How do you connect cause and effect?

Peace be upon the late Rabbi Shlita.
How does science come to the conclusion that thing A caused thing B? There are many things that could have caused it, and why specifically because of a specific thing? Like the joke about how once some scientists wanted to test a fly. They cut off its wings and told it to “fly.” Of course, the fly didn’t fly away. They came to the conclusion that a fly without wings can’t hear.
I hope I was able to explain myself.