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I just recently, finally, began annotating my books and dog-earing pages after having run the gamut of other annotative methods--taking notes on my phone, taking notes in a corresponding notebook for the text, using index markers/sticky flags, etc. etc. Direct annotation is by far the best and most effective method I've found unless I intend on conducting an ultra close reading of a text, in which case I will take detailed notes in a notebook, in addition to annotating the pages directly.

A sort of paranoid fear of distorting my subsequent readings of a book has always made me hesitate marking them directly--a second reading is often a chance to catch subtitles you missed the first time around--I've always feared that having my annotations screaming at me while reading would render finding these subtitles impossible, those slippery nuggets making their escape under rivers of pen ink.

Ultimately, I couldn't deny myself the inherent use-value of direct annotation--so it won out over my fear. Yes, it's true that my annotations will perhaps make me miss things I otherwise might've noticed on a second read, but they'll also remind me of ideas I'd previously had which might've otherwise been lost to time, or are more difficult to parse out and re-associate with a given piece of text using the other methods.

So I accede to the wisdom of DFW, a great lot of famous scribblers, and Tim Parks; I read with pen in hand and ink on page.

On a side note, where you wrote "subtitles", did you mean subtleties?
To their credit, it was a nonetheless subtle mistake. :)
My elementary school library class teacher is turning over in her grave.
An ebook reader that lets you annotate using a stylus and then subsequently disable/enable the annotations seems like a good middle ground.
Not an ebook reader per se, but goodreader on iOS is by far the best pdf note taking app around. Not only does it have a gamut of styles of highlighting, but then you can export the whole mess and it makes for a wonderful synopsis of a book, complete with page references.
I have yet to see an effective use of an e-book for books that are meant to be reread not from front to back but by chapters...

Examples would be technical books and philosophy books.

I inherited my dad's book collection. The more interesting ones (to me) are the ones where he wrote notes in the margins, often amplifying or disagreeing with the author.
Didn't Warren Buffet say that Benjamin Graham's margin-annotated Intelligent Investor, or was it, Security Analysis, was his most prized possession.

Otherwise, what funny coincidence in the examples of this article: C.S. Lewis "Lion ..." which I just finished reading to my daughter yesterday, and DFW, who we just finished electing Pres. Gentle.

The Great Concavity - it's coming.

On one hand, I'm in favor of critical thinking. On the other, I kind of want to say "just leave me alone and let me enjoy the book!"
My first thought was, "wow, what a wonderful excuse to buy a really nice edition and also the paperback to just carry with you and mark up". Yeah ereaders and so on, but as users of notebooks know there's no substitute for pen/pencil and paper.