The is part of a paper I am writing to extend the debate with David Kyle Johnson

The debate appears in Gregory Bassham ed. C. S. Lewis's Christian Apologetics: Pro and
Con. (Brill Rodopi, 2015).

Now I think it important here to point out one very important area of disagreement between myself and Johnson. Johnson firmly accepts supervenience and causal closure, but he thinks that insisting that the supervenience base mechanistic is in fact a non-standard definition of naturalism. He writes:

In reply, Reppert might insist that property dualism is not a naturalistic theory because it is also violates his first tenet of naturalism by including mental properties at the basic level of analysis. But this simply reveals that he has chosen a (non-standard) definition of naturalism to load the dice in his favor—to preclude naturalism from doing the one thing he says it must do. In reality, this tenet does not actually express a necessary component of naturalism (which is that nothing exists beyond the natural world). Not only is naturalism not necessarily mechanistic (a possible world of chaotic matter would still be naturalistic), but neither a mechanistic world nor a naturalistic would preclude mentality existing at the basic level of analysis—as property dualism and the identity theory reveal. Simply put, the mental is not necessarily supernatural, as Reppert seems to assume.

            Well, I would simply have to ask how mental causes came to start operating in a naturalistic world. Given theism, minds operate in the world because they are products of divine creation (even if there was an evolutionary process involved). Or perhaps there is an Absolute Mind that is not distinct from the physical world, so that what appears to be nonmental really is not nonmental. This is the perspective of Absolute Idealism which Lewis embraced when he was first persuaded by Owen Barfield of the difficulties the Argument from Reason poses for naturalism. Or mind might be fundamental to the universe in some other way, and Thomas Nagel in Mind and Cosmos and elsewhere has been casting about for how that might be. But it should be noted that, while being very explicit about avoiding supernaturalism, he is being ferociously attacked by advocates of standard naturalism, precisely for trying to fit mind into the foundation of his view of the universe. As one commentator points out,

The critics have focused much of their ire on what Nagel calls "natural teleology," the hypothesis that the universe has an internal logic that inevitably drives matter from nonliving to living, from simple to complex, from chemistry to consciousness, from instinctual to intellectual.

In short Nagel is upbraided by many of his collegues for his failure to adhere to the what I am calling the doctrine of mechanism, the doctrine that the mental must be excluded from the suprervenience base.

Or, perhaps there are emergent laws, such that, once biological systems get complicated enough to produce brains, the matter in those brains stop acting like the matter in the rocks flying down the hill toward my head, and instead start acting as if they had purposes they were fulfilling. But the individual parts of my brain don’t obey logical laws, so it looks like this form of emergentism not only involves emergent properties and emergent laws, it also seems to include emergent substances. This certainly is going to be regarded as blazing heresy by the mainstream naturalists, who agree with Francis Crick:

 ‘You,’ your joys and your sorrows, your memories and your ambitions, your sense of personal identity and free will, are in fact no more than the behavior of a vast assembly of nerve cells and their associated molecules. Who you are is nothing but a pack of neurons.” 

            The mainstream naturalistic position is that mentalistic explanations are not allowed in the supervenience base. That is the essence of Darwin’s dangerous idea. Long before writing Darwin’s Dangerous Idea, Daniel Dennett spelled out the fundamental commitments of naturalism when he wrote:

Psychology of course must not be question-begging. It must not explain intelligence in terms of intelligence, for, instance by assigning responsibility for the existence of intelligence to the munificence of an intelligent creator, or by putting clever homunculi at the control panels of the nervous system. If that were the best psychology could do, then psychology could not do the job assigned to it.[10]

And again:

Darwin explains a world of final causes and teleological laws with a principle that is entirely independent of "meaning" or "purpose." It assumes a world that is absurd in the existentialist's sense of the term: not ludicrous or pointless, and this assumption is a necessary condition of any non-question-begging account of purpose.[11]

In fact, in Darwin’s Dangerous Idea, he explains the difference between cranes and skyhooks as follows:

"Let us understand that a skyhook is a "mind-first" force or power or process, an exception to the principle that all design, and apparent design, is ultimately the result of mindless, motiveless mechanicity. A crane, in contrast, is a subprocess or special feature of a design process that can be demonstrated to permit the local speeding up of the basic, slow process of natural selection, and that can be demonstrated to be itself the predictable (or retrospectively explicable) product of the basic process."

In fact most of the book is spent upbraiding not religious believers, (who he probably considers marginalized anyway)  but thinkers who say they are naturalists but have not fully and completely applied the dangerous idea, such as Chomsky, Penrose, Searle, and Gould.

            If we think about it, if we are naturalists, how did things happen in the world before brains came on the scene? What principles of causation were operative? Presumably nonmental ones. Wouldn’t it take a miracle for brand new principles of causation to enter the universe? And miracles are, of course, anathema to the naturalistic mind.