More Words, Deeper Hole

It's scientific materialism (or, perhaps more accurately, materialist monism) versus dualism in that context. It's the monism they object to, rather than the materialism per se.
http://www.newscientist.com/article/mg20026793.000-creationists-declare-war-over-the-brain.html

Schwartz and Beauregard are part of a growing "non-material neuroscience" movement. They are attempting to resurrect Cartesian dualism - the idea that brain and mind are two fundamentally different kinds of things, material and immaterial - in the hope that it will make room in science both for supernatural forces and for a soul.