I’d agree. Annotations are a tool and can be used for both positive and negative outcomes.

Related somewhat to my bible example above, one could view the individual texts of the New Testament as annotations to the Hebrew bible, in which case they changed a movement from being a religion of Jesus to a religion about Jesus—one which not coincidentally makes him one of the best known people to have ever lived (see: http://pantheon.media.mit.edu/rankings/people/all/all/-4000/2010/H15).

In the case of my earlier genealogical example, the books of the New Testament go back and parallel the lineages of the Old Testament to draw a direct line from King David to Jesus spanning roughly a 1000 years. This is seemingly suspect for a man who would have most likely been an illiterate and poor carpenter, but certainly served the purposes of Greek, Jewish, and Aramaic writers of the time, particularly against the ruling patriarchy of Judea and Rome at the time.

A well known popular culture version of this appears in the title of the book and film Harry Potter and the Half-blood Prince as well as a primary plot point in which Potter actively eschews a beaten up copy of a potions textbook, but to his pleasant surprise find a heavily annotated text that helps him significantly in his studies.

https://harrypotter.fandom.com/wiki/Severus_Snape%27s_copy_of_Advanced_Potion-Making

Google has accelerated this by using search to better link pieces of knowledge in the modern world, but scholars have been linking thoughts manually for centuries.

Other great examples include teaching and scientific progress. Owen Gingerich details annotations in all the extant copies of Copernicus in his text The Book Nobody Read: Chasing the Revolutions of Nicolaus Copernicus. There it seemed obvious that the moving state-of-the art of science and teaching was reflected in the annotations made by professors who handed those annotations down to students who also copied them into their textbooks.

In some sense this is a textual equivalent of the directors commentary tracks on DVDs from the 1990's in which one could watch films with overdubbed running commentary of the film's director (and often cast, producers, et al. as appropriate).

The first time I recall seeing such journalistic annotations was on the web in The Smoking Gun (http://www.thesmokinggun.com/) which generally annotated court documents that were the source of newsworthy tidbits—generally relating to celebrities or gossip pages.

But why not mix them together the way the IndieWeb has done?! A few people are using the new W3C recommendation spec for Webmention along with fragmentions to send a version of comments/marginalia/annotations to sites that accept them and have the ability to display them!

A good example of this is Kartik Prabhu's website which does this somewhat like Medium does. One can write their response to a sub-section of his post on their own website, and using Webmention (yes, there's a WordPress plugin for that: https://wordpress.org/plugins/webmention/ ) send him the response. It then shows up on his site as a quote bubble next to the appropriate section which can then be opened and viewed by future readers. Example: https://kartikprabhu.com/articles/marginalia For those interested, he's opensourced the code to help accomplish this: https://github.com/kartikprabhu/marginalia

While annotation systems have the ability to overlay one's site, there's certainly room for serious abuse as a result. (See an example at https://indieweb.org/annotation#Criticism) It would be nice if annotation systems were required to use something like webmentions (or older trackback/pingbacks) to indicate that a site had been mentioned elsewhere, this way, even if the publisher wasn't responsible for the resulting comments, they would be aware of possible attacks on their work/site/page.

Compare this with the fragmention: http://boffosocko.com/about/website-philosophy-structure/#I+try+to+follow