Over in the main site, there's a post by Jason Rantanen about Whiteserve v. Computer Packages, here. He points out that Judge Mayer, sua sponte, would have held some claims invalid for lack of patentable subject matter.
There's an argument that this is not a validity defense, which I find interesting. Briefly, we're dealing with a statute, not common law, and so the statute matters. Under the statute, there are specifically enumerated defenses. See Aristrocrat Tech. v. Int'l. Game Tech, 543 F.3d 567, 661-63 (Fed. Cir. 2008). If a statutory requirement is not identified as an invalidity defense, then it's not. Id.
Section 282 lists a number of things as defenses, but lack of patentable subject matter under Section 101 is not expressly listed. You would have to argue that it's implicit, I guess, in "non-infringement" under 282(1). But that seems to be a very loose reading of the statute (I wrote a book on statutory interpretation and won't bore you with a lot of the mumbo jumbo).
Wait, you say, it's long been recognized as a defense. Maybe, but a lot of statutes are read wrongly for a long time. E.g., Central Bank of Denver v. First Interstate Bank of Denver, 511 U.S. 164, 177, 191 (1994) (overruling 60 years of judicial decisions authorizing a statutory cause of action on the ground that Congress in fact had not authorized it).
What's the ethics angle in this? Heck, I don't know, except that under our system, the statute matters. Someone explain to me how we can get to an invalidity defense under the statutory language, based on 101...?