I read the link that you gave to Sean Carroll’s views on the issue of Science and Religion. What is interesting is that his views reminded me of another set of views that I came across on about.atheism.com
This view is one that you can see, or get hints of, from Carroll’s views as well. It is a very sad position because it shows a lack of understanding of the logic of scientific discovery/methodology, but it also ignores some very basic things they are taking for granted that not even science can give them. The basic point is that you will see some atheists proclaiming science as if it is true. And from this fictional basis they base their world views, and try to pass it off on others as superior in its fictional basis.
Science deals with theoretical systems that are neither necessary nor impossible. This means that it deals with theoretical systems that are contingent, i.e. possibly true or possibly false. Mathematical and logical systems are examples of necessary and the negation of mathematical and logical systems are impossible. There are an infinite amount of theoretical systems that are contingent, but there is only one theoretical system that can correspond to the actual system that is our “universe”.
Science is not the only branch that deals with theoretical systems that are neither necessary nor impossible, since metaphysics deals with them as well. But there is a line of demarcation between scientific theoretical systems and metaphysical theoretical systems. This is that scientific theoretical systems are empirical & empirical systems are possibly true or possibly false, and empirical systems can’t be shown actually true (or probably true) and can be shown actually false. Metaphysical systems can’t be shown actually true (or probably true) and can’t be shown actually false.
The empirical systems all have the ability to be shown false and never shown true, and the systems are held so long as either there is no observation or experiment that contradicts what the system says, or we find a system that makes the same predictions in the same domain and also make predictions that go beyond the domain covered by the other empirical system.
All empirical systems contain things within them that can’t be observed by human beings, since they are of a universal nature, i.e. relationships that hold at all temporal and spatial events without exception. There is no way to verify that such things are true, so whatever science would talk about would be those things that can’t, in principle, be experienced by human beings. So whatever is brought up in science can never have any evidence for the truth of such a position, but a falsifying occurrence can obtain. Since there are an infinite variety of empirical systems that would, also, be consistent with any observation that may be obtained, there is no way to tell which system corresponds to reality. Systems we hold or use are probably false, but possibly true.
Furthermore, science relies on a couple of methodological principles, which make no claims for reality and are themselves not open to scientific investigation. They are rules that say act as if there exists at least one causal relationship between all temporal and spatial events without exception. From this methodological rule we have causality to help us obtain the processes that we need in order to conjecture our empirical systems and put them to the test by rigorously testing our hypothesis in situations in which it makes a prediction contrary to a competing empirical system. We eliminate those that can’t stand up to the competition by giving a false prediction, while the other system didn’t give a false prediction. None of this makes any claim to ultimate reality, and probably false.
Science and religion or metaphysics are just fine, but they have separate domains in which they operate. The problem comes down to categorical mistakes, which Carroll and some other atheists make, along with some theists.