In Ayn Rand's personal journals about her relationship difficulties, she refers at times to her "stomach feelings," by which she seems to mean what most of us would call "gut feelings." She worries over whether her stomach feelings might be telling her something important. Indeed, they are. These feelings are correctly warning her that her relationship is doomed and that her loved one is acting fraudulently toward her. She is thinking very hard on this topic, but her feelings have run ahead of her thoughts and reached the correct conclusion sooner.
In Atlas Shrugged, she wrote: "An emotion that clashes with your reason, an emotion that you cannot explain or control, is only the carcass of that stale thinking which you forbade your mind to revise."
This was different. The emotion was not the carcass of stale thinking, not the empty echo of old premises. Rather, the emotion was the warning message from a subconscious that was integrating vast amounts of information, including things like body language and vocal tone and facial expression.
For what it may be worth, there is a cranial nerve (the vagus) that connects to the stomach. Some speculate it's involved somehow in our experience of "gut feelings".
Otherwise it's hard to understand how your digestive system
Could pick up clues after your brain had missed 'em.