The supernatural and science

In the comments on the OP about the “war” between science and religion some interesting points were raised, which I thought deserve their own OP. One commenter noted:

“Science and religion are not at war. They are different magisteria. Each is a way of looking at reality. Science looks at reality through the natural realm. Religion looks at reality through the supernatural realm. As long as they each stick to their own realm, there can be no conflict. Religion opens itself to challenge by science when it makes claims about interaction between the supernatural and the natural realms.”

However, when we look at Christianity, we see that Christians make many claims about their God and other mythical beings from the supernatural realm constantly meddling in the natural world, e.g.:

  • God created and sustains the universe.
  • God completely floods the earth, destroys cities, sends plagues, and helps warlords.
  • God performs miracles and answers prayers: He heals the sick, makes sure the right team wins, prevents accidents, finds parking spots, turns gay people straight, etc.
  • God provides human embryo’s with a “soul”, which survives after death.
  • The devil and his minions wreak havoc on earth, mainly by tempting and misleading people to do bad deeds.
  • Angels protect and guide humans, and they convey divine messages to humans.
  • The Holy Spirit inspires believers to live better lives and allows them to interpret scripture.

All of this meddling with the natural world should be observable if we look closely enough. Which means: we can gather knowledge about these supernatural interventions in the natural world by using the scientific method. And from the knowledge about these interactions we can derive scientific theories* about the supernatural realm and about the nature of God.

*) Note: a scientific theory is a coherent group of propositions formulated to explain a group of facts or phenomena and repeatedly confirmed through experiment or observation; it is not “just a theory” in the colloquial sense.

Question:

Why do or don’t you agree with the position that the study of an interventionist God falls squarely in the realm of science?