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What were once quiet concerns whispered among peers at American universities have become a steady drumbeat of angst ringing out across the proverbial quad. Everyone, it seems, is aware of the woeful state of the academic job market for newly minted PhDs. Graduate students who’ve dedicated five, even seven, years of their lives in training for their chosen fields—even at top universities—often face a stark absence of professorial prospects. A fresh-faced PhD in, say, history, biology, or the classics might get only a couple of job interviews, even zero, never mind an actual job offer in academia.

Without a university position in hand, these highly educated would-be professors generally have two options: bounce from one part-time teaching job to another or take a job doing something else entirely. And while some—those with engineering and science doctorates, mostly—have the option of well-paid work in the private sector, others do not, and admit to feeling shame and frustration that they didn’t make it in academia. At conferences and in the higher-education press, they bemoan a broken system: one that generates experts with training they cannot use without that all-important title of professor.

What if there was an alternative? The Ronin Institute, a three-month-old experiment founded by one of these would-be academics, is asking that question, hoping to revolutionize academia by connecting unaffiliated scholars to research funding and giving them credibility at the same time—no university required.

“We want to change that perception,” said Jon F. Wilkins, the institute’s founder. “If you’re a physicist and you’re not at a university, but you’re an engineer, or you’re doing physics, or actively pursuing your field of study, you should feel like as much of a scholar, or a physicist, as someone who is doing so as a professor somewhere.”

Wilkins, who earned a doctorate in biophysics from Harvard University in 2002, focuses on theoretical evolutionary biology, trying to understand, among other things, how and why our genes dictate behavior. But a few years ago, this 41-year-old academic without a tenure-track job began pondering a different issue: the unharnessed brainpower of the highly educated underemployed. He wrote about it on his personal blog, galvanizing support among his peers. And a few months ago, from his home in Montclair, N.J., Wilkins decided to do something about it, launching the Ronin Institute.

The goal, Wilkins says, isn’t just offering up a short-term solution to the current scarcity of academic jobs. It’s suggesting a new system altogether, named for ronin—the samurai who broke with the code of feudal Japan, refusing to commit suicide upon the deaths of their masters. “The analogy is, if you’re not employed by a university and you’re an academic, you’re supposed to say, ‘Well, I’m not an academic anymore.’ You’re supposed to sort of commit professional suicide at that point,” Wilkins said. “And what we’re saying is, ‘You know what? No, we can do this. We don’t need a master.'”

The academic job market for many post-docs is bleak. While the number of people obtaining PhDs has been rising—between 2000 and 2010, doctoral degree production increased in most every field, according to the Council of Graduate Schools—the percentage of professors holding traditional tenure- track jobs has been shrinking. An analysis of federal employment data, conducted by the American Association of University Professors, found that the percentage of college instructors holding such jobs is nearly half what it was 1975, with the slack taken up by adjuncts who receive no benefits and little job security, and are paid, often at low rates, per course. These trends have flooded the marketplace with scholars who have flagging hopes of landing stable, long-term academic jobs.

Many, of course, find work in other industries. And comparatively speaking, few holders of doctoral degrees will go totally unemployed. But many end up in jobs for which they are untrained, or over-trained. The Center for College Affordability and Productivity, a nonpartisan think tank that has been critical of the rising cost of a college education, estimates that in 2008 16 percent of those holding doctoral or professional degrees, such as law degrees, were working in jobs that required less than a bachelor’s degree.

But the issue isn’t just a lack of jobs for would-be academics. To do research, young scholars usually need to find full-time academic jobs. By training more people than it can employ, the current system leaves untapped brainpower languishing.

In a white paper published this month by the Ewing Marion Kauffman Foundation, Wilkins and coauthor Samuel Arbesman, a senior scholar at the foundation, are suggesting an alternative. Academics, they argue, need not be professors with experiences “steeped within the ivory tower.” They can be “fractional scholars”—a term they coined—pursuing their interests on their own, outside of academia. “Many, many PhDs have the ability to do it,” said Arbesman, who has also written for Ideas. There’s just one issue. “Within the current culture,” he said, “you need some sort of institutional affiliation.”

That’s where Wilkins and his nascent institute come in. Since obtaining his doctorate a decade ago, Wilkins has held a series of research posts, first as a junior fellow in the Harvard Society of Fellows and then as a professor at the Santa Fe Institute, a small interdisciplinary research group.

He was applying for jobs last year, he said, and not having much luck, when he got a break: His wife, a writer, landed a book deal. The book contract, along with a grant Wilkins already had, suddenly gave him a window of opportunity to launch the institute he had been considering.

Wilkins incorporated the Ronin Institute in February, attracted several scholars to sign on, and has begun seeking grant money for an idea that he believes is long overdue—not just for academics in the social sciences and the humanities, but even for science-minded scholars like himself. “I’m a theoretical evolutionary biologist,” he said. “What I need is a pad of paper and a laptop.”

He hopes the institute will help connect similarly minded people to the funding they need by supporting grant applications and, at times, perhaps even disseminating small amounts of money to researchers. “Say you left academia and you took a few years off to have kids and now you want to get back into it,” Wilkins said. “Well, one of the things you need to start doing is, you need to start going to the meetings, getting reintroduced to people.”

Wilkins wants to be able to fund such trips—as well as small research projects. And to do that, he’ll be asking for funding from foundations, philanthropists, and other donors. The institute’s overhead is low; Wilkins plans to keep it a virtual entity for the foreseeable future, which will free up more money for the researchers themselves. Still, it won’t be an easy task. To make it work, Wilkins said, the institute is hoping to raise enough money to have a working budget of tens of thousands of dollars. And then there is the prickly matter of selecting the independent scholars. Wilkins doesn’t plan to take all comers; he simply can’t.

“The danger of something like this,” he said, “is that it could easily be a magnet for crackpots—people out there not working at universities and it’s not because of lifestyle. It’s because they’re just crazy or not very good.”

Wilkins isn’t the only one rethinking the status quo. Last year, while researching the glut of PhDs in the marketplace, the journal Nature examined several potential solutions to the problem, including training PhDs on how to succeed in the private sector (some have little experience working in teams) or focusing less on dated definitions of what counts as success in their fields. (One new buzzword, Nature pointed out, is “transdisciplinary.”) And a handful of institutes, such as Santa Fe where Wilkins worked until recently, have set up outside university walls to create small research clusters around specific topics.

The challenge for Wilkins, going forward, will be part fund-raising and part changing the perception that serious researchers must be university professors. Ralph Haygood, one of the independent scholars who’s supporting Wilkins, believes the latter won’t be easy.

“If someone is a tenured faculty member at a university, it is a reasonable supposition that they know what they’re talking about,” said Haygood, who earned a doctorate in population biology from University of California, Davis, but stopped applying for academic jobs five years ago, he said, in order to start his own business. “And so, anytime anybody comes along and wants to talk about doing science outside academia, there is a certain amount of wariness.”

The key to overcoming that, Haygood said, is attracting credible people, whose work has been published in respected journals, to the institute. And the other key, according to Wilkins, is making clear that they aren’t trying to replace traditional academic institutions but to complement them, while helping people like Kristina Killgrove.

Killgrove, 35, earned a doctorate in anthropology from the University of North Carolina at Chapel Hill in 2010. Her focus is studying human skeletal remains. Her most recent research analyzed the remains of commoners who lived in Rome during the Roman Empire—heady, interesting stuff that, she said, helped her land an adjunct professor position last fall at Vanderbilt University.

But the job did not last. Within a few months, Killgrove, her husband, and young daughter were back in North Carolina. And though she is still hoping to find a full-time faculty job this spring, Killgrove is hedging her bets. Like Haygood, she has signed on with the Ronin Institute.

She believes in the premise, she said. And she knows the money is out there. Last year, Killgrove said, she used the Internet to raise $10,000 to finance her latest project. And if she doesn’t get that full-time faculty position, she hopes the institute might help her in at least one small way this year: raising money to send her to professional conferences. “I do that out of pocket,” she said, “because I want to tell people about my research.”