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There's a Youtuber named Elizabeth Filips that covers topics like this a lot. She has some interesting ideas about note taking and organization that sound a lot like what you're asking.

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Discussion

I retain significantly more of what I read if I talk about it with others. And this doesn’t have to be person to person. When I finished a book, I immediately look for threads on it to see what people have said about it. Sometimes someone will bring up something challenging the ideas in a book, sometimes people give further context to something, sometimes people will just interpret something entirely differently making me go back and reread to see if I can get their perspective on it etc. It’s basically repetition for me.

I even do this with fiction books. I’m a very literal reader. I don’t look for symbolism or between the lines meanings during my first reading. I prefer to just read for the story, and then go back and look for meaning. Threads afterwards help a lot with forming my own opinion.

Looks like chatgpt wrote this

I mean every book has major themes you can use to rationalize the smaller events. In Of Mice and Men, why did they come to Curley's farm? Because Lenny is on the run. What theme does this inherit? That dreams are repeatedly deferred by our sometimes literal heavy-handedness. And it's a fragile, costly balance between toeing the line like George and harboring these dreams at all, like Lenny does. You can read a book at face value but if you want to teach a book you need to keep track of themes and larger conversations.

yup taking down some notes will help you collect your ideas and You can later visit these ideas and explore them again.

Highlight passages that stick out to you and journal/discuss based on that. I also love to relate the themes/moral of the story to songs.

Basically.you have to read it like 3 times.

The first time, you just read it normally. A lot of stuff probably won't make sense because it's explained in later chapters or expanded on elsewhere etc. So you're not going to understand anything by reading it slower.

After the first read, you should have an understanding of the general concepts and the sort of main point of the book. Usually there is a problem, a proposed solution, some arguments to support the solution and then a conclusion or wrap up of it all.

Then you read it a second time, more carefully now, with the knowledge of your first read. This time, you should be able to understand better how the author is linking various ideas, identify some threads that continue through the chapters and how the arguments are built.

With the second read you should have a good idea of the problem, how the arguments are structured and how they build together to support whatever the author is trying to say.

In the third read (which tbh, is optional unless you really want to get to the nitty gritty and truly understand) you should read it and take note of the language, specific vocabulary the author uses for concepts, more critically look at the arguments and whether they make sense etc.

I'll just add some additional stuff in case it comes useful. This is a good way to read academic papers etc. You take advantage of the fact that they're structured the same, so if you're looking for relevant research, you can skim a bunch of papers because you know where the problem, arguments, methods, conclusion etc are. And if it's not relevant to you you can move on without needing to read an irrelevant paper in detail.

Once you recognise that certain types of books, papers, journal articles etc. All have a specific structure and purpose, it becomes a lot easier to extract information from them at whatever level of detail you want.

EDIT: regrading your comment that you remember the main idea but missing something, it sounds like you should pay more attention to the arguments. You can flip to the last chapter and get the main idea, but the actual meat and potatoes is actually the arguments of how they came to that idea. For example many philosophers are often summarised by some pithy sentence like "life is pointless" but the core is actually all the work they did to set up their final idea.

In college for one of my history courses, the professor had us keep a notebook/journal and required us to write a thesis of each chapter in our own words and a couple of paragraphs summarizing the text.

I used one of those little Composition Notebooks and ended up doing the same for each class. Very helpful.

as it always has.
Highlighter and notepad with pencil.
Underline the important parts, use the additional notepad.
Then read again. end.