The following is a para from a book. I don't understand why the author uses 'the' before things which he did not mention earlier. For example, in 'where is the mud', I am not sure which mud she is talking about.
I put the whole para, just to give you some reference for the sentences in question.

'An example from personal experience: Science fiction and fantasy writers seem to do a lot of stories that concern caves. These really bug me, as I like to go in caves, and most of these stories get every damned detail wrong. Caves in fantasy all seem to be airy, well-lit places full of perfect marble staircases and veins of pure gold -- which generally are not found in the limestone formations where caves usually form. When a story takes me into a cave like that, I ask myself -- Where is the mud? Where is the darkness? Where is cool, slightly clammy air? Where are the loose rocks on the floor, and the smell, and the bats? Even if the writer has, in reality, gotten it right, it is too late. Once I am in that state of mind, it will do no good at all for the writer to have five thousand pages of documentation on the principles of natural cave formation in igneous, ore-bearing, and metamorphic rock.'