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The two coaches of the most high-profile athletic programs at the University of Colorado would like to see significant changes made to the NCAA’s Academic Progress Rate system monitoring student-athlete eligibility and retention.

Football coach Jon Embree and men’s basketball coach Tad Boyle say they support the ideas behind the APR, but they dislike, and in some cases very much disagree with, some of the repercussions when a program fails to make the grade.

“I like the concept, it’s just they’ve got to clean up some things that are blatant inequities in it to make it fit right,” Embree said.

The NCAA is in the first year of instituting higher standards and tougher punishments for failing programs. The three-step penalty process starts with the loss of practice time and scholarships and moves to bans from postseason play in addition to the other penalties.

The NCAA announced Wednesday that 35 teams from various schools and sports will not be eligible for the postseason in the coming school year because of failing APR grades. The list included 10 men’s basketball programs, 2011 national champ Connecticut among them, and three football programs.

“I think the APR can be very deceiving first of all,” Boyle said. “It’s based on two factors, eligibility and retention. I feel as a coach, you have control over eligibility in terms of the players that you recruit and how you handle them going to class and disciplining them internally for not taking care of their own business.

“I think as a coach you have very little control over retention.”

All 16 of CU’s sports programs reported passing grades when the report was released Wednesday. Embree’s football program raised its score from 919 last year, a score that would fall below the new standard, to 938 this year. Boyle’s program reported a perfect score of 1,000 for the second consecutive year.

All nine seniors on Boyle’s roster over the past two years have graduated. Embree said there are only a couple of his 28 seniors from last season’s team who haven’t earned their degrees and all are expected to do so by the end of the fall semester.

Boyle pointed out that his program “dodged a bullet” this year when freshman Damiene Cain left the program in the middle of the year unexpectedly because of personal problems. Cain was recruited as a scholarship player but never was put on financial aid because of his personal problems. Non-scholarship athletes don’t count toward the APR score.

Another Buff, guard Shannon Sharpe, recently decided to transfer from Boyle’s program. If Cain and Sharpe both counted toward the APR, the score for men’s basketball next year would drop substantially because of the small squad size — two of 13 scholarship players leaving.

Sharpe’s transfer will prevent the men’s basketball team from reporting a third straight perfect score at this time next year.

“When you’re dealing with a small squad size like basketball is, it can very tricky and very dangerous,” Boyle said. “I don’t like APR. I’ve never believed in APR but I’ve got to live with APR.

“What I’m interested in is graduating the kids who matriculate through our program, the ones who are tough enough to stick through it and fight through the tough times, which there are going to be no matter what sport you play. If you fight through those tough times and you get to your senior year and you’re not graduating, then I think the coach should be held responsible and I think there should be penalties in place for that. But I don’t think there should be penalties in place for kids getting homesick or at the first sign of adversity, kids deciding they want to leave.”

Another issue Embree and Boyle say isn’t fair under the current system is making players who weren’t in the program at the time low scores were posted pay penalties. For instance, the freshmen on the Connecticut basketball team next year will be robbed of a chance to play in the NCAA Tournament even though they had nothing to do with creating the problem.

While Boyle believes in judging coaches and programs based on whether they graduate players, Embree said he didn’t mind the previous punishment structure that cut the number of scholarships a program was able to offer if it reported failing grades.

“That’s hard since it’s not real time situations and issues, I think that makes it hard,” Embree said. “That why when they were doing scholarships it was probably a little more fair from the standpoint of it just affected what you could bring in the next year or the next couple years.”

Boyle has been a college coach for the past 18 years and has dealt with APR since its inception in 2004. Embree was at UCLA for the first two years of the APR and then spent five years in the National Football League. He, perhaps, hasn’t had as many opportunities to be annoyed or frustrated by the system.

Embree said he views the APR as another tool to help him communicate with and motivate his players.

“I think that helps coaches trying to get kids to understand they are there to graduate and get their degree,” Embree said. “When you have something like that, sometimes players need a reason why they’re supposed to what they’re supposed to do. When a kid knows he has an impact on the program, not just on the field, but what can happen if a team doesn’t do what he’s supposed to do or if a group of them don’t do what they’re supposed to do that is can have a negative effect on the program. I think that’s good, and I think it’s good, too, that some coaches have to take a more active role in what their students are doing and making sure they are doing what they need to do to graduate.”