The phrase "head thinks, heart knows" reflects the common idea that the brain uses logic and intellect while the heart represents emotion and intuition. It suggests that sometimes our emotional or intuitive feelings, which come from the heart, provide a deeper or truer understanding than our rational thought alone. The phrase can also be understood through a new scientific lens, as research indicates the heart sends signals to the brain via the vagus nerve, suggesting the heart's "knowledge" may even precede the brain's processing. 
The phrase is a modern quotation attributed to Joe Dispenza. A similar sentiment is found in a quote attributed to the 17th-century French philosopher Blaise Pascal: "The heart has its reasons which reason knows not", meaning that some truths and motivations are understood through feeling and intuition, not logic. It suggests that while reason is a powerful tool, it cannot fully grasp all aspects of human experience, like love, faith, or the fundamental principles we intuitively accept.
- From online source with editing
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Being a person born very sensitive, I'm very aware of the meaning of the phrase. And more, I would like to add another dimension of my own: "head thinks, heart knows, and stomach acts". As my stomach seems to have its own rule to take or not to take food, regardless of what my head thinks or my heart knows.
So I would think there are possibly multiple "brains" in the human body, one for head, one for heart, and more for other organs. I don't have any scientific theory, peer reviewed or not, just a hunch from my heart. "Head thinks, heart knows". 
Wish All a good Friday!
