Theists hold that there exists an omnipotent, omniscient, and morally perfect person (God) who created the universe. Metaphysical naturalists, on the other hand, hold that the universe is a closed system, which means that nothing that is not part of the natural world affects it. Metaphysical naturalism (N) denies the existence of all supernatural beings, including God. Therefore, N entails that any true scientific explanations must be naturalistic (i.e., non-supernatural) ones.
In my post, “Evidential Argument from the History of Science,” I appeal to evidence (E) regarding the nature of scientific explanations. E1 states the overwhelming number of plausible scientific explanations for physical phenomena which do not appeal to supernatural agency. While readers may think of the topics that are standard fare for “science and religion” discussions (such as biological evolution, mind-brain dependence, etc.), the scope of E is much broader than that. To put the point somewhat crudely or simplistically, imagine a library that contains textbooks for all of the sciences, e.g., physics, chemistry, biology, astronomy, medicine, etc. Suppose that the textbooks summarize all currently plausible scientific explanations for those fields. The percentage of such explanations which make no appeal to supernatural agency is extremely high, while the percentage of such explanations which do appeal to supernatural agency is, at best, very small.
Furthermore, E2 states that the history of science contains numerous examples of naturalistic (i.e., non-supernatural) explanations replacing supernatural ones and no examples of supernatural explanations replacing naturalistic (i.e., non-supernatural) ones. Of course, one hears about specific scientific questions which (allegedly) do not have a plausible naturalistic (i.e., non-supernatural) explanation, such as cosmological fine-tuning, the origin of life, and consciousness. But that in no way denies the point that there have been numerous examples of naturalistic explanations replacing supernatural ones and no examples of supernatural explanations replacing naturalistic ones.
The central claim of the evidential argument from the history of science (AHS) is its premise (2), which states E is antecedently much more probable on the assumption that naturalism is true than on the assumption that theism (T) is true. In symbols:
(2) Pr(E | B & N) >! Pr(E | B & T).
And, for convenience, here again is the entire structure of AHS in its logical form.
cl does not find AHS in the least bit convincing. In his words, “there is so much wrong with this argument he does not where to start.” As I read his reply, his entire response to AHS is based upon his denial of (2), which he supports with three objections.
First, he presents a dilemma: natural explanations “work” either because of their utility or because they allow us to get the job done. This is a weak objection. Natural explanations “work” in the sense that they are plausible scientific explanations for physical phenomena which do not appeal to supernatural agency. The sheer quantity of such naturalistic explanations is much more probable on N than on T. N entails that all true scientific explanations are non-supernatural explanations, whereas T is compatible both with true non-supernatural scientific explanations and with true supernatural scientific explanations.
Second, he correctly observes that I reject what he calls “intrinsic methodological naturalism” (IMN) and instead accept something like what he calls “provisional methodological naturalism” (PMN). What, then, is the problem?
Lowder defines a “supernatural” person or cause as one who exists outside of “the spatio-temporal universe of natural entities.” Well, science can’t investigate anything outside the spatio-temporal universe of natural entities! At most, a scientist could posit a “supernatural” explanation for hitherto unexplained phenomena—then get beat over the head with God of the gaps retorts. So Lowder’s PMN seems to lead directly to fallacious thinking.
Third, cl argues that AHS begs the question. How, precisely, does AHS beg the question? According to cl, AHS claims that
the history of science is evidence for naturalism / atheism because natural explanations replace supernatural ones, but that premise presupposes that the explanations are ultimately natural (read: godless).
The word “ultimately” is key here. Suppose we have data about some scientific phenomena, which we call our evidence E. Assume that current scientific wisdom says that hypothesis H1 is the best explanation for E and that H1 does not make any appeal to supernatural agency. For example, E could be, “objects dropped from the roof of a house fall to the ground,” and H1 could be gravitational attraction. H1 could have an “ultimate” supernatural explanation just in case H1 is best explained by another hypothesis (call it H2), which does appeal to supernatural agency. For example, a theist might say, “H1 is true because God wills it to be true.” Let us call H1 an example of a primary explanation and H2 an example of an ultimate explanation, i.e., an explanation for one or more non-ultimate explanations.
Contrary to what cl claims, E1 and E2 do not claim that plausible scientific explanations are ultimate explanations. In fact, to avoid any misunderstandings, we can make this explicit with alternative wordings of E1 and E2.
E1′. The percentage of plausible scientific explanations for natural phenomena which have naturalistic primary or non-ultimate explanations is extremely high.
E2′. The history of science contains numerous examples of naturalistic primary or non-ultimate explanations replacing supernatural ones and no examples of supernatural primary or non-ultimate explanations replacing naturalistic ones.
Not only are E1′ and E2′ logically compatible with theism, but E1′ and E2′ are also compatible with all of these primary or non-ultimate explanations having a further, ultimate explanation which appeals to supernatural agency. Thus, this objection, like the two before it, fails.
Using the alternative wording provided by E1′ and E2′, it should now become even more clear why (2) is true. N entails that all true scientific explanations are non-supernatural explanations; if N is true and a primary scientific explanation has a deeper ultimate explanation, that ultimate explanation is also non-supernatural. In contrast, T is compatible with both true non-supernatural explanations and with true supernatural explanations (primary, ultimate, or otherwise). In other words, if N is true, true scientific explanations have to be naturalistic, whereas if T is true, true primary scientific explanations could have directly appealed to supernatural agency. Thus, E1′ is antecedently much more probable on the assumption that N is true than on the assumption that T is true, and hence strong evidence favoring N over T.
 By “plausible,” I mean “has a high epistemic probability.”
 Earlier in this series, following Draper, I used the expression, “modest methodological naturalism.”