James Sire describes naturalists as monistic materialists who deny the existence of immaterial entities and their ability to act in this world. Though naturalism can be characterized in broader term, which I will address briefly later in this paper, Sire's characterization is really of materialism. Ontological or metaphysical naturalism is defined in The Cambridge Dictionary of Philosophy as the view that everything is composed of natural entities constructed of properties as the sciences allow.  The worldview I wish to address is the version of naturalism that holds that all abstract entities are determined by the factual or descriptive judgments of science. I will label this view materialism.
Materialism requires that all entities in the world are physical or physically determined. However, most materialists want to preserve free will of human action. Materialists deny the existence of universals, yet most still attempt to find a place for objective morality in their worldview. My thesis is this: Materialism is a monist ontology that attempts to account for moral and mental properties, but cannot; these properties require a pluralist ontology to maintain their irreducible qualities. Two common strategies of materialism to accommodate these properties are functionalism and reduction, but these strategies do not adequately capture these facts about the world. Given that failure (and that of other strategies that are beyond the scope of this paper), we should seek a worldview that accomplishes the task.
Many materialists offer a defense for morality and mind in terms of functionalist and supervenience theses, which are part of a monist account of ontology. (Though these are not the only strategies to defend morality and mind in materialism, they are very common and I will restrict my critique to these.) The strength of this sort of justification for moral realism will depend upon the virtues of functionalism and supervenience. However, these two theories fail to account for moral facts and can provide no adequate grounds for moral realism; a monistic worldview is insufficient for this sort of property. Only ontological pluralism is explanatorily sufficient to justify real moral facts.
Materialism denies that moral realism requires ontological pluralism. Moral facts are just like other kinds of physical facts that science can account for. To justify this thesis, materialism must be able to give an account for the reality of morality in wholly physical terms.
The primary way that materialism describes morality is in terms of functionalism. A functionalist theory of moral value describes moral facts as facts about human well-being and flourishing. Supervenience is a way of accounting for the existence of moral properties in a monistic universe. If these are undermined, there is inadequate justification for moral realism and the worldview fails to account, not only for what it claims to account for, but a feature of the universe that it seems prima facie obligated to explain.
Is causal supervenience sufficient to explain moral facts? Materialism draws a comparison between the supervenience of moral properties with mental properties supervening on physical properties. They are both understood in causal terms of the physical properties that they supervene on (whether or not they are ontologically reducible to these properties).
Materialism may be able to tell a story about how moral properties supervene on physical properties, but this account cannot capture the irreducible features of morality that we are referring to when we speak of morality. Describing moral entities in terms of causal properties of the physical facts does not mean that the nature of moral facts are physical. Moral facts are unnatural entities in materialism. Supervenience does not explain how real moral facts, which have no physical features, come from unconscious matter. Morality cannot be deduced from the composition of physical structures. Correlation between moral and physical states does not answer the question of why morality arises from physical states at all.
Materialism explains morality in terms of the causal interaction among elements of the physical system. Physical states are causally sufficient for mental states, either ontologically or in an emergent way. Extending physical categories to include moral facts is not adequate when the moral facts bear different kinds of features than the physical facts, such as a sense of oughtness, a central feature of morality. When we carve the world up at the joints and find unique moral facts, that has metaphysical consequences.
Materialism has no persuasive reasons why we should accept the causal identification of moral and physical categories except that it is stipulated in a materialist worldview. It attempts to stretch the categories of the physical world to encompass any facts we find in the world, but materialism will not accommodate ontologically unique facts. Moral facts resist this reduction.
Supervenience also presents a problem for moral responsibility. J.P. Moreland points out that "it is part of the nature of libertarian acts that there are no sufficient conditions for such acts to occur or for the chances to be fixed for such acts to occur."  Supervenience requires a necessary causal connection between a brain state and an action, and cannot allow for free moral agency. Supervenience is not explanatorily sufficient to allow for this feature of morality.
Materialism also defends a functionalist account of moral realism. Functionalism is a causal role in which a mental state plays a role in the activities which are characteristic of the person as a whole. According to functionalism, moral facts are just like other scientific facts that have natural explanations based on physical laws. Basically, morality is a matter of inputs and outputs that perform a certain function, that in the case of morality brings about human flourishing and well-being.
Functionalism would account for pain as a mental state that has the tendency to result in certain outputs, such as tissue damage or injury-avoidance behavior. Similarly, there are moral states of the brain that fulfill certain functions; in fact, they just are functional properties. Moral properties are moral in virtue of the causal role they play in human activities. Morality is that which provides for the survival and well-being of humans. The physical states that contribute or interfere with these functions are the ones on which moral properties supervene.
Functionalism treats mental states as secondary properties; that is, they are properties of properties. A mental property is a property in virtue of playing the right causal role. A pain is not a pain unless it disposes one to have certain outputs (e.g., tissue damage or injury-avoidance behavior). Inverted qualia arguments demonstrate the weakness of functionalism, underscoring the failure of functionalism to capture the subjective, non-physical features of morality.
Two creatures could be in the same functional state, but be in different moral states.
To take a moral example, Smith and Jones on separate days each trip Brown as he runs down the sidewalk to cross the street. What Smith and Jones can see that Brown cannot is an oncoming semi-truck. They both exhibit the same functional output, but the morality of each act is wholly different. Smith trips Brown because he is next in line for Brown's job and wants to ensure that he will fall in front of the truck; but Jones trips Brown to save him from running in front of the truck. Both Smith and Jones exhibit the same functional output, but the moral facts are quite different. Functionalists define mental states as second order properties, but the inverted qualia argument shows that the mental state is first order, not second in determining the morality of an action. Functional roles are not non-rigid designators; they do not always refer to the same moral state.
Materialism makes morality a dispositional concept that is about the relevant behaviors or desires. Morality turns out to be a term that is apt to produce certain types of behaviors that are conducive or detrimental to human well-being. Morality is not morality unless it disposes one to behave in a certain way. This seems backwards. The case of pain might be clearer. We avoid pain because it hurts; we do not call it a pain because of avoidance behavior. We call an action moral based on the mental state, not only or even primarily because of the behavior output.
In addition, human well-being and flourishing are teleological terms which materialism cannot adequately account for. Well-being can only be a material concept in functionalism, such as survival. But that does not seem to be what we mean when we talk about human flourishing. It seems to connote achieving an intended purpose, yet final causes are done away with in modern science. Flourishing and well-being seem more at home in a pluralist ontology.
Naturalism, as a larger category than materialism, can give a more credible account for moral realism than the narrower thesis of materialism. Naturalists that allow for essences and teleology can account for morality as part of human flourishing and natural properties of the universe, but this requires a pluralist ontology. Naturalism in a classic sense of this word (ala Aristotle) is a "thick" naturalism that hold that things have natures and essences. Value is irreducible to physical properties. Value, such as moral properties, can be found in natures; fact and value are linked, and morality flows from this view. It is metaphysically and normatively rich.
But the question is which worldview is the most natural home for moral realism? Christianity is a worldview that provides a reasonable explanation for immaterial properties. It is superior to classic naturalism in that it gives a personal source for morality and a personal explanation for moral obligation. Morality may be understood as a natural property, but it seems unique that these properties require minds of a certain sort to perceive them (i.e., animals do not seem to behave in moral ways so must not perceive these properties). It is a unique feature of human minds to perceive these properties and to understand the obligatory nature of moral properties. The mind, then, also requires a reasonable explanation and this is best understood in terms of a personal Creator who made our rational minds to function similar to His. 
Materialism also attempts to explain mental properties in the same terms as moral properties, that is as functional states or supervening properties of physical properties. Evolutionary and atomistic theories are adequate to explain the nature of the world, including minds. Consciousness is an obvious feature of the world, therefore, materialism makes room for consciousness as a biological feature that arises from evolved physical forms.
John Searle addresses the problem of mental properties in the scientific model of consciousness.  Materialism holds that consciousness necessarily rises at a certain level of brain complexity. But why does consciousness arise at all on brains? How does something intrinsically subjective and first person generate from a purely physical, third-person kind of material?
Materialism mistakes the correlation of minds and brains with causal necessity. Brain states are not modes of consciousness. There could be a world in which there were highly evolved brains functioning like incredibly sophisticated computers, but no consciousness. Brain states and mental states are not the same thing. Inverted qualia examples, as given for moral states, illustrate this, as well.
Materialism attempts to maintain moral properties in their ontology and free will along with it. But if mental states are causally dependent on physical states, then physical necessity is required and free will is lost. In a materialist world, mental states have no causal powers; it is a bottom-up atomistic world in which free will cannot be maintained. Free will requires a pluralist ontology in which minds are causally efficacious.
The strength of materialism's explanation for moral and mental properties rests on the strength of the supervenience and functionalist theses. These theses are part of a materialist worldview that cannot account for the uniqueness of moral and mental properties or the real nature of human actions. Ontological monism cannot provide adequate justification for the properties. If moral and mental properties are to be maintained in a robust sense that fit our prephilosophical understanding, then we should embrace the metaphysical implications of these facts and look for grounds in a pluralist ontology. Naturalism in a the broader sense can make more sense of these properties, but the are most adequately justified in a Christian worldview that gives a personal explanation for moral and mental facts, and the implications of these properties.
- Sire, James, The Universe Next Door 3rd ed., Downer's Grove: InterVarsity Press), 53-55.
- Post, John F., "Naturalism," Ed. Robert Audi, The Cambridge Dictionary of Philosophy (Cambridge; Cambridge University Press), 517.
- Moreland, J.P. and Scott Rae, Body & Soul: Human Nature and the Crisis in Ethics (Downer’s Grove, IL: InterVarsity Press), 149.
- I credit Howard Short with this insight.
- Searle, John, The Rediscovery of the Mind (MIT Press).