For me, as a person of faith, the chief virtue of this "naturalistic" scientific method is that it let's God be God.  As a "born again," evangelical Christian I believe that everything that the scientist studies was created by God.  That means the material universe is not ultimate reality.  God created it, transcends it and exists beyond it.  God is not part of the "furniture" of the universe.  God is not an "object" that can be observed, tested, manipulated or controlled by any conceivable experiment.  Science, therefore, can say nothing about God.  It has no competence to pass judgment on God -- either to prove or disprove his existence.  The "methodological" naturalism of modern scientific inquiry means that science is necessarily neutral in regard to the religious and metaphysical questions that deal with the ultimate meaning and significance of reality.  Those questions are outside the sphere of its methodology.

Whenever conflicts arise between evolution and religion, they arise where evolution is discussed in the context of philosophical and religious inquiry.  Religion does not "bracket out" questions about the ultimate nature, meaning and significance of reality -- it makes them central.  Unfortunately, there is no agreed upon methodology by which philosophers, theologians and people of faith determine the answers they give to these questions.  In the field of religion there is a wide variety of interpretations about the meaning and significance of evolution.  

There are Fundamentalist Christians who interpret evolution as an attack upon their faith.  There are Fundamentalists, Evangelicals, Mainline Protestants and Catholics who interpret evolution as the process by which a sovereign, loving, and personal God chose to exercise a constant and continuous creative power and providence.  There are liberal Christians who interpret evolution as the process by which God is spelling himself out in the world process or developing his being through cosmic time.

There are also atheists, some of them scientists, who interpret evolution to mean that faith in God is superfluous or superstitious.  These atheistic "metaphysical" naturalists are making a faith statement that science can neither prove nor disprove.  Such people are nowhere near as numerous or as influential as some people think.  Many, if not most, scientists are people of deep religious faith who use scientific methodology in the laboratory and in their scientific work but remove the "brackets" in their private philosophical and religious lives.  When they remove the "brackets," most see no conflict between their faith and science.

Common to all these interpretations is adherence to some basic premise or organizing principle that is accepted by faith.  As long as people are free to choose where they place their faith, a conflict of "interpretations" is inevitable.  Conflicts of "interpretation" will end only in the eschaton -- when the "perfect comes" and the "partial" will be done away (1 Cor. 13:8-13).

Every conflict between evolution and religion boils down to a debate over religious and philosophical "interpretations."  Science cannot resolve these issues.  Resolving these debates requires open dialogue between people of faith.

Whenever I am engaged in such dialogue, I share some personal beliefs and opinions and talk a little about the journey that I have made as a Christian in regard to opinions about evolution.

I grew up in an Independent, Fundamental Baptist church.  Those are the Baptists that think Southern Baptists are liberals.  I grew up believing what I was told about evolution by people that I trusted -- and they told me that evolution was an attack upon God, the Bible and everything holy.  They indoctrinated me in creation science and taught me all the standard arguments for proving the existence of God.

I have since grown out of that kind of faith -- not because someone first convinced me that evolution was true, but because I came to realize that the God they wanted me to worship was too small.

There are at least two things that led me to this conclusion.  

First, I found that my mentors did not know how to distinguish the inspired and revealed truths of the Bible from their private interpretations of the Bible.  For people who take the Bible seriously, the question is not whether the account in the book of Genesis is inspired and true -- the question is what kind of truth does it reveal and how should we interpret it.  For those of us who are Protestants, there are no infallible interpretations of scripture.  There are just interpretations that are better than others at taking into account all that we know about God and the universe.

Second, I found that my mentors were limiting God in at least two ways.

First, they imposed finite human understandings of time on God.  The question is not whether God could create life forms in an instant.  God is free and able to create in any way that is pleasing to Him.  Burger King may be bound to let you "have it your way," but God is not.  

Science indicates that God created the universe and life in processes that took billions of years.  Why should that be surprising?  God lives in eternity.  It is mortal men with their short life spans who are impressed by billions of years of cosmic time, God isn't.  He transcends time.  A thousand years is like a day to him (2 Peter 3:8).

I decided that interpretations that insist that the earth had to be created 6000 years ago are inadequate for more than scientific reasons, they are inadequate because they are overly anthropomorphic for theological reasons.  

The second way of limiting God is also anthropomorphic -- by anthropomorphic I mean making God in the image of man, rather than letting God be God -- the second way limits God by insisting that He must create human beings in a way that completely distinguishes us from the rest of God's creation.  The question is not whether God could do so.  He could do it that way if he wanted to, but he is not bound to do it that way.  

Science indicates that we share most of our genetic structure with primates.  What violence does that do to the Christian understanding of man?  God is not an organism.  He does not have a genetic structure.  God is Spirit.  The image of God in man does not refer to our physical form or body; it refers to our spirit.  Our uniqueness is in our spiritual capacity to enter loving relationship with a God who loves us.  

Theologically, it makes no difference whether God decided to form our physical bodies through long stages of biological development or by a special creative act.

Ultimately, I've learned to be cautious about what many of my well meaning but misguided preachers and mentors taught me about faith and science.  Now I try to remember a few simple principles:  

1.    Live by faith.  

2.    Don't limit God.  

3.    Don't tie faith too closely with any scientific view.  

4.    Exercise interpretive humility in both science and religion.  

God is the only one whose view of the world is final and complete and He's the only one who has all the answers.