"Atheism of the gaps" or how to misrepresent atheism and abuse philosophy

I am an atheist. That means I don't believe in god(s). I also don't believe in Santa Claus, the tooth fairy, Bigfoot, the Loch Ness monster, or leprechauns.

When I say that I don't believe in leprechauns it means that I don't devote any time at all to the idea that leprechauns might exist and I don't alter my life in any way to allow for that possibility. If you ask me in casual conversation, I might say that leprechauns don't exist.

But I will give you a different answer if you are a philosopher or someone steeped in philosophical musings. In that case I will be careful not to say that lepechauns don't exist because I'm well aware of the fact that you can't prove a negative.

You have to be very careful what you say when you are around those people because they can be very picky about that sort of thing and they love to catch you making "metaphysical" claims that you can't logically defend.

The same rules apply to gods. Don't you dare say that gods don't exist or you'll be accused of (gasp!) metaphysics. This is why all intelligent atheists define atheism as not believing in god(s) and not as denying that gods exist.

Theists often propose very scientific-sounding arguments for the existence of god(s). Scientists often refute those arguments by showing that they don't meet the standards expected of good science. That does not mean that scientists have proved that gods don't exist. It only means that the defenders of gods have not been convincing.

In my regular searches for articles on junk DNA I stumbled across a paper by Daniel Akhondi¹ that was published on the PhilPapers website. I have no idea whether these are high quality philosophical papers or not (but see below). Here's the abstract.

Akhondi, Daniel (2026) Atheism of the Gaps: The Jump from Science to Metaphysics [website]

This paper introduces "Atheism of the Gaps" as a methodological label for a recurring pattern of reasoning in which a scientific explanation is taken to support a metaphysical conclusion about the non-existence of God. In contrast to "God of the Gaps," where ignorance is used to infer divine action, this paper identifies a symmetrical error: the leap from "we know how" to "therefore God is not." The paper argues that the epistemic success of a scientific explanation does not, by itself, entail any broader metaphysical conclusion. To substantiate this, it distinguishes between scientific, philosophical, and metaphysical levels of explanation, and proposes a principle of epistemic humility as a neutral criterion for evaluating arguments on both sides. The argument is illustrated through the case of junk DNA and debates over biological function, where concepts such as non-functional, useless, suboptimal, and having no role in survival are shown to be conceptually distinct and incapable, without independent argument, of supporting conclusions about design or atheism. The paper further offers a fourfold typology of this error - Functional, Explanatory, Optimization, and Epistemic Gap Atheism - and derives two methodological principles: the insufficiency of scientific explanation and the non-automatic transfer from scientific propositions to metaphysical conclusions. Finally, it specifies conditions under which an argument would not be an instance of this fallacy. The paper concludes that neither theistic nor atheistic metaphysical claims should be regarded as following directly from scientific explanations alone, and that the proposed methodological framework has the potential to be extended to other philosophical and even legal domains.

You can see right away that Akhondi is confused about the meaning of atheism—he assumes that atheist scientists are making an argument for the non-existence of gods instead of just refuting arguments for the existence of gods. He also seems to be a bit fuzzy when it comes to simple logic. Here's an example ...

For example, the proposition "Phenomenon X is explained through natural process Y" is a scientific proposition. But the proposition "Therefore X has no need for God" is no longer merely a scientific proposition. The proposition "Therefore God has no role in X" is a metaphysical or theological claim, and finally the proposition "Therefore God does not exist" is a much more general claim about reality. Therefore, even if the first proposition is completely correct, its correctness does not in itself guarantee the correctness of the subsequent propositions.

It's true that scientists are often satisfied with naturalistic explanations and we often say that phenomenon X is explained by natural processes. It's also true that some theists will argue that phenomenon X requires the existence of gods so when we say that the natural process is sufficient to explain phenomenon X it means we have no need to postulate the existence of supernatural beings. That's a rejection of a very extraordinary claim by a theist. It's a perfectly reasonable scientific argument against a scientific claim. There's no reason to quibble about whether the scientists are entering the realm of philosophy unless you are nitpicking in order to defend your belief in gods.

You could quibble if a scientist said "Therefore God has no role in X" but that's really just quibbling. Any reasonable scientist confronted with such quibbling would immediately correct the statement to say, "Therefore you have not demonstrated that God has a role in X." This is not a (gasp!) metaphysical or (double gasp!) theological claim.

Similarly, no intelligent scientist will say that "Therefore God does not exist," especially religious scientists who routinely refute the pseudoscientific claims of the Intelligent Design Creationists.

The rest of the article is extremely disappointing and it leads me to wonder whether this is a genuine peer-reviewed philosophical paper. Call me skeptical. The brief section on junk DNA shows a profound misunderstanding of the science behind the junk DNA model. It focuses on the idea that lack-of-function is not the same as no function (i.e. junk) in order to preserve the idea that at some point in the future we may discover functional roles for most of the DNA in our genome. Daniel Akhondi seems to believe that the concept of junk DNA is based on ignorance or lack of knowledge about the genome rather than on facts and evidence about function.

---

1. As far as I can tell, he is a Ph.D. student in medical research at Tarbiat Modares University in Tehran, Iran.