Haven't read the book yet (as I just heard of it from the post), but sounds interesting. I am also currently working on a piece of fiction with some similar themes, and was wondering if you could share some thoughts on how you manage references to real world entities and technologies in the story? What sort of balance did you find between history, science, and fiction?
I guess I would say that the story is the important thing, not the themes or real-world references or whatever. It's a novel, so above all, the story has to be compelling and the characters have to be believable and at least somewhat interesting.
With regard to real-world people, places and things, I was just aiming for verisimilitude, to make the setting (and the science and computer science) believable to people who knew the territory.
I've seen two major developments beyond the traditional published-once book. This article talks about one of them: "Unfinished", whether for fictional works with multiple editions or edited versions (as in this article), or for non-fiction references continuously updated to cover the latest version of the topic they document. However, this article still assumes a punctuated series of versions in essentially complete form, intended to be thought of as a complete book, even though the author may release a new version in the future.
There's a step beyond that sense of "unfinished": the future of the book is in progress, actively being written and edited. There's something particularly fun about reading the first few chapters of a book whose ending is not yet written, providing feedback, having a conversation with the author, and seeing that feedback reflected in the next update. See a typo, or a plot hole? Post a comment with a bug report. Having that experience with software was what hooked me on Open Source; however, that experience is not by any means limited to software, and it's quite a thrill for books (fiction or non-fiction) as well.
Having that feedback and update channel pervasively available really changes your outlook on prose, as it does with software. I've long since stopped putting up with software for which I can't file a bug report and ideally write a patch. Imagine a world where a significant fraction of books work the same way.