Science v. Religion

This has been a common theme for me but recent events have made me think about it again. Last night I picked up a book and started reading A Jealous God: Science’s Crusade Against Religion. I didn’t even make it through the introduction before I became convinced that this is just another one of the many books written by Christian conservatives that attempt to paint scientists as immoral and godless. If that is not the case then I apologize to the author. I would recommend that she not set that tone if she expects anyone other than someone who already believes her way to read it.
I get to work early so I can read the news on a couple of my favorite sites before the rest of the crew shows up. While reading I learned that The Catholic Church has fired its head astronomer for speaking out against Intelligent Design. Claiming that it wasn’t based on science, which I agree, Father Coyne was concerned that trying to link God with this theory was demeaning to God.
In my review of How We Believe I explained how Michael Shermer believes that people are in one of three different stages in their relationships with God and science. First, they believe that the two are in conflict. Second, they believe that the two are harmonious. And third, they believe that the two exist in completely different spheres. From what I have read it appears that Coyne was in stage two or three and he was fired by a Vatican firmly entrenched at stage one. In spite of some of the steps that the Vatican has taken in the last century to make amends with science, I see this as a huge step backward.
I just do not understand why religion is so afraid of science. Contrary to books like Godless and A Jealous God I do not believe that science has the same animosity towards god. Granted there are exceptions, however for the most part I think scientists just treat religion as being irrelevant to their work. Science is based on physical laws and testability. Basically they take a logical positivist philosophy. Basically that if it isn't physically real then it isn't testable and is not the domain of science. Since they refuse to place an ultimate value judgment on it religion takes offense. I believe this offense is needless and irrational. From personal experience I can say that there came a tremendous peace both to my spirit and my intellect when I stopped trying to make the two worlds harmonize. When, if ever, will religion as a whole learn this lesson?