My approach to the margin note/marking conundrum:
I primarily use digital sources. Most e-book software has an option to just look up your mark ups, and to extract them. This makes things easier. What I’m describing here works with physical books as well, so I will describe different processes for physical and e-books as necessary.
I use mark-ups as a ‘look at this passage a second time’ marker. I use two markers (Marker colors or marks like a cross and circle on margin). One is for ‘moderately interesting’, another is for ’resonated strongly. For the first category, use a marker color that can be overwritten by the second (like yellow, and dark red for interesting stuff).
Reading happens in two passes for me:
First pass, I read the chapter, book part or whole book from front to back, marking anything of note. If I have something to say, it goes into the marginalia (or as a comment for e-books). This is typically just things like ‘?’ or ‘contradiction > p. 53’ ; so short it takes under a second and keeps you in the book.
Second pass, I read only the marked passages and marginalia/comments. In the second pass I work straight into my preferred note taking method (in my case, I use the Zettelkasten method with Evernote as the software).
On the second pass, I copy interesting pictures etc. out of the book either by photographing them with a smartphone for the physical books, or using Windows Clipper to crop them out in case of e-books (WIN+SHift+S) - there’s a similar tool for every OS and device under the sun.
I often use the red passages as direct quotes (with proper sources and page in the external notes!). The yellow passages are getting summarized in the notes. I also try to answer/solve the marginalia in my head and to add them to the notes, as they’re often very insightful.
This way, initial reading is a lot faster and pain-free. On the second pass, you also know the gist of the book and are more easily able to compress the marked information and to sort nice-to-know, have-to-know and irrelevant (that’s why I use two colors; anything unmarked → probably irrelevant). Remember: marking is just for finding things, it’s not note taking on its own. So re-read as quickly as possible. The intervals for re-reading (if after each chapter or after finishing the book) depends on how dense the book is.
This technique can of course be combined with other techniques like pre-reading and skimming Adler talks about in his book. For skimming, I mark interesting passages to re-read vertically down the margin, usually whole paragraphs. For e-books, I mark the first few works of a paragraph. Then I proceed as usual, or do not read non-premarked passages at all.
The book as well as the Zettelkasten method in itself doesn’t directly solve the problems you stated in your article. It isn’t a system that tells you what to extract out of the books you read. There’s a lot of discussion of what to extract and how deep to extract in forums, and the tequnique itself doesn’t prescribe anything.
The main problem the ZK tries to solve isn’t curation of what to extract from your sources. Instead, it tries to solve the problem of information siloing that happens when you take classic notes about books that are separate from each other. Later, the ZK becomes an Ideation tool—with enough notes in the system, you can work out new knowledge and ideas just be connecting things that weren’t connected before.
It’s not about mechanical steps, either. It’s a change in how to record and organize notes. Instead of one book > one long note about the book, you ‘atomize’ knowledge into many smaller notes. Each of these notes are like mini-Wikipedia articles about a specific thing. Than you re-connect the notes, like in the world wide web. One book leads to many notes, and one note can have references to many books.
Examples of note titles, just to give you an idea: ‘Reading as forgetting’; ‘the brain isn’t for retention’; ‘information bottleneck of the brain is an advantage’; ‘GTD: Getting it out of the head as central paradigm’; ‘deep learning in AI’. Those are all closely interconnected but have totally different sources. Each of those notes is between 100-300 words long.
A few observations of mine on what to take notes on:
The overarching structure of the book, as well as central ideas. I often extract that via reading techniques (reading TOC and end/summary chapters), skimming) or by reading a summery of the book.
Everything that solves a current problem I have (especially when I read a book for a specific reason, like learning)
Everything that connects to already existing notes (often, this is just a new reference to an old note).
Everything that resonates with me or makes me excited.
Sometimes, I have 4-5 new ZK notes for a 300 page book. Sometimes I make 5 new ZK notes for one page alone. The more valuable the source, the more time I will spend with it.
One interesting thing about the ZK principle is that it’s additive. If I read a few books about a subject, I don’t need to note down the basics that I read again and again. Instead, I can focus on adding the nuances and Individualities that each book adds on top of the basics. This way, there are note trails that are almost like discussions: ‘Author A says this is so-and-so’, ‘Author B says this is this-and-that’, ‘comparison Author A, Author B’, and so on. Very satisfying, and a huge boon of the technique.