The phrase is most often used to describe bits of scientifically-discovered, objective truth that, for one reason or another, our so-called "right brain", intuition, emotions, and the sum of our cognitive processes outside of deductive rationality interpret as 'false' or 'wrong.'
Of course, the subjective nature of intuition make it impossible to say with any objective accuracy what is counter-intuitive -- what is counter-inuitive for one may very well not be for another, since the sources of intuitive 'knowledge' are very much open to debate and epistemological inquiry.
Examples of counter-intuitive theories
The twentieth century has seen a number of counter-intuitive theories developed, most notably:
- Quantum mechanics, which suggests that instead of being made out of particles, the universe is best described by complex-valued wave functions which behave very differently to particles in many situations.
- Relativity theory is also counter-intuitive, because it reformulates the conventional ideas of separate "space" and "time", "mass" and "energy" into a four-dimensional universe with non-Euclidean properties which is hard to visualise.
It is interesting to observe that, at scales and energies in the range normally associated with human experience, these counter-intuitive theories closely approximate the world of "common sense" folk physics and human intuition. However, in situations far removed from normal human experience, the predictions they make are quite different, and yet can be very precisely verified by experiments in the real world, suggesting that they are more "true" than the theories which preceded them.
Attempts to unify these theories, such as string theory and M-theory, are even more counter-intuitive, even from the viewpoint of many physicists whose intuitive abilities have expanded to take into account the earlier theories.