@TheCobbler,
The scientific process works like this.
1) You start with existing knowledge
2) You start to think about a question that either hasn't been answered, or has something that doesn't exactly fit with the current theory.
3) You develop a hypothesis.
4) You define your hypothesis in a way that can be tested.
5) You develop an experiment that can
disprove your hypothesis. You run the experiment and get results.
6) You publish the results, and you get feedback from other scientists.
7) Other people figure out ways to test the hypothesis (each test has the possibility of disproving it)... they publish their results and the experiments are reproduced.
8) After the hypothesis has been tested, and the scientific community believes it has reach the limit, it is accepted as theory and the existing knowledge advances.
Intuition fits into steps #2 and #3. That's where intuition stops. Intuition allows you to develop a hypothesis, but it is usually wrong.
There is a saying in science that "incredible claims require incredible proof". Scientists who understand the atomic structure and chemical properties of water are going to find it hard to believe there is an "essence" or a "fairy soul". These scientists are experts and they are almost always right.
But you are right to say that "almost always right" doesn't mean "always right". But that is why science is based on experiment.
Show me a fairy... and I will believe in fairies. Until then, I will believe in atoms.