It has always seemed to me that, philosophically speaking (and logically, for that matter), there can — by their very nature — be no conflict between science and metaphysical issues.
Science, as a discipline, involves only things that can be observed, measured and quantified. However, as any logician will tell you, failure to prove something does not constitute proof of anything. Metaphysics involves things that cannot be measured, observed, quantified, or shown to exist or not exist using scientific methods. Therefore, there can be no discussion of metaphysics based on science, and “science” as a discipline cannot have an opinion pro or con on metaphysics.
Logic and observation can confirm scientific principles, but even in those cases it can only predict probable outcomes based on observation. Those who believe in metaphysical matters can believe whatever they want, and science can neither prove nor disprove it. Thus, it seems to me that no conflict exists except in the minds of those who desire it.
If I want to believe that a metaphysical influence caused the primordial soup to combine in a certain way and guided the development of life in certain directions using scientific principles, I can’t be proven wrong, and that position does not conflict with science. However, if I maintain that the Earth was created some 6 millennia ago, in contradiction of myriad scientific indications to the contrary, that is based solely on my opinion and the opinions of those who prefer to believe as I do. We call those opinions “faith”, and whether or not we agree with them, we must honor them if we expect our beliefs and opinions to be honored.
The conflicts between the two occur when folks who don’t understand these essential differences attempt to conflate one with the other. One can have all the opinions one wants. Those have nothing to do with either science or metaphysics. They are, rather, interpretations, colored by what one prefers his or her reality to be. There is certainly reason for concern when such beliefs affect the lives of non-believers, but that is an entirely different matter. Blindly refusing to consider the beliefs and concerns of the other side is unworthy of anyone, regardless of the issue, and does nothing to resolve problems.