I learned from Austin Kleon that writing notes in the margins of a book is a fairly common habit, and that it has a name: marginalia.
Other than the Bible, I've always struggled with the idea of marking up a book with my own thoughts and ideas. To even underline some text with a highlighter makes me nervous. And my subsequent readings of a marked up book always feels less special, as if I've used up some of the ideas with a yellow pencil.
This is partially why I'm now doing sketch notes of some of the non-fiction I'm reading. This is a horribly slow process, but I do feel that I'm thinking about the text as I render it, and that is the point: to learn from what I read. It's too easy today to simply skim an article and not put any thought into it.
Slow down, learn more.