Not rule out, but question naturalistic mechanisms that are highly unlikely, or currently unexplained in certain areas of biology, mainly concerning origins of life.
When using the scientific method (SM) you question the theory that you are putting forward. If Behe is putting ID forward then he needs show how he questioned the mechanisms of ID. He never does that.
Relativity was not supported by the collapse of Newtonian mechanics. Germ theory was not supported by pointing to the lack of evidence for evil spirits. Each of these was supported by testing the theory itself. The ID method (IDM) does not test ID. It claims to test everything else BUT ID. That is a significant depature from the SM.
That they cannot be produced by naturalism could be Behe’s opinion, or any religious individual’s opinion, but the science of ID is justified in observing that it’s highly unlikely that they arose by only naturalism.
As has been pointed out, the conclusions made by Behe or others is secondary to the main argument here. In the IDM the ID claims are not directly tested as they would be in the SM.
If the scientific method has any relationship at all with Occam’s razor, then the ID studies that Behe proposed in Darwin’s Black Box (particularly as described at the end of Chapter 10) unquestionably follow the scientific method.
Occam's Razor states that the explanation with the fewest unevidenced assumptions is the one to go with. ID makes a ton of unevidence assumptions compared to naturalistic explanations. For evolution we have the OBSERVED mechanisms of evolution. No such mechanisms for ID have been put forward. We don't even have any evidence for the designer itself. All of it is assumed without any evidence to support it.
In many instances it is implied that order cannot be studied scientifically if it happened by a supernatural cause, that means there is evidence for order arising from purposeless naturalistic processes. So in some instances, a process of elimination is currently used in practice of the scientific method.
Can you name one of these instances? Can you point to a generally accepted scientific theory that is supported solely by the falsification of competing theories?