With Moreland's case for dualism already crumbling under the weight of compelling scientific evidence to the contrary, the powerhouse of his last three "recalcitrant facts" losses traction. The next "fact" against naturalism he unleashes is rationality. Apparently to him, rationality can only exist if a rational god made us in his image.
Moreland describes the Christian god as being fundamental and rational who "created his image-bearers with the mental equipment to exhibit rationality and be apt for truth gathering in their various environments." (p. 41) He quotes Christian philosopher Victor Reppert saying, "The necessary conditions for rationality cannot exist in a naturalistic universe."  Moreland offers two reasons why naturalism precludes rationality: (1) the necessity of the enduring, rational self and (2) the need for room for teleological (goal-directed) factors to play a role in the thought processes. (p. 41) He backs up (1) with a quote from British philosopher A.C. Ewing about how enduring states of "I" are required to process things like propositions and their different constituents:
to compare two things the same being must, at least in memory, be aware of them simultaneously; and since all these processes take some time the continuous existence of the same entity is required. In these cases an event which consisted in the contemplating of A followed by another event which consisted in the contemplating of B is not sufficient. They must be events of contemplating that occur in the same being. 
This notion of there being no enduring self under naturalism underpins this argument. Subatomically, the atoms that make up our bodies are jumping from position to position following the laws of quantum mechanics, but those atoms that make up your body existed for billions of years, and were forged in the hearts of stars that have long since died. Who says the information carried by your atoms of your mental states and identity cannot endure? Moreland is assuming that with each nanosecond, we should be a completely different person unless we have a soul to ground our sense of memory and identity. But if memory is physical, at least in part, then brain states would preserve that memory from moment to moment, and physical damage to the brain would erase it. That's basically what we see with people who've experienced brain trauma.
Moreland defends (2) with another logical argument (p. 42):
(1) If naturalism is true, there is no irreducible teleology.
(2) Rational deliberation exhibits irreducible teleology.
(3) Therefore, naturalism is false.
He offers two examples to back this up (p. 42):
- The glass broke because the rock hit it.
- I raised my hand because I wanted to vote.
There are also some problems for the dualist approach towards having rational faculties. How does the dualist explain the fact that our rational faculties don't always work properly? How does he explain mental illness? How does he explain the tendency for confirmation bias and for the general inept use of logic on the part of humans - if - we are designed to be rational? These are more easily explained under naturalism than theism. So far the only explanation I've heard is original sin - a belief one must take entirely on faith since there is no evidence to support such an event, and all the evidence goes against it.
4. Unified selves
In this section, Moreland attempts to argue that since naturalism posits that all we are is simply just a particular arrangement of atoms, it cannot "countenance a substantial, enduring metal self." (p. 42) It seems we've heard this already from him. We are indeed particular arrangements of atoms. Put a person into a blender and mix their atoms around until they're nothing but goo and you can say that the person is no more, in the same way that smashing a computer into thousands of little pieces will result in something that looks nothing like what we can call a computer. A "simple soul is not an option for a naturalist" as Moreland declares, but it's nothing really problematic either. Every naturalist expects that when they die their atoms will be recycled into other things, and they will have ceased to be. "I" is just a temporary label we attach to particular arrangements of matter, just like we do to inanimate objects.
Moreland says that "most naturalists banish entities with no causal powers from their ontology, so a soul with no causal powers is tantamount to a nonexistent entity." (p. 43) Through my many debates with theists over the existence of supernatural entities, like demons, whose causal influences are indistinguishable from natural causes, I can say that any immaterial entity (especially if it resembles what superstitious people have believed) is likely the figment of someone's imagination. This of course includes any notion of the soul.
5. Intrinsic, equal value and rights
Alas, we have arrived at the final "fact" that is supposed to demolish naturalism once and for all. Here Moreland states that god "possesses intrinsic value, and his loving, just character is the source of objective moral obligation." And since god has these traits, we have "equal value and rights simply as such." (p. 44) It is the moral argument perhaps that gets me heated the most. I suppose, under Christian theism, we have such rights and value because god gave them to us. In other words, god says we're really special, and this is apparently the source of our value. But not only would this actually be an example of extrinsic value - value given from outside, and not intrinsic value, if god said we weren't special anymore, would our value suddenly evaporate? It would seem so on theism. Furthermore, human rights seem to be in conflict with the rights god has endowed us in the Bible, which, among a litany of other things, affirms that some people are slaves and should accept their place (Ephesians 6:5, 1 Peter 2:18, Titus 2:9). Apparently god does not approve of recalcitrant slaves. That's a "recalcitrant fact" theists have to lie to avoid dealing with. So the Christian view is actually out of sync with human value and rights on the most basic humanist views of ethics.
Moreland then quotes the philosopher of science Michael Ruse in a passage about morality under the naturalistic view. This quote has been used by many apologists. Ruse says in part:
morality is a biological adaptation no less than are hands and feet...Considered as a rationally justifiable set of claims about an objective something, ethics is illusory.......such reference is truly without foundation. Morality is just an aid to survival and reproduction . . . and any deeper meaning is illusory. 
The ontological foundation of moral values are in our intentions and actions and their consequences and I've made the case repeatedly on this blog that the Euthyphro Dilemma destroys any notion that goodness is grounded ontologically in god or that god is needed to know right from wrong. What the Christian theist yearns so strongly for is a moral law giver so that they can have god on their side when arguing morality, and use that to claim victory. This is evident in Moreland's writing. It's kind of like getting into an argument with your coworker over company policy and feeling vindicated if the boss happens to agree with you. But morality to me always seemed to be more than simply what's merely commanded, and was better tuned to "the distinction between right and wrong as it relates to conscious beings, with right actions being those that intend to positively affect conscious beings, and wrong actions being those that intend to negatively affect conscious beings when it cannot be avoided." This was my definition of morality I gave in my post, A Case For Secular Morality.
That's not all. According to Moreland, "the appearance of simple, intrinsic value" he says, "counts against naturalism and for Christian theism." (p. 44) But that's like saying the appearance of solid matter counts against atomic theory. We can say that human beings alone are the one species who have discovered their evolutionary past, who can contemplate the concepts of zero and infinity as well as some of the greatest mysteries of the cosmos, and who have the greatest capacity for emotional stimulation. That, one could say, is what gives human beings intrinsic value on a naturalistic supposition.
Next Moreland goes onto say, "naturalism cannot account for the high, equal value and rights of human persons" and that some secular philosophers like Peter Singer have acknowledged that the best or perhaps only way to do so is in "the metaphysical grounding of the Judeo-Christian God." (p. 45) But why Yahweh as opposed to the Zoroastrian god Mazda? Or why not allah? Those gods could do just as fine a job. If fact, any god could do if you're going to adopt a divine command morality. And the Christian argument that Yahweh loves everyone, even sinners, does nothing to mitigate the fact that he approves of slavery and unequal treatment for women. (Plus it's a false argument.)
The concept of natural rights is a tricky one. Rights always have to be upheld by persons. Nothing "natural" awards them to you. And if they come from Yahweh, why did it take an American revolution started by men to decide these rights? You'd think that our salient rights would also be found in the Bible, but they aren't. They actually contradict the Bible. And basic rights are not designed to correlate to our talents and merits; we can all enjoy the same basic human rights despite the fact that we're all unequal in our abilities. Human rights are derived from the knowledge that we'd all be living in a world with greater well being and less unnecessary harm by adopting them. Given this naturalistic understanding, Moreland's dilemmas seem less impressive. So the question he poses from the political philosopher Joel Feinberg is already answered: why should we treat all people equally in any respect in the face of manifest inequalities of merit among them?
Lastly, Moreland takes his aim at evolutionary theory once again. This time he tries to argue that evolutionary theory makes equal human value and rights hard to justify. He presents a long quote from the philosopher of biology David Hull in which he says that species having "natures" is a metaphysical category, and that Darwinian evolution removes that. Hull's argument isn't clear and I'm not sure I even agree with it. He states, "Perhaps all people are "persons," share the same "personhood," etc., but such claims must be explicated and defended with no reference to biology. Because so many moral, ethical, and political theories depend on some notion or other of human nature, Darwin's theory brought into question all these theories."  But why think human nature is metaphysical, when it certainly does relate to our biological evolutionary past?
To further the point, Moreland then goes onto quote atheist James Rachels that Darwinism undercuts any attempt to defend the notion of intrinsic human dignity.
The doctrine of human dignity says that humans merit a level of moral concern wholly different from that accorded to mere animals; for this to be true, there would have to be some big, morally significant difference between them....But this is precisely what evolutionary theory calls into question. 
I don't know Moreland's view on evolution, and it would've been helpful if he mentioned in his chapter whether he accepts it in whole or in part, or not at all. He seems to be making the case that evolution is not compatible with concepts of human dignity, but if Moreland's case forces one to deny evolution in favor of some sort of creationism, his argument falls apart. His only hope is to embrace some sort of theistic evolution, which has plenty of it's own problems. Now to Rachels' point, we are indeed animals but we've evolved greater intellectual, rational and emotional capabilities, and that's what separates us from all the other species. That's why we don't hold other animals to the same legal responsibility we do to humans. This theistic notion that says if evolution is true, then we're just no different from bacteria is completely baseless.
Moreland concludes that of his five recalcitrant facts, "not a single one of these five fits naturally in a non-ad-hoc way" under naturalism. Furthermore, he says "naturalists can't appeal to emergence to solve their problems because (1) this is just a label for the problem to be solved and not a real solution and (2) it begs the question against Christian theism in a most egregious way." (p. 47) Hopefully, I have shown this not to be the case, and that it is actually Christian theism and it's necessary adoption of dualism that suffers the greater problems given the data. The science of consciousness is a burgeoning field. We are no where near close to solving its most perplexing mysteries. As such, there is nothing wrong with calling it emergent given that we already have well supported evidence to believe it is completely contingent on the physical brain.
Moreland's cited references:
 Victor Ruppert, C.S. Lewis''s Dangerous Idea (Downers Grove, Ill.: InterVarsity Press, 2003) p. 70.
 Michael Ruse, "Evolutionary Theory and Christian Ethics," in The Darwinian Paradigm (London: Routledge, 1989) pp. 262-99.
 David hull, The Metaphysics of Evolution (Albany: State University of New York, 1989) pp. 74-75.
 James Rachels, Created from Animals (Oxford: Oxford University Press, 1990) pp. 171-72 Cf, pp. 93, 97, 171.