A pair of philosophers named Stewart Goetz and Charles Taliaferro have written a fine introduction to the metaphysical point of view philosophers call naturalism. They title the book simply Naturalism, and in a relatively brief but instructive 122 pages Goetz and Taliaferro walk the reader through the major varieties and implications of naturalistic belief and the criticisms to which naturalism is most vulnerable.
Philosophical naturalists hold that nature is all there is, there is no supernature, no God that acts in the world. The world (i.e. the universe) is "causally closed" to any outside intervention. Although it's possible to be a naturalist who believes that nature is god, in actual practice naturalists are invariably atheists.
There are two basic kinds of naturalism, strict and broad, but adherents of both are united in believing that there are only physical causes acting in the world. Whatever minds or souls may be they're ultimately reducible to material stuff.
All subjective experience (pain, pleasure, purposes, etc.) is either illusory or simply the physical consequences of electrochemical events in our neurons, sort of like the light and sound produced by exploding fireworks. There's no immaterial mind or soul that causes our choices. There are no immaterial purposes for which we act. What we do is strictly determined by the chemical interactions occurring in the brain.
For the philosophical naturalist, mind is simply a word we use to describe the function of the brain, just as we use digestion to describe the function of the stomach. Or, to switch metaphors, mind is like photosynthesis. Photosynthesis is not a material structure which exists in the plant but is rather a physical process involving chemical reactions occurring in the chloroplast. If we understand the chemistry of the plant cell we know everything we need to know to understand photosynthesis. Likewise, if we understood the brain well enough we would understand mental phenomena like purposes, beliefs, sensations, even the nature of understanding itself. We are, as Francis Crick once put it, nothing but a pack of neurons.
Throughout the book the authors consider what naturalism has to say about the soul (mind), values, and conscious experience and they offer some very convincing (to me) counter-arguments to the naturalist hypothesis. Perhaps the most persuasive goes something like this:
If all of our conscious experience is explicable in terms of chemistry and physics then if someone knows all the relevant science involved in seeing the color blue they would know what blue is even if they've never seen it. Of course, that's not the case. Imagine a man blind since birth who is a brilliant scientist and manages to teach himself every detail of the chemistry of seeing color. He knows every physical fact about what occurs in the process of vision. Would he then know what blue looks like? Suppose he suddenly gained his sight and the first thing he sees is the sky. Would he know what he was seeing?
The answer to these questions is almost certainly no. Conscious experience consists in more than just the physical facts of brain chemistry. There is something it is like to see blue that cannot be known simply by learning chemistry. There's something more involved in experiencing blue than just chemical reactions. Consciousness and the experiences we have as conscious beings must be more than simply the material processes which occur in the brain.
Perhaps the relationship between brain and mind (or soul) is something like the relationship between a television set and the signal that the set translates into an image on the screen. Our brains are like the tv, but just turning on a tv is not enough to have a picture (conscious experience). We must also have a signal and even though both can exist without the other the image, or conscious experience, can't exist unless both television and signal, brain and mind, are functioning properly and together.
At any rate, I recommend Naturalism by Goetz and Taliaferro to anyone with at least an introductory philosophy course under his or her belt and an interest in gaining a deeper understanding of the consequences of the logic of contemporary anti-theism.