Described in the book initially as a circular slab made of coquina and stone with a rectangular opening onto descending stairs, the biologist’s companions all rationally call it a tunnel. That said, the biologist labels it as a tower before even that most basic description, illustrating something tall rather than deep. The word, which effectively describes the exact opposite of what it’s labeling, is used for the duration of the first volume so that as a reader when you see “tower” you picture a tunnel.
What’s more is that through our implicit trust of the narrating biologist, who is incredibly sympathetic despite her cold demeanour and air of mystery, we understand that her dissonant naming is involuntarily affected - a result of being in Area X. She almost immediately admits, through the description of her nomenclature logic, that her insistence on the word “tower” is insane:
“At first I only saw it as a tower. I don’t know why the word tower came to me, given that it tunneled into the ground. I could easily have considered it a bunker or a submerged building. Yet as soon as I saw the staircase, I remembered the lighthouse on the coast and had a sudden vision of the last expedition drifting off, one by one, and sometime thereafter the ground shifting in a uniform and preplanned way to leave the lighthouse standing where it had always been but leaving this underground part of it inland. I saw this in vast and intricate detail as we all stood there, and, looking back I mark it as the first irrational thought I had once we had reached our destination.” p.7
By describing a tunnel as a tower, VanderMeer manages to familiarize readers with negation. By virtue of being wholly visible, a tower has perceivable limits. A tunnel does not have this. Only the parts that have been experienced can be said to even exist, and beyond that anything else is implied or expected based on hope or human estimate. Additionally, by invoking the negative label, the author has avoided the awkward unspeak pitfall of having to write out things like “I fell up and to the right, sliding down, (or was it out?)” Since tower implied height instead of depth, the mind-bending is taken care of in passages like this:
“With the tower, we knew none of these things. We could not intuit its full outline. We had no sense of its purpose. And now that we had begun to descend into it, the tower still failed to reveal any hint of these things. The psychologist might recite the measurements of the “top” of the tower, but those numbers meant nothing, had no wider context. Without context, clinging to those numbers was a form of madness.” -p22
Annihilation and its subsequent volumes (Authority and Acceptance) go on to require the reader to continue thinking difficult, contradicting thoughts, and it is because of the tower that it all works out to such great effect. The Southern Reach Trilogy can be called a magnificent achievement in horror simply for its depiction of that impossible place with a builder that cannot be imagined, a place that cannot exist yet feels so real.