See, e.g., Bayer AG v. flousey Pharms., Inc., 340 F.3d 1367, 1377-78 (Fed. Cir. 2003) (granting motion to dismiss and holding that a patent claiming research processes is not infringed by the manufacture of a product)
Background - Bayer vs Housey was a ruling about the interpretation of a section of the law (271g) that prohibits the importation of a product "made" abroad using processes patented in the US. In this case Housey's assertion was that Bayer had used Housey's patents to discover a useful drug thence imported.
Bayer vs Housey ruled that only patents used in the manufacturing were intended to be covered by the law - patents used in discovery were not protected by law.
Altogether agree, as is captured elsewhere on these boards, that if:
a) the Momenta patents were only used in discovery
OR
b) in proving to the FDA as a one-time event that the aL is acceptable
Then Momenta's case is much weaker - but given the FDA's concerns in these matter either of the two above conditions is true.
PS Amusingly the OCR they use in electronically capturing the legal rulings stinks.