During our Roundtable, I focused my short remarks on much of the content of this series, speaking about the apophatic tradition, the causal joint, and providence. But before getting to those reflections, I listed out some mysteries faced by reductive materialism. We might call these "mysteries of science."
Again, as I asked in this series, "What is a mystery?" One way to define a mystery is any question that, in principle, reductive materialism cannot answer. That is to say, a question that falls outside the boundaries of science. In such cases we are denied a mechanistic account, and without knowing "How it works" we're left with mystery.
So, what are some of the mysteries science faces? Where does a reductive materialism hit a wall of explanation?
First, being itself, the question of existence, is a mystery. Why is there something rather than nothing is a persistent mystery that science cannot answer.
Second, science itself is a mystery. By that I mean that science can never, in principle, get behind its own equations. Even if science were able to reduce down to a single "God Equation," a grand "theory of everything," it would still face the question: Why this particular equation? And why these particular variables? To even write down such an equation demands some givens, givens which themselves cannot be accounted for. In short, science itself is mysterious.
Third, mathematics is a mystery. Many mathematicians are what are called "mathematical Platonists." According to mathematical Platonism, mathematical truths are objective aspects of the universe. That is to say, mathematical truths are like material "facts" in how they exist independently of human minds. For example, the Pythagorean Theorem existed and was true prior to its discovery. And yet, no scientific account can be given to explain the existence and truth of the Pythagorean Theorem.
Fourth, consciousness is a mystery. No third person, mechanistic account can explain first-person, subjective experience. At best, we can establish a correlation between a neurological event and a subjective experience (like the taste of apple pie), but a correlation is not a causal explanation. No brain scan will tell you what apple pie tastes like. For an exhaustive tour of this debate, read David Bentley Hart's All Things Are Full of Gods: The Mysteries of Mind and Life.
Fifth, free will is a mystery. By definition. Of course, some deny the existence of free will. But the point to observe here is how, if you adopt a stance of scientific materialism, free will is ruled out before you even begin your investigation. Simply because if you assume materialism you're committed to offering a mechanistic view of neuroanatomy which, by definition, nullifies free will. In short, the issue of free will concerns metaphysical axioms which cannot be adjudicated by science. To say that "science disproves free will" is nonsensical for science, in assuming materialistic reductionism, denies free will axiomatically. Even more broadly, this is also why any "account" of free will, an attempt to explain how it "works," is also doomed to failure.
Sixth, the transcendentals--the true, the beautiful, and the good--are mysteries. Hume's Dictum is one example, that you cannot get an ought from an is. No amount of scientific analysis can determine moral duties or imperatives. You cannot extract an ethical claim from a descriptive claim. Another issue concerns the axiomatic nature of moral judgments, what might be called their "universality." Moral judgments, to be moral judgments, cannot be subjective, mere personal preferences. Also, attributions of value, like human dignity, cannot be extracted from materialistic descriptions. Of course, like free will, one can deny the existence of the transcendentals. But insofar as we operate, implicitly or explicitly, in the light of the transcendentals--making moral judgments or acting in light of human dignity--this falls beyond the scope of scientific materialism.
In summary, while this series focused primarily upon what might be called "theological mysteries," there are also "scientific mysteries," locations where reductive materialism cannot give an account or, in the giving an account, rules out the reality in question.