Shipwrecked by the sea change in their industry, many journalists are looking to philanthropy and academia as safe harbors. Numerous nonprofit ventures have been launched; others are on the drawing board. We are in the early stages of an era of experimentation, innovation, and cross-fertilization. The movement to nonprofit models has been so swift that we are only just beginning to wrestle with threshold questions about how such arrangements may affect the practice of journalism.

For the purposes of this essay, I will consider the Chicago News Cooperative, but the questions I raise apply to the entire emerging world of nonprofit journalism. The Chicago cooperative is largely staffed by former Chicago Tribune editors and reporters, and it received start-up funding from the John D. and Catherine T. MacArthur Foundation. Its board includes, among others, Newton Minow, a prominent lawyer and former chair of the Federal Communications Commission; Peter Osnos, founder and editor-at-large of PublicAffairs Books (and CJR’s vice chairman); Martin Koldyke, businessman and former chair of WTTW public television; and Ann Marie Lipinski, vice president for civic engagement at the University of Chicago and a former editor of the Tribune.

Since mid-November 2009, the cooperative has contributed two pages of local content on Fridays and Sundays to the Chicago edition of The New York Times, with some of its articles running in the national edition. It plans to launch a revamped Web site and is expected to provide content to other outlets, such as WTTW.

With both the Tribune and the Chicago Sun-Times having made severe cutbacks, the cooperative assembled its own newsroom to cover the city and state. Putting aside the issue of whether this model is cost-effective and sustainable, a key question is: Will its funding design give rise to persistent inducements to self-censorship?

This question was brought to a point for me by a piece by James Warren in the January 10 edition of the Times. A former managing editor at the Tribune, Warren writes a column that appears twice a week. (Full disclosure: prior to his taking the Chicago News Cooperative column, Warren and I had several exploratory conversations about a possible collaborative journalistic venture.)

Against the background of Mayor Richard M. Daley’s recent political woes—the lost Olympic bid, a deepening fiscal crisis—the theme of Warren’s column was that the mayor and the city have something to be proud of: the University of Chicago.

Warren takes as his text a recent book by Jonathan Cole, the former provost of Columbia University. The Great American University: Its Rise to Preeminence, Its Indispensable National Role, Why It Must Be Protected is an ode to America’s research universities. In conversation with Warren, Cole singled out the U of C as “our closest approximation to the idea of a great university.” Warren closes the column with the observation that “there is reason to be proud and protective” of the university.

From one perspective, this is an unexceptional column. From another, it’s unsettling, when one considers that Ann Marie Lipinski, Warren’s former editor and a board member of the news cooperative, is a vice president at the university. It’s also worth noting that Cole’s book was edited by another board member, Peter Osnos, and published by PublicAffairs, the publishing house he founded.

There is nothing improper about Warren’s column. For sins in past lives, columnists are condemned to struggle every few days to be engaging and provocative. It’s a difficult dance to do. In view of their unceasing hunger for ideas and material, it seems only fair to exempt them from various forms of conflict of interest. In any case, Warren subsequently appended to the column (on the Times’s Web site) an acknowledgment of Osnos’s role as publisher of the Cole book, though not the nature of Lipinski’s position at the university.

But the important question here is not the issue of transparency. Rather, the question is: In view of how the news cooperative is constituted, will it bring sustained critical journalistic scrutiny to bear on the University of Chicago?

It may seem ungenerous of me to press this point, in view of the fact that Warren quotes Cole as saying that the Kalven Committee Report (PDF), drafted in 1967 by my late father, Harry Kalven Jr., a law professor at the U of C, is “the greatest expression of ‘the sacred values’ of a great university.”

I am indeed grateful to Warren for retrieving this salute to my father. The two-page document that has come to be known as the Kalven Report is titled “Report on the University’s Role in Political and Social Action.” Written at a time when students were demanding that universities take a stand on the Vietnam War and other issues, it addresses the question of when, if ever, it is appropriate for the institution to take public positions. While allowing for the possibility of exceptions, the report eloquently articulates the principle that the university cannot take collective action on the issues of the day without endangering the conditions of freedom of inquiry and discussion that are its reason for existing.

For present purposes, what is striking is the sharp dichotomy between those core values and the way the institution conducts—and explains—itself when it acts as a corporate entity. Like other urban universities, it gets into disputes with the neighbors. Recent controversies have included stealth real-estate dealings by the university in a neighborhood west of campus, charges that its medical center systematically deflects the poor, and debate over its plan to destroy a large community garden in order to make temporary use of the site as a staging area for a construction project. (I have participated in the latter as both reporter and advocate.)

Such issues fall within the domain of Lipinski in her role as vice president for civic engagement. The university describes her mission as “overseeing an effort to create a new model for an urban research institution acting in partnership with its city.” In practice, Lipinski stands at the center of a formidable apparatus for managing public perceptions of the university in the service of its institutional agenda. Her office promotes university programs and, when controversies arise, is deployed to do damage control.

The issue here is not Lipinski. She is doing her job as defined by her employer. It is, rather, whether the news cooperative will be encumbered when a story about the university requires penetrating the official narrative promoted by the Office of Civic Engagement? Or to put the question another way, would the Chicago News Cooperation place on its board the chief of public relations for a major corporation or government agency it covers? How is this different?

Similarly, how will the cooperative cover its funders and philanthropy in general? The MacArthur Foundation is a major force in Chicago and beyond, yet it receives remarkably little sustained scrutiny from the press. Will it receive even less now that journalists are clamoring for its support? (More disclosure: MacArthur is also among the funders of this magazine.)

Beyond the question of how journalists will cover the foundations that fund them is a question of how they will report on public policy areas that those foundations have invested in. A case in point is the Chicago Housing Authority’s “Plan for Transformation”—the demolition of high-rise public housing and its replacement (now largely stalled) with so-called new communities. Over the last decade, the MacArthur Foundation has strongly identified itself with these policy objectives. It describes its relationship with the city in this context as a “partnership.” The embodiment of that partnership is Julia Stasch. As Mayor Daley’s chief of staff, she was the architect of the city’s plan for public housing. Then, in 2001, she joined the MacArthur Foundation as vice president for human and community development, where she has had a central role in making some $65 million in grants related to public-housing “transformation.”

In view of the news cooperative’s dependence on MacArthur funding, will it investigate the realities on the ground for public-housing residents? If the facts so dictate, will it challenge the official narrative the city and foundation have worked so hard to construct? Is it prepared to risk damaging a key funding relationship in pursuit of an important story involving some of the city’s poorest, most vulnerable residents?

Over the last ten years, the MacArthur Foundation has, in effect, policed the parameters of permissible discourse about public housing in Chicago. As the major funder in this area, it has provided support to virtually everyone working in the field (including, briefly, me). At a glance, one might imagine this reflects a commitment to robust debate. In fact, it more resembles a political machine that absorbs and thereby neutralizes potential challengers. For the most part, this dynamic appears to be less the result of deliberate strategy than a byproduct of grantsmanship.

Imagine you are the executive director of a nonprofit working on public-housing issues. Support from the MacArthur Foundation accounts for a significant portion of your budget. You are disturbed by city policies that you believe harm public-housing tenants. MacArthur strongly supports those policies. Will you voice your concerns? Publicly? Privately? If so, how forcefully? You need to be realistic. You want to sustain the work of your organization, you have a payroll to meet, and you must answer to your board. The best course, you tell yourself, is to retreat to fight another day.

Viewed in isolation, this may seem an exercise in common sense. Yet such decisions, in the aggregate, can have a devastating impact on public discourse about important issues. As journalists join the nonprofit world, will we be able to resist the siren song of such calculations? The danger is not so much that foundations will dictate what gets covered and what does not. That is relatively easy to resist. It is that we will seek to ingratiate ourselves to funders in order to stay afloat. It is precisely because the stakes are so high, with careers and enterprises in the balance, that the pull toward accommodation is so intense.

Self-censorship is subtle and insidious. It is often hidden from those practicing it as well as those subjected to it. Amid all the decisions that go into producing any journalistic artifact, it can easily be disguised as editorial judgment or realism about limited resources. After all, there are many worthy stories for the news cooperative to tackle that do not overlap with MacArthur’s interests. When we back away from, or soften, a story that might alienate a funder, will we even recognize what we are doing?

In raising these questions, I do not mean to impugn the integrity of particular reporters and editors—or to claim some higher moral ground. In my career, I have accepted support from a number of funders with definite agendas. And I am currently seeking to raise funds for the journalistic initiative with which I am associated, the Invisible Institute.

Nor do I mean to romanticize the old regime. In traditional newsrooms there are many pulls toward self-censorship: anxieties about alienating advertisers and subscribers; skittishness about proposing stories that challenge the crotchets of powerful editors and publishers; concern about maintaining access to institutions and individuals one covers; and so on.

This is familiar terrain. Good journalists navigate it with self-awareness, resourcefulness, and, when need be, cunning. The new kinds of potential conflicts in the emerging nonprofit journalism, by contrast, are largely uncharted. As we enter this gravitational field, the only way to keep our bearings is to challenge ourselves and one another to remain alert to the risks.

By the same token, philanthropy needs to examine its own practices. These days many foundations are disinclined to provide general operating support to their grantees. They prefer to fund specific projects bearing on the policy areas that concern them. That is the essence of their craft: to create incentives that draw work to a particular area. The danger in the journalistic context is that such incentives will also act as disincentives—as invitations to self-censorship.

Promises by foundations not to interfere and assertions of editorial independence by nonprofit ventures mean little. Only a strong sense of journalistic vocation can trump the otherwise compelling cost/benefit logic of grantsmanship. And the only meaningful expression of such clarity of purpose is the work itself. If we are prepared to err in the direction of biting the hand that feeds, perhaps journalism and philanthropy will co-evolve in ways that benefit both, yielding forms of patronage that effectively underwrite the First Amendment. Paradoxically, this is among the ways the conditions that imperil journalism also create an opportunity to recover its best traditions.

Jamie Kalven is the editor of A Worthy Tradition: Freedom of Speech in America by Harry Kalven Jr., and the author of Working With Available Light: A Family’s World After Violence. He has reported extensively on public housing and on police abuse in Chicago.