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"Sarawak Chamber was so big, Mad Phil explained, that it almost certainly contained new passages—particularly in the roof, where no one had ever searched. Although it’s tempting to think of caves as similar to mine shafts—tunnels that slope relatively straightforwardly down—natural caves are nonlinear and expand and contract according to the movement of rocks, the meandering of water, the work of chaos.

Concepts of “up” and “down” assume subtler meanings underground, where directions can be utterly inverted over a few million years. If someone is exploring the down part of the cave, another caver might try looking up. And up was Mad Phil’s specialty."

I've done some caving and I'm pretty sure that the situation here is that there may be stream passages that once exited into the chamber through the roof. They probably no longer carry water, or they would already be obvious.

For, example, the caving term for a vertical shaft that is discovered from its lower end is "aven", and it doesn't imply that the whole landscape has been turned upside-down by geological forces.

http://www.speleogenesis.info/directory/glossary/?term=aven

"aven

1. A hole in the roof of a cave passage that may be either a rather large blind roof pocket or a tributary inlet shaft into the cave system. A feature described as an aven when seen from below may equally be described as shaft when seen from above, and the naming of such a feature commonly depends purely upon the direction of exploration. Many avens close upwards to impenetrable fissures but may still be important hydrological routes; few caves are without them. In parts of France, aven is equivalent to the British term, pothole [9].

2. (French.) A vertical or highly inclined shaft in limestone, extending upward from a cave passage, generally to the surface; smaller than an abime. Commonly related to enlarged vertical joints. Compare cenote; natural well; pothole.

3. (British.) A vertical extension from a shaft in a passage or chamber roof that tapers upward rather like a very elongate cone [10]. Compare dome pit."

"Vadose" is another technical term that applies to the regime of erosion in which water is trickling down towards the water table. That's obviously something that can very much happen in the rock above the ceiling of the chamber. (Vadose erosion is usually contrasted with phreatic erosion, which refers to tunnels which are literally dissolved through the rock below the water table.)




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