When should we disregard explanations that are intuitively appealing?

When they get in the way of explanations that are even more intuitively appealing.

When they don’t take into account all the factors.

When they prevent you from doing your own homework

I think @janbb takes it too far – we’ll never have “all the facts.” I think it’s more accurate to say “when it runs contrary to the wealth of evidence” in addition to @ninjacolin‘s answer.

Of course, I’m going to modify my answer slightly to take into account the fact that I don’t think any explanation should be disregarded permanently – filed away in a drawer yes, but if disregarded permanently, we may later find ourselves without tools necessary to create better knowledge models in the future.

@iamthemob I guess what I was trying to say was that when there are known factors that contradict the explanation.

When there is a painful truth hiding in the background of that appealing explanation.

Whenever they declare/imply an absolute (i.e. ‘always,’ ‘never,’ ‘all’ e.t.c. )

When the explanation is not consistent with the facts.

Sometimes the intuitively appealing explanation is adequate to the task, even when a more accurate explanation is available. We’ve known for centuries that it’s more accurate to say that the Earth rotates on its axis than to say that the sun moves across the sky. But the latter better expresses our intuitive reading of the situation and is actually perfectly adequate for most purposes. It feels a little forced to perceive the situation in the more accurate way, so the older, more naive model persists. That’s a flagrant example, but there are many more subtle instances.

Explanations are like tools. Sometimes a crude tool will do the job just as well as a precision instrument, and it may be closer to hand. For other jobs, the crude tool won’t cut it; then you need to seek one better fitted to the job.

In the pure sciences, the criteria are much stricter. All explanations are tentative and invite challenge.

When the explanation is not based on reason or is morally wrong.