes (Luhmann limited himself to at most 2) that serve as "entry points" to the topic.

The entry points are often notes that give overviews to the topic. Luhmann would make these notes to be an annotated list of notes that cover various aspects of the topic. His entry-point notes would have list length up to 25.

Between notes, there are two kinds of links: sequential and horizontal. In fact, sequential links are really just horizontal links that you annotate as "sequential".

For example, consider this note:

Following: [link 1] [link 2]... Content content [link 3] content content [link 4]... Followed by: [link 5] [link 6] ...

After reading this note, you can go along the sequence and read "Followed by" notes, or take a sideways stride and follow the horizontal link [link 3].

The advantage of marking some links as sequential is that you get clear sequences of thought that you can easily follow, but they are by no means essential. You could just make horizontal links.

Ideally, you should make the network of slip-box notes to be like a small-world network, with a few notes having many connections, and some notes having "weak ties" to far-away notes (Granovetter, Mark S, 1977 The Strength of Weak Ties).

How to write a paper

Don't brainstorm, since brainstormed ideas are what's easily available, instead of innovative or actually relevant. Especially don't group-brainstorm, which tend to become even less innovative due to groupthink effects (Mullen, Brian, Craig Johnson, and Eduardo Salas, 1991, Productivity Loss in Brainstorming Groups: A Meta-Analytic Integration).

Instead, do a walk through the slip-box and select a linear path. That gives you a draft from which you can polish into a paper.

Work on several papers simultaneously, switch if bored. This is a kind of "slow multitasking", which is good multitasking. Luhmann said

When I am stuck for one moment, I leave it and do something else... I always work on different manuscripts at the same time. With this method, to work on different things simultaneously, I never encounter any mental blockages.

When you need to cut out something that you really like, but just doesn't belong to the paper (such as something that is not relevant to the argument), you can make a file named "maybe later.txt" and dump all the things that you promise to add back later (but never actually do). This is a psychological trick that works.

How to start the habit of using slip-boxes

Old habits die hard. The best way to break an old habit is to make a new habit that can hopefully replace the old habit.

For getting into the habit of using slip-boxes, you can start by making literature notes. Once you have that habit, making permanent notes would be a natural next habit to take on.