If you’re reading this, it’s likely you’re an apologetics nerd and already have some idea what Natural Theology and Skeptical Theism mean. For everyone else, and even the nerds, it’ll be helpful to provide a quick explanation of how these terms are being used. It’s actually a lot simpler than it sounds (welcome to Apologetics!).
Many believe that Natural Theology (NT) and Skeptical Theism (ST) are at odds with each other. After explaining the terms, I’ll explain why, from my perspective, this conflict actually helps the Theist and hurts the Naturalist.
Natural Theology and Skeptical Theism
Natural Theology is a branch of theology concerned with giving rational arguments for God’s existence. One of my favorite arguments from NT is the fine-tuning argument. Roughly, it states that the universe is designed. Not just that it was created, but that it was designed for some specific purpose, namely, the evolution of embodied moral agents (like us). If you want to learn more about the argument check this and this out. Importantly, the arguments from Natural Theology don’t assume the Bible is true, accurate, or inspired (hence why it’s called “natural” theology).
The basic idea behind Skeptical Theism, which is actually a terrible name for it , is that there’s no reason to think our knowledge of goods is representative of all the goods there are. This term usually pops up in the context of the problem of evil. Think about some really terrible case of widespread suffering (like the Lisbon Earthquake). Some are stretched to find a reason God would have for allowing and permitting suffering to this degree. Isn’t God all good? Why would He allow so much suffering?
The phenomenological experience of not seeing a reason God would have is sometimes used to draw the conclusion that therefore God probably doesn’t have a reason (and therefore probably doesn’t exist). Skeptical Theism (again, terrible name) comes in and says, well, wait a second, just because we can’t see a reason doesn’t mean God has no reason. We are limited in what we know, so it’s unsurprising that we, limited in time and space, can’t see a reason. That’s the basic idea.
The alleged conflict between Natural Theology and Skeptical Theism might not be obvious, so let me expose that a little. If ST is true and we have no reason to think our knowledge about the kinds of goods there are is representative, then it’s puzzling how we can say it’s likely that God, for example, would want to bring about a universe with embodied moral agents. Let me make this a bit more formal. The fine-tuning argument I cited above is famously defended in the following way (don’t worry about the symbols, I’ll explain them below):
(2) ~(Pr (LPU | T&k) << 1).
(3) Therefore, LPU confirms N over T.
In English, (1) says that the probability that a life-permitting universe (like ours) would exist given Naturalism is very, very low. Premise (2) says it’s not the case that the probability that a life-permitting universe would exist given Theism is very, very low. Most responses to this argument focus on (1). They want to say that actually the probability a life-permitting universe would exist on Naturalism isn’t that low. Other people (including Christians) have argued that affirming ST means rejecting (2). If we don’t know that horrendous evils are unlikely on Theism, then surely we can’t know that a life-permitting universe is not unlikely on Theism. Hence, the Skeptical Theist can’t affirm (2).
If we really are limited in what we know about God and his ways, then we can’t say with any confidence what God would or wouldn’t do given the opportunity. Maybe God would create a universe with embodied moral agents; maybe he would create a world full of beautiful inanimate objects; maybe He wouldn’t create anything. It’s not like we are just flipping a coin here–the probabilities involved are literally inscrutable. We don’t know what we don’t know. The most responsible thing to do is to withhold judgement altogether.
That’s the alleged conflict.
Before moving on let me make one caveat: I am not agreeing there is a genuine conflict here. I’m only laying out what I’ve seen and heard from other smart people.
Resolving the Conflict
As I see it, there are basically four ways this can go, and none of them benefit the Naturalist . We’ll evaluate each option from the perspective of the Theist and the Naturalist.
Option 1: Accept Conflict, Accept Skeptical Theism
This is the route that Hud Hudson takes. Note that Naturalists can accept Skeptical Theism as I’ve defined it. (This is part of the reason why ‘Skeptical Theism’ is such a bad name.) Keep in mind I’m not saying there is genuine conflict, but let’s assume there is. What can be done at this point? Well, if we accept Option 1, then we can’t affirm a premise that includes knowledge about what God would or wouldn’t do. This leads Hudson to deny Robin Collins’ version of the Fine-tuning Argument.
Theist: The upshot of accepting Option 1 is that it deals a death blow to the problem of evil (the strongest argument atheists have). The downside is that it means one cannot affirm certain arguments from NT. Importantly, however, this doesn’t mean they can’t affirm any arguments from NT. They could still affirm a whole host of arguments (e.g., the Kalam Cosmological Argument, the Contingency Argument, Craig’s deductive version of the Fine-Tuning Argument, the Moral Argument, the Ontological Argument, Plantinga’s argument from knowledge and proper function, and many others). Affirming Skeptical Theism doesn’t magically get rid of Natural Theology. Not by any stretch.
Naturalist: The upshot of accepting Option 1 for the naturalist is just the opposite. It means that fine-tuning arguments (and any argument utilizing such premises) should be rejected. That’s good news for Naturalists looking to reject the argument. The bad news is that, as mentioned above, there’s still quite a bit of NT to contend with. Affirming ST does very little to make Naturalism plausible. More importantly, affirming ST means that one can no longer base one’s Naturalistic belief on arguments from evil (which I take to include arguments from divine hiddenness).
Overall, this option looks pretty favorable for the Theist and not so favorable for the Naturalist.
Option 2: Accept Conflict, Reject Skeptical Theism
Most atheists already reject ST, so this is the option they’ll take. It’s also the route that, believe it or not, many Christian philosophers take (Trent Dougherty is a great example). Rejecting ST means that one can utilize premises about what God would or wouldn’t do. NT is no longer limited, the problem of evil is no longer off the table. Let’s see where this gets us.
Theist: The upshot of accepting Option 2 for the theist is that they can now run their favorite argument for God (and by that I mean Robin Collins’ fine-tuning argument). The downside is that the problem of evil is back. The way I see it, the probabilities weigh so heavily on the side of Theism, probabilistic versions of the problem of evil couldn’t even make a dent. That’s even granting there’s no great good we could identify, granting that animal suffering is a big problem, and the rest of it. There’s no scenario here where the probabilities tip in favor of Naturalism. 
Naturalist: The upshot for the Naturalist is that the problem of evil is back. Hooray! Downside is that, as I’ve already said, so is Collins’ fine-tuning argument. Boo!
Here again, this option doesn’t help the Naturalist. In my opinion, it actually makes matters much worse.
Option 3: Accept Conflict, Alter Skeptical Theism
An interesting option is to alter Skeptical Theism. This option seeks a version of ST that undercuts the problem of evil while leaving all of Natural Theology on the table. John DePoe is a philosopher currently working on this (see his paper on “Positive Skeptical Theism”).
Theist: For those inclined to this view, this is a great option (in terms of benefits). Problem of evil is gone and all of NT is back.
Naturalist: This is the worst option for the Naturalist. No problem of evil, no response to the second premise of Collins’ fine-tuning argument.
Option 3 is a devastating hit to the Naturalist.
Option 4: Deny Conflict
Some Skeptical Theists deny there is a conflict between ST and NT. While ST might locate certain cognitive limitations, it doesn’t locate the kinds of limitations needed to reject (2) of Collins’ fine-tuning argument. This is a real option and is constantly being explored.
Theist: This is a great option for those unwilling to compromise on truth (and those unwilling to prematurely Moorean shift). Here again the problem of evil is gone and all of NT is back.
Naturalist: This is another bad option for the Naturalist. No problem of evil, no response to the second premise of Collins’ fine-tuning argument.
Options 3 and 4 are equally devastating to Naturalism.
Any way we look at this alleged conflict, it doesn’t look good for the Naturalist. Option 1 does away with the problem of evil and still allows for many arguments from NT. Option 2 leaves the problem of evil on the table but is heavily outweighed by the fine-tuning argument (again, see ). Options 3 and 4 are both the best options for the Theists and worst options for Naturalists; they leave the problem of evil in the dust and all of NT on the table.
The alleged conflict between Natural Theology and Skeptical Theism is not one that Naturalists should be happy about.