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Isak has expressed his desire to consider leaving St James' Park and was notably absent from the team's trip to the Far East due to a minor thigh injury and uncertainty over his future.
Liverpool have been courting the Swedish striker for some time and have lodged an official bid believed to be in the region of £110million, which Newcastle promptly declined.
Shearer, speaking on The Rest is Football podcast, conveyed his understanding of the situation: "No, I'm not angry at all towards him.
I understand how football works, I know what happens in and around the game.
"I probably understand his mentality.
Probably two different things." But I know what football is about and I know how it works, and obviously Liverpool have been into him or his agent."
If Isak cannot be reintegrated, Shearer believes Newcastle should sell promptly and reinvest in strengthening Howe's squad following a tumultuous summer transfer window.
He added: "I just thought it might have happened next year and if it really is impossible for Eddie to turn him around and he says no, and it sounds like that is the case, I want him to be out now, you get your big money for him, whoever's prepared to pay that and you get other people in, hopefully beforehand, and then you move on.
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"As I said, no individual is bigger than any football club, and if he doesn't want to be there, fine, get what you can and get him out and say thanks very much for the memories, off you go."
Isak was accompanied at Newcastle by compatriot Anthony Elanga, a £55m acquisition from Nottingham Forest, though the club have failed to land a string of targets, including James Trafford, Bryan Mbeumo, Liam Delap and Joao Pedro.
They secured Aaron Ramsdale on loan from Southampton over the weekend, but Shearer concedes it has been a 'really poor' summer thus far for the Magpies.
"Up to now it's been a disastrous window for Newcastle," Shearer added.
"It was meant to be the time we kicked on with heavy investment and hopefully go to another level.
It's been anything but that to be honest.
"They've missed out on several first-choice targets, so up to now it's been really poor.
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