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Even if the text is separated into chunks with comment space following each, that's still not the same as being able to star or underline a particularly provocative sentence with a word or two (or just a "?" or "!") in the margin. This is even more important in some ways if you're a peer reviewing a text than if you're making jottings for your own later use. Perhaps if there were a browser plugin that would allow you to highlight and comment on any text, Word-style? (There probably is one already.) So that each time you come back to the page your comments will be right where you made them? Would that recapture something of the way I interact with my bound books now?