There is a gaping hole in the latest effort to reinvigorate the search for extraterrestrial intelligence (SETI), one so big it could hold an estimated 357 million boxes of cornflakes.

The hole opened last week when tech billionaire Yuri Milner announced the Breakthrough Listen initiative, a 10-year, $100-million shot in the arm for SETI, operated through Milner’s Breakthrough Prize Foundation. The initiative includes funding for unprecedented amounts of SETI time at three world-class observatories: the Green Bank Telescope in West Virginia, the Automated Planet Finder telescope in California and the Parkes Observatory in Australia. What’s missing from the partnership is the Arecibo Observatory in Puerto Rico, which at 305 meters wide is the biggest and most sensitive single-dish radio telescope in the world. SETI godfather and former Arecibo director, astronomer Frank Drake, once calculated that the instrument could not only hold all those cornflakes, but also receive (or send) radio messages throughout much of the galaxy.

The omission at first seems inexplicable, because SETI and Arecibo are inseparably intertwined. Drake, a key player in Breakthrough Listen, famously used the telescope in 1974 to transmit his “Arecibo message” toward the globular star cluster M13. The message was meant to be an interstellar postcard from our culture, and included pictographic figures of our planet, our solar system and even the recipe for DNA. Today, the observatory remains the primary source feeding data to the groundbreaking SETI@home citizen science project, which uses idle computer time to scour the data for alien signals. Like Drake, SETI@home is also a key part of the Breakthrough Listen initiative, and will be distributing some of the project’s new data to its millions of volunteers.

The foundation was and still is interested in partnering with Arecibo, Scientific American has learned. But according to Arecibo Director Robert Kerr, that partnership is currently being prevented due to a poison pill inserted by the observatory’s owner, the National Science Foundation (NSF). The situation is a startling example of a cash-strapped federal agency seeking to offload an expensive, world-class facility to the private sector—at the potential cost of compromising its ability to perform world-class scientific research.

Driven by budget cuts, for years the NSF has sought to preserve its extensive program of research grants and to support newer facilities by divesting from older ones, including Arecibo, encouraging each one to find outside funding partners or to otherwise risk closure. The NSF reviews and approves all possible partnerships, provided the partnership does not interfere with an observatory’s obligations to the agency. For instance, the NSF also owns Green Bank and is seeking to divest from it as well, even though the state-of-the-art facility offers astronomers the world’s largest fully steerable radio dish (Arecibo is much bigger, but cannot be aimed at all parts of the sky). The NSF approved Green Bank’s Breakthrough Listen partnership, allowing Milner to purchase 15 percent of the telescope’s observing time for SETI, although NSF officials say even with that cash infusion Green Bank’s continued operations remain in jeopardy.

According to Kerr, Breakthrough presented Arecibo with a contract for a similar partnership, but negotiations stalled when the NSF informed Kerr and the rest of Arecibo’s Executive Governing Committee that the deal would be considered part of the agency’s divestment strategy. That is, to accept money for Breakthrough Listen, Arecibo would first have to forgo further funding from the NSF, which currently provides some $4 million a year through a cooperative agreement that expires in September 2016. (The observatory also receives funding from other sources, including about $2 million a year from NASA, which uses Arecibo to monitor potentially dangerous near-Earth asteroids.)

Even with the Breakthrough money promised by the foundation, Kerr says, the NSF’s divestment “might well result in the cessation of science operations at Arecibo, and possibly closure.” If Arecibo managed to stay open after divestment, Kerr says, it would struggle to fulfill the proposed Breakthrough Listen contract, which does not include funding for basic operational costs such as electrical power for the telescope.

James Ulvestad, director of the NSF’s Division of Astronomical Sciences, disputes Kerr’s characterization of the situation. Arecibo, he says, is “incredibly valuable,” and the NSF would be “quite pleased” if the observatory could partner with Breakthrough. Even so, he would not rule out the possibility of the observatory losing NSF funding through a future Breakthrough partnership. The decision, Ulvestad says, hinges on details of the proposed partnership that Arecibo’s management have yet to provide to the NSF.

“We don’t have any hard and fast rule that says if you get some new partner that brings in a dollar, then we’re going to take a dollar away from you,” Ulvestad says. Instead, he says, the NSF evaluates any possible partnership based on how it affects the agency’s broader mission. The NSF mandates that all of its telescopes, including Arecibo, must conduct a program of observations proposed and selected via peer review by the U.S. astronomy community. “We’re in the business every day of making priority choices of where to spend a limited pot of money,” Ulvestad says. “If some fraction of [Arecibo’s] time isn’t being spent on open-user community science anymore, we have to think… Should we be giving them the same amount of money to do less of our mission?”

Kerr rejects the NSF’s position as a catch-22 cleverly designed to further the agency’s budget-cutting goals. As appealing as the Breakthrough Listen observations at Arecibo might be, they would be taking place outside the realm of peer review, and would thus not contribute to that portion of the NSF’s mandate. The further cuts to NSF-mandated science observations that would likely be required to fulfill a Breakthrough Listen partnership could consequently provide the NSF with a convenient excuse to justify divestment. “This new situation waxes unscrupulous,” he says. “The NSF now insists that we do commercial, non–peer-reviewed science so they can divest—and show positively that Arecibo no longer does mainstream radio astronomy and is thus unworthy for NSF investment. Amazing.”

In all likelihood, Breakthrough will continue to court Arecibo, seeking a middle ground between the struggling observatory and the NSF. In addition to Breakthrough Listen, Milner has formed a sister initiative for which Arecibo seems custom-made. Dubbed “Breakthrough Message,” the $1-million effort is an open competition to design digital messages to send to extraterrestrial civilizations. Milner, Drake and others involved with the project are careful to note that Breakthrough Message does not presently include plans to unilaterally transmit those messages—a practice that many astronomers now view as irresponsible and potentially dangerous because it could attract the attention of hostile advanced civilizations. But it is undeniable that transmitting targeted messages would require much less time on Arecibo than a broadband, wide-field search for talkative aliens, meaning it could more easily coexist with ongoing NSF and NASA peer-reviewed science observations.

The NSF, for its part, seems to have a vested interest in playing along. A full divestment and closure of Arecibo—which was built in a giant limestone sinkhole deep in the Puerto Rican jungle—would obligate the agency to dismantle the observatory and return the area to its “natural state.” Two NSF-commissioned engineering studies since 2008 have priced that endeavor at around $100 million—the same price tag as Milner’s entire decadal SETI effort.