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After three kicks, Penn State did not run an offensive play in what was a manipulation of a new rule that starts the clock rolling as soon as it is kicked.
"It was a hell of a call!" said Alvarez, the school's athletic director who hired Bielema. "If Joe Paterno does that everyone says it's genius. There are rules. Good coaches take advantage of them. Do you not think Joe Paterno would have done it if he'd known the rule?"
Wisconsin won the game to improve to 9-1. Alvarez said he and Bielema discussed exploiting this loophole back in the summer, when they visited with officials.
"It's a bad rule," Alvarez said. "I think what you'll see next year is the clock stopped in the final two minutes of each half."
NCAA Associate Director for Playing Rules Administration Ty Halpin said that, by rule, Penn State could have accepted a 5-yard penalty where it ended up with the ball.
"But think about where Penn State would have started with the ball," Alvarez noted. "They caught it at the 5-yard line."
Game officals have also been instructed to give out unsportsmanlike penalties if they believe the offsides are clearly intentional.
"Officials are not going to use that until it is very clear the team is circumventing the rule," Halpin said. "You can argue that in this case, but the game officials are in a tough spot here because by rule, what Wisconsin did was legal."
Grant Teaff, director of the American Football Coaches Association, said his organization and the NCAA are compiling feedback and analysis on the new clock rules, which have been widely criticized by coaches.
"I can assure you this scenario is a big topic of discussion at officials' meetings this morning," Teaff said. "There are other rules that can be exploited. If within the rules, the question becomes is it unethical or does it just take advantage of a rule? I can assure you this will be discussed."
Said Alvarez: "Bret's just a smart coach. We're looking at winning ten games this season for just the second time."
Alvarez said that although he loves his role as an administrator, he has not ruled out the possibility of coaching again.
"Never say never," Alvarez said. "I'm like most guys who cut the cord. I miss it at times. The day to day involvement with the assistants. The games."
Alvarez has been mentioned as a possible successor in Miami if president Donna Shalala fires Larry Coker.
Joe Schad covers college football for ESPN.