By Michael Hurley, CBS Boston

BOSTON (CBS) — I’ve long contested that it would be truly impossible for any human being to read the entire Wells report without arriving at the conclusion that entire process was a sham. U.S. District Judge Richard Berman’s behavior in court on Wednesday only further cemented this theory.

The judge, who continues to urge both Tom Brady’s and Roger Goodell’s sides to reach a settlement, seemingly showed his hand that he might have chosen a side in this case. And it does not favor the NFL.

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Of course, it would be dangerous to reach absolute conclusions of the judge’s thought process based solely on his line of questioning in a public forum. He did caution against that very process just last week. Plus, there have been many hours of discussions behind closed doors, so from the outside we will never be able to get the entire story.

However, after a line of intense questioning of the NFL, it would be difficult to draw any other inference. Berman is simply not buying the NFL’s case.

For the second straight week, Berman poked holes in the NFL’s case, which is based entirely off the questionable Wells report and complicates matters by twisting those findings in decisions made by Roger Goodell — decisions which were later upheld … by Roger Goodell. This line of questioning took place after legal experts predicted more talk about process and “the law of shop” and less focus on the logical holes in the Wells report for this second meeting, so it’s clearly a source of much doubt for Berman.

Berman went so far as to accuse the NFL of taking a “quantum leap” when taking Ted Wells’ finding of “general awareness” and later deeming Brady to have “approved of, consented to, and provided inducements in support of … a scheme to tamper with the game balls.”

NFL attorney Daniel Nash contested that not only was Brady aware of a plan to deflate footballs, but he was actively involved in it. Berman’s response was concise: “Why doesn’t [the Wells report] say that?”

Berman also openly took issue with Goodell’s decision to suspend Brady for four games, stating simply, “I have a little trouble with that.”

For one, no similar punishments have ever been handed out. There’s also the unclear measure of how much of that suspension relates to alleged awareness of football deflation and how much relates to non-cooperation. Lastly, Berman didn’t quite see eye-to-eye with Goodell’s assessment that awareness of football deflation could be equated to steroid use.

Nash tried to state that it had to do with “integrity of the game,” but Berman wasn’t sold.

“I still don’t see how the four games is comparable to a player using steroids,” Berman flatly stated.

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Still, this is not exactly news. The holes in the NFL’s case are obvious and have been obvious for months to anyone who’s paid close enough attention. By raising those issues, Berman was just being a reasonable person more than he was acting as a man of the law. But it was on one point in particular where Berman was employing his legal expertise. And it’s on that point that the NFL should be very worried.

Berman raised an issue with the NFL for not allowing Brady’s side to call Jeff Pash as a witness during the appeal hearing in late June. Pash is the NFL’s executive vice president and the league’s general counsel, and he was named as the co-lead investigator with Ted Wells, who testified that Pash edited the final report before its public release.

The NFL refused to allow the NFLPA to call Pash as a witness, claiming his testimony would have been irrelevant. Berman not only disagreed with that sentiment but also recalled some arbitration awards that have been overturned for the refusal to allow a party to call a witness.

It’s this point made by Berman that resonated loudest on Wednesday, because it’s this issue that may ultimately sink the NFL.

Despite Wells’ insistence that he acted as an independent investigator, he testified that Pash added “some kind of wordsmithing” to the final report. That makes Pash a key part of the story, not only because Pash is a high-ranking NFL official, but also because the NFL based its entire reasoning for Brady’s suspension on the Wells report. Pash was, without a doubt, a key witness who should have faced the NFLPA’s questions on June 23 in New York City. But the NFL was making the rules that day, and the NFL said Pash was off-limits.

Berman pointed out that by preventing the union from questioning Pash, there are clear and obvious questions about the fundamental fairness of the arbitration hearing. And if the judge rules that the arbitration hearing was fundamentally unfair, then the NFL’s case of “we can do whatever we want, because we have a CBA, and there’s nothing you can do about it” gets thrown out the window.

(As an aside, the gall of the NFL to preemptively file this suit in New York City in an effort to secure a favorable judge, only to tell that judge that he has no authority and must defer to Goodell’s decisions as commissioner, is truly remarkable.)

Again, Berman has not made a ruling. He has not indicated how he will rule. In fact, he continues to stress his desire for both sides to settle.

But if the two sides aren’t able to reach an agreeable settlement — and that still seems like an impossible conclusion — then it continues to appear that the NFL’s insistence that its decisions cannot be questioned is an argument that will lose to the case made by Brady’s side, which is based in legal precedent and basic fairness.

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We can’t know for certain, but it seems to this point that Berman agrees.Read more from Michael Hurley by clicking here. You can email him or find him on Twitter @michaelFhurley.