Changes in patent rules — in the courts, in Congress and in federal regulations — have forced general counsel to take sides against each other and caused some outside attorneys to sound an alarm.

“A number of remarkable events have occurred in the intellectual property world just this year that have the potential to change the landscape,” said John R. Harris, a patent attorney and partner in the technology/intellectual property group of Morris, Manning & Martin. “It’s scary to me because I represent clients on both sides. The U.S. has the best patent system in the world. What I’m afraid of is that they are about to throw the baby out with the bathwater.”