It's interesting that historically, atheism was associated with the belief that the universe, life,and human were always in basically the same state that they are today. It was not until the discoveries of biologists in the 19th century that atheists accepted the idea of common descent.
It would have to be argued that the assumption that divine intervention is impossible, or too improbable to be considered, is on a par with the assumption that the literal truth of the Bible is not immune to empirical counterevidence[sic], and that just as the latter is a constitutionally permissible presupposition of the teaching of science, so is the former. In other words, not considering divine intervention a possibility is just a basic epistemological condition of modern science, a condition of scientific rationality, and cannot be constitutionally suspect, in spite of the fact that it is a religious assumption.
This is part of the issue leading into this error: the notion that science says divine intervention is impossible. Science actually says divine intervention is unmeasurable and unpredictable, therefore not useful as predictive element. It's ruled out of science because of being undetectable and non-useful.
Judge Jones cited as a decisive reason for denying ID the status of science that Michael Behe, the chief scientific witness for the defense, acknowledged that the theory would be more plausible to someone who believed in God than to someone who did not.12 This is just common sense, however, and the opposite is just as true: evolutionary theory as a complete explanation of the development of life is more plausible to someone who does not believe in God than to someone who does. Either both of them are science or neither of them is. If both of them are scientific hypotheses, the ground for exclusion must be that ID is hopelessly bad science, or dead science, in Kitcher’s phrase.
This is wrong because Nagel has missed the chain of reasoning. Being an atheist dos not make you more likely to accept evolution, as opposed to believing in a static universe for example. Being an atheist means you are more likely to accept that the naturalistic explanation, the one that has been tested and proved, without adding any sort of need to superimpose a additional beings into the process, but it does not guide to to a specific natural proof. The evidence leads you to evolution.
That would be true if ID, like young earth creationism, can be refuted by the empirical evidence even if one starts by assuming that the possibility of a god who could intervene cannot be ruled out in advance.
Nagel has this relationship backwards. It is precisely because it makes claims that can be refuted that YEC is at least making scientific claims. I have yet to hear one ID claim that was capable of being tested, much less refuted.
So far as I can tell, however, no such refutation has even been offered, let alone established.
Nagel does not say what there is to refute.
What have been offered instead are necessarily speculative proposals about how the problems posed by Behe might be handled by evolutionary theory, declarations that no hypothesis involving divine intervention counts as science, and assurances that evolutionary theory is not inconsistent with the existence of God.
Nagel is apparently not aware that there have also been direct refutations of many of Behe's claims the types of evolution that have or have not occurred, corrections to his description of fitness spaces, etc.
It is also emphasized that even if evolutionary theory were false, that would not mean that ID was true. That is so, but it is still not a sufficient reason to exclude it from discussion.
The reason to include ID is to provide positive, testable evidence for ID. 20 years after Edwards, the ID movement has not even come up with a testable prediction. So what's to discuss?