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(Reuters) - New England Patriots quarterback Tom Brady on Thursday formally appealed a four-game suspension for his role in "Deflategate" after his team, one of America's most high-profile sports franchises, delivered a blistering rebuttal of an NFL investigation into the matter.
National Football Commissioner Roger Goodell later said he would personally hear Brady's appeal, overruling the league's players union, which called for an independent arbitrator to hear the case when it filed the appeal on Brady's behalf.
"Given the NFL's history of inconsistency and arbitrary decisions in disciplinary matters, it is only fair that a neutral arbitrator hear this appeal," the union said in a statement announcing Brady's move.
League spokesman Brian McCarthy said Goodell would act on the appeal "in accordance with the process agreed upon with the NFL Players Association in the 2011 collective bargaining agreement."
Brady's appeal pits the NFL's most popular player against the most profitable sports league in the United States at a time when it is reeling from criticism over its handling of players involved with domestic violence and a concussion settlement for retired players that could ultimately cost $1 billion.
The league suspended Brady without pay for the first four games of next season, fined the club a record $1 million, and forced the Patriots to give up two draft choices for purposely deflating footballs used in the team's 45-7 victory over the Indianapolis Colts that put it into the Super Bowl.
In a website created to dispute the investigation findings, the Patriots said the report's conclusions were "incomplete, incorrect and lack context."
Two days after independent investigator Ted Wells steadfastly defended his conclusions implicating Brady and two Patriots employees in the scheme, the team fired back.
"There is no evidence that Tom Brady preferred footballs that were lower than 12.5 per square inch and no evidence anyone even thought that he did," according to the team's counterclaim, written by attorney Daniel Goldberg.
Goldberg represented the club and was present during all interviews of team personnel conducted at Gillette Stadium.
The Patriots also included Nobel Prize Laureate Roderick MacKinnon's "scientific conclusion" that challenges the Wells report's rejection of scientific explanations as to how the footballs could have naturally lost air pressure.
Wells said he believes a series of text messages by two Patriots employees implicated Brady, a three-time Super Bowl most valuable player, who is married to Brazilian supermodel Gisele Bündchen.
The Wells report identified the two Patriots employees, officials' locker room attendant Jim McNally and equipment assistant John Jastremski, as the ones who deflated the footballs.
The Patriots, who suspended both indefinitely last week, have not said whether they will appeal the club's penalties.
"Texts acknowledged to be attempts at humor and exaggeration are nevertheless interpreted as a plot to improperly deflate footballs, even though none of them refer to any such plot," the Patriots said in the 20,000-word rebuttal, posted on Wellsreportcontext.com.
The Patriots said the word "deflator" used in the texts cited by Wells in his report was taken out of context.
"Mr. Jastremski would sometimes work out and bulk up -- he is a slender guy and his goal was to get to 200 pounds," the team, which has until May 21 to appeal its punishment, said in the rebuttal.
"Mr. McNally is a big fellow and had the opposite goal: to lose weight. 'Deflate' was a term they used to refer to losing weight."
Deflating the balls would likely allow Brady a better grip, especially in the cold and wet conditions during the AFC title game in January. New England subsequently defeated the Seattle Seahawks 28-24 to win the Super Bowl.
Experts believe Brady has a chance to get his suspension halved, as the penalty is severe by NFL standards. For example, the league assesses the same suspension for first-time violators caught using performance-enhancing drugs.
In addition, the league is on a losing streak of sorts after penalties on two high-profile players involved in domestic abuse, Peterson and former Baltimore Ravens running back Ray Rice, were reversed on appeal.
Brady has denied any knowledge of how the balls lost air after being examined by a NFL referee. He refused to surrender his phone to Wells but Brady's agent, Donald Yee, said the quarterback had a lot of personal information on it and did not want to hand it over.
The team and its fans are showing few signs of throwing in the towel. On their Twitter account, the Patriots changed the avatar to the back of Brady's No. 12 jersey.
Patriots fans this week set up a website to seek donations to pay the team's $1-million fine and had collected $15,691 by Thursday afternoon.
Reporting by Steve Ginsburg in Washington; Additional reporting by Curtis Skinner in San Francisco; Editing by Alan Crosby and Clarence Fernandez