The future of the Boston Red Sox farm system is in limbo, with their affiliate the Lowell Spinners one of 42 minor league teams that could lose their big league ties under a proposal put forth by Major League Baseball.

Negotiators from Major League Baseball and Minor League Baseball are set to meet Thursday following weeks of public sparring over the plan.

Spinners owner Dave Heller told WGBH News it's unclear to him why the Spinners are on Major League Baseball's cut list.

"Lowell meets or exceeds every facility standard there is," Heller said. "They [Major League Baseball] say they want minor league teams that are closer to their major league affiliate. Well, goodness gracious — you can’t get much closer to your major league affiliate than we are."

Major League Baseball has offered several explanations for why it wants to shrink the minor leagues, which includes 160 teams in all. Among the reasons is the contention that some clubs are too far from their major league affiliates, and some stadiums too dilapidated to nurture future major league players. But the distance between Boston and Lowell is just 30 miles, and LeLacheur Park is relatively new; it opened in 1998, with new lights and a new field all installed in the past five years.

A now-public letter addressed to MLB officials that was signed "Minor League Baseball" last month outlined the central disagreements Minor League Baseball has with MLB's proposal to end Major League teams' affiliations with the minor league teams. In MLB's public response to the letter, Deputy Commissioner Dan Halem elaborated on MLB's position on short-season minor league teams like the Spinners, who begin play in June.

In the letter, Halem argues that under the contraction plan put forth by MLB, short-season teams would cease to be viable for a variety of reasons, including an amateur draft that MLB wants to shorten and reschedule from June to July.

MLB officials did not respond to multiple requests for comment by WGBH News.

MLB is promising that the Spinners and other teams set to lose their ties to their Major League clubs could compete independently, in what it's calling the Dream League. That's a non-starter for Heller.

"If we're not tied directly to the Red Sox, what kind of community support is there?" he said. "Our entire focus is saving the Spinners."

Heller has the backing of Massachusetts Rep. Lori Trahan, whose district includes Lowell.

In an interview, Trahan suggested that she believes the Spinners losing their Red Sox affiliation would mean the city losing the team as they know it.

"It would be psychologically devastating to this community," Trahan said. "The Spinners are as much a part of Lowell and Greater Lowell as the national park, as the Merrimack River, as the university."

Trahan has partnered with Republican Rep. David McKinley of West Virginia to form a task-force to save the minor league teams slated for contraction. Right now, they’re pushing a resolution calling on Major League Baseball to scrap its plan.

Community leaders in Greater Lowell and Spinners season ticket holders are calling for more, with many saying a grassroots campaign is needed. Heller has expressed support for the idea of a grassroots campaign, but said he believes that hearing from Trahan and others in Congress would be more effective. The Spinners haven't done much to push a ground-up campaign online, with the contraction plan getting little attention on the team's social media accounts.

"Far more than the feelings of individual season ticket holders or Spinners fans, I think that hearing from members of Congress is going to be at this point in time more meaningful to MLB," Heller said.

No matter where Major League Baseball stands, a looming and awkward question is how the Red Sox feel about the Spinners’ place on the cut list. It’s a question raised by John Chemaly, owner of Trinity EMS, one of the Spinners' corporate sponsors.

"If they approved already the deal to eliminate the Spinners, I’d like to know why," Chemaly said. "What have we done wrong? And do we have a chance to change your mind?"

Major League Baseball says all 30 of its teams, including the Red Sox, are on board with the contraction plan. But while Heller is blunt with his disapproval of MLB's proposal, he avoids criticizing the Red Sox.

"The Red Sox would like to see Lowell survive," he said. "I think the Red Sox like having us here."

Red Sox CEO Sam Kennedy said the team is "very, very committed to Lowell. We’ve had a great relationship and we hope it’ll continue."

But Heller said that last summer, Major League Baseball sent out an informal survey to its 30 franchises, asking them to pick four of their minor league teams they would want to save if contraction were to happen. Heller says he doesn’t know how the Red Sox answered, or if they did, but he says he doubts they picked the Spinners.

Kennedy did not say how the Red Sox responded, or whether the team even received such a survey. Major League Baseball did not respond to requests for comment.

The Spinners' ambiguous status doesn't sit well with season ticket holders like Larry Norman. Norman, of Billerica, Mass., said if the team loses its affiliation with the Red Sox, he'd be heartbroken.

"I haven't missed a game in 16 or 17 years," Norman said. "This is my summer vacation, coming to the games."