We might observe that X causes Y, and A is just an effect of X while B is an effect of Y. When we observe this, we come up with explanations as to how it happe

We might observe that X causes Y, and A is just an effect of X while B is an effect of Y. When we observe this, we come up with explanations as to how it happened, describe it using mathematics or chemical symbols or whatever is appropriate. In this way, science is done. There are still a lot of mysteries out there today. Scientists are working on explaining them.