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.

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.

I have read How to take smart notes by Söhnke Ahrens, in its German original language. A few observations I've made:

• The book, despite its English title, isn't really about note taking in general. It describes how to implement one specific note-taking technique, the Zettelkasten (ZK), or slip box, method. The premise is that you need to do knowledge work in order to write something like a master thesis or scientific paper.
• The strength of this method is to avoid putting knowledge you extracted from books into information silos. Instead, extracted notes are free-flowing and interconnected.
• This doesn't really solve the problems you mentioned on their own, especially the one about not knowing what to read more carefully and what to gloss over. However, in the ZK technique, you can really easily combine notes of multible sources. I usually just extract notes from a summary about the book somewhere. After that I read the book and I fill in the gaps around the summary notes and append interesting things to already existing information. Depending on the information richness of the book source, that's either almost nothing new compared to the summary extraction (and quick work) or a lot of new details & information (and takes longer).
• The weakness of the ZK method is that it can be very time consuming (moreso than other note taking methods), depending on how much you want to extract from the source. There's also time on administrative things like connecting and organizing notes. You will also need a computer for the note-taking work; you can read/listen to/watch the source as usual. The technique is applicable to all kinds of sources, I also extract from lectures, audio books and YouTube video.
• There's a lot of 'why' and argumentation for the Zettelkasten technique. The argumentation however is really shallow and mainstream, and glosses over a lot of ground in passing.
• This would be awesome for someone who needs directions on where to look next, and would be a good beginning for source-hopping. However, if you've read books that go into more detail or even the sources themselves, it feels like name dropping.
• An example would be the short sub-chapter on habit formation ("Make it a habit" ), which feels like a introductory chapter of a graduate thesis rather than a book that is supposed to be riveting.
• Also, I'm personally not a fan of the distinction between long-term, project and short-term notes in context of the ZK.
• The writing style is very structured and feels German to it's core. You instantly feel that a scholar is writing, instead of a science educator.
• This is a welcome change to most popular science or self-help books, who are way too long and anecdote-ridden.
• When you follow the book from front to back, it feels like a step-to-step introduction on how to work on books with the ZK method.
• The structure follows a three part approach:
• The introduction, which includes general things like the goal and approach of this book, and also preliminary steps to set up. It gives very practical tips on setup.
• The second part talks about principles and theory. This is the part I'm not too happy with, as it's too shallow and short.
• The last third, "The six steps to successful writing" is about the implimentation of the technique and how this approach is different from more traditional reading and knowledge work. The goal isn't the extracted knowledge per se, but to use that in other writing projects - the book assumes academic writing.

I'm personally an avid fan of the Zettelkasten and use it extensively, together with Progressive Summarization (Tiago Forte) for the preliminary work on short-form written sources (and Cornell method for lectures/video sources). This book serves as a neat primer for getting started, or to think about your second brain from another perspective. However, it's not word class literature and the English version reads a little awkward in my opinion.

I have personally used this book to build a skeleton of information, before filling it in with blog posts from https://zettelkasten.de/ . However, reading https://zettelkasten.de/posts/overview/ is a good alternative for that.