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I felt a sort of idealistic giddiness upon enrolling in “Prisons & Punishment,” a government course introduced during my senior year of college. It was exciting to attach a resonant cause to academic inquiry, and about 95 percent of my classmates—Republican and Democrat—identified as supporters of criminal justice reform. Our professor had a childhood friend who was wrongfully imprisoned for murdering his parents and then exonerated 17 years later. “This will be the most important course you take in college,” the professor said on the first day of class.

I was startled to learn that several classmates would later complain that the class featured liberal advocacy. No, I thought, our class is passionate but intellectually rigorous; objectivity doesn’t preclude empathy, and how could studying the dehumanization of millions be reduced to a political stance? In hindsight, was it contradictory for me to do something with unabashedly moral convictions, then proceed to defend that ideology as neutral?

Around the same time, The New York Times’ Bill Keller was exploring his own version of this paradox, only on a much grander scale. He had stepped down as the executive editor of the Times in 2011 and initially landed on its Op-ed page, where he’d been condemning the “international scandal” of American prisons and punishment. Now, he was leaving to oversee a nonprofit that would aggressively investigate those issues. Many admired this sense of journalism with purpose. His new operation, The Marshall Project, sought to emulate ProPublica, whose mission is rooted in reporting with “moral force.”

Morality plays an interesting role in editorial judgment. Political bias is eschewed, but moral bias is essential; investigative work is often directed by a sense of right and wrong. The Marshall Project, a journalistic enterprise with an expansive focus on criminal justice, was inspired by moral outrage, with the explicit purpose of promoting reform. It may not call its work advocacy, but it is unavoidably ideological—not a political disposition, as the taboo version of “ideology” connotes, but more of a moral temperament. “While we are nonpartisan,” its mission statement reads, “we are not neutral.” And so, although Keller’s team of talented reporters may follow the same rigorous reporting standards as the Times, they are fundamentally different institutions. One is on a crusade, however virtuous that mission may be.

Keller gave instant credibility to The Marshall Project, less for his personal scholarship on criminal justice than for his devotion to editorial standards. I asked former Times Public Editor Clark Hoyt about nonprofits such as The Marshall Project, and he began, “I think Bill is a person of unquestionable integrity, and any organization he is going to be in charge of is one in which I would have a great deal of confidence.”

Since its launch last November, The Marshall Project has published 36 articles in collaboration with other outlets, from the Times and the Washington Post to the Atlantic, New York Magazine, and Vice. It employs nine reporters, many with extensive experience covering a justice system notorious for lacking transparency. Though being a nonprofit eases some financial pressure, an annual budget just under $5 million requires constant fundraising, and proof that the money is well placed.

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This summer should have helped that cause. The project has been especially prolific, mixing in-depth longform with cleverly packaged work on the Web. The Marshall Project is not yet an established brand, and a recent reader survey revealed that most people learn of it by seeing its work elsewhere. Still, as one of the most prominent single-subject journalism nonprofits, The Marshall Project is worth appreciating—in context. It’s a shining example of a suspect variety. No one is questioning the quality of its work, and Keller’s credentials make his organization’s journalistic rigor and fairness reliable. The question of nonprofits is more about the next generation out, and whether the Marshall Project’s model will breed cause-driven journalism unfit for partnership with the news sections of objective outlets.

In an interview at their Midtown Manhattan newsroom in July, Keller indicated considerable editorial self-awareness of this dilemma over the past nine months, but that hasn’t led him to waver on mission or methodology.

“We’re not offering loaded stories or polemical screeds about the state of the criminal justice system,” he said. “We’re offering reported pieces with the kind of discipline and skepticism that a place like The New York Times would expect. There are lots of pitfalls and dangers in this crazy landscape we live in now, but I don’t think partnering with more specialized news organizations is inherently problematic.”

Partnerships are essential to the publishing model of journalism nonprofits, whether cause-driven like The Marshall Project or more generalist like ProPublica. They fill a need for costly investigative reporting that’s increasingly unaffordable for commercial outlets. The for-profit gets top-notch investigative work produced by experts virtually free of charge, and the nonprofit gets free access to a large audience. Yet, their purposes diverge. Regardless of whether these arrangements have been benign so far, they present, by nature, an entanglement of editorial interests that legacy outlets must carefully weigh against the financial incentives.

Keller was editor at the Times in 2009 when it partnered for the first time with a nonprofit. “Traditionally, the Times has been deliberately self-contained,” he said. “I was lucky enough to be executive editor—lucky and unlucky, I guess—at a time of ferment and reinvention and experimentation.” The inaugural effort was a ProPublica story on medical chaos in the aftermath of Hurricane Katrina, and the two organizations would share a Pulitzer Prize for Investigative Reporting.

Today, Keller finds himself on the other end of the equation, at the right hand of Marshall Project founder Neil Barsky, a former Wall Street Journal and New York Daily News reporter and successful hedge fund manager with an epiphanous commitment to criminal justice reform. In 2012, Barsky read two books on criminal justice, “The New Jim Crow: Mass Incarceration in the Age of Colorblindness” and “Devil in the Grove: Thurgood Marshall, the Groveland Boys, and the Dawn of a New America,” that inspired him to try and shake the country into a moral reckoning.

“It was as clear as the nose on your face,” Barsky recalled during a recent interview in his office, a bigger space down the hall from Keller’s. (Barsky also chairs CJR’s Board of Overseers.) “That was the whole irony, the whole scandal. Nobody discovered anything—there were thousands of professionals who’ve spent their careers in criminal justice reform. What struck me was not the dysfunction, it was the complacency.”

While Barsky was refining his plan of action the following year, Keller had just written his weekly column at the Times around a dialogue with Glenn Greenwald, the Guardian journalist who had recently joined The Intercept, a journalism venture launched with $250 million from eBay founder Pierre Omidyar. They debated the nature of responsible journalism and the role of advocacy. “This suffocating constraint on how reporters are permitted to express themselves produces a self-neutering form of journalism that becomes as ineffectual as it is boring,” Greenwald wrote.

Keller answered:

“I believe that impartiality is a worthwhile aspiration in journalism, even if it is not perfectly achieved. I believe that in most cases it gets you closer to the truth, because it imposes a discipline of testing all assumptions, very much including your own. That discipline does not come naturally. I believe journalism that starts from a publicly declared predisposition is less likely to get to the truth, and less likely to be convincing to those who are not already convinced.”

Not long after seeing this, Barsky began corresponding with Keller. In one of those early emails, Barsky noted, “In the Glenn Greenwald, Bill Keller debate, I would side with Bill Keller.”

The editorial approach they settled on for The Marshall Project, though, involves more nuance. Barsky’s chief objective was to promote criminal justice reform. But when creating The Marshall Project, was he out to produce journalism for its own sake, or as a means for achieving something else?

“My motive was, I want to have an impact,” Barsky explained. “And having been a journalist, and having an understanding of the impact of journalism, I chose the vehicle of journalism to make that impact. Now, other people here might wake up in the morning and say, I want to create great journalism and I hope it has an impact. I get here and I say, I want to make an impact, and journalism is a great way to do that.”

When I posed this distinction of journalism as a means or an end, it was the one time Keller began by asking, “What did Neil say?” He then answered, “I sort of come from the school of a good story is its own reward.” Still, he has frequently observed that journalism is often assessed by the consequences of the reporting.

This question of impact is one of particular concern for cause-driven nonprofits. After all, their reason for being is to produce action, societal change, not simply to inform the public as conventional media aim to do.

Impact is a nebulous concept, but it’s what Marshall Project donors expect as the return on their investment. Toward that end, The Marshall Project recently developed a list of four “buckets” for measuring impact, according to Audience Editor Blair Hickman, formerly of ProPublica. They’re based on the Center for Public Integrity’s “glossary of offline impact indicators.” The first of these is “Institutional change,” which could mean, for example, a Marshall Project story leading to a government investigation being initiated. Next is “Community,” such as a school incorporating the project’s work into its curriculum. Third is “Civic or legal change,” such as a legal decision being reversed; and the last bucket is “Amplification,” which might mean a politician mentioning Marshall Project work.

ProPublica helped popularize this focus on impact. The organization was founded in 2007, with former Wall Street Journal editor Paul Steiger at the helm, and a benefactor couple pledging $10 million annually. It investigates issues “in the public interest” without getting caught up in playing off the news, which might be more likely to draw readers in bulk.

The proclivities of readers don’t always turn toward serious, lengthy projects, as The Marshall Project has discovered. Three of the most-read stories on the Marshall Project website have been Keller’s an interview with David Simon, former Baltimore Sun police reporter and creator of HBO’s “The Wire,” in light of the Baltimore riots; an interview with Equal Justice Initiative Executive Director (and Marshall Project advisory board member) Bryan Stevenson, in the wake of the Charleston shooting; and “What’s in a Prison Meal?” a collection of recreated illustrations of standard servings at prisons accused of skimping on food.*

ProPublica’s general manager, Richard Tofel, authored a compelling white paper on impact. Audience size matters, but the composition of that audience determines the potential for change. In an interview with CJR, he elaborated, saying reach is not per se impact, and distribution through partners is more important than reinforcing the ProPublica brand. Barsky speculated that a recent Washington Post collaboration on parole board dysfunction may have been read by nearly every member of Congress. The prison food piece, on the other hand, utilizes a graphic approach that’s appealing to mainstream readers who don’t have the appetite for 8,500 words.

Nonprofits see themselves, in part, as an antidote to diminished funding for investigative work. Yet ProPublica and The Marshall Project don’t prioritize the neediest news outlets when selecting partnerships. The Times and the Post are among the few newspapers that can still afford deep-dive reporting, but their large, impactable audiences make them attractive collaborators. “We don’t care when we partner with someone if their profit margin is in the red or 30 percent,” ProPublica’s Tofel explained.

The Marshall Project does a balance of partnerships, from those where the partner simply publishes the journalism to others where the collaboration runs deeper. As one example, in late June, The Marshall Project partnered with New York for the cover story “This Is Rikers.” New York reached out to Marshall Project News Editor Raha Naddaf, a former editor at the magazine, about doing a story on the notorious New York City prison. One New York reporter joined seven from The Marshall Project. The two outlets jointly collected, edited, and arranged dozens of testimonials from people connected in some way to Rikers.

“One of the reasons why it worked so well was that it really was a true collaboration,” explained Jared Hohlt, editorial director for print at New York. “They bring an incredible expertise on the subject, and reporting power, and Raha understood what our needs would be in terms of creating this as a magazine package.”

To Hohlt’s knowledge, this was the magazine’s first major partnership with a nonprofit. While he enjoyed dividing the labor for this project, he said he could imagine a scenario when all of the reporting is done by the partner, but never without thorough editing and fact-checking from New York.

“One of the advantages of magazine journalism is that obviously we’re not out there endorsing presidential candidates or anything, but we are comfortable with pieces that push certain opinions,” Hohlt said when asked about the possibility of advocacy creeping into work done by partners. For other legacy outlets, the distinction is of graver consequence.

How do reporting standards align if one partner exists to promote reform? “I don’t think the reporting ethics do match if one has a clear imperative,” said Geneva Overholser, former ombudsman at the Washington Post, director of the USC Annenberg School of Journalism, and now a senior fellow at the Democracy Fund. “You might be able to find a role where they gather data, for example, and be comfortable with that. If the imperative is that people be well informed about what’s happening with global climate change, then that’s an imperative that I, as a journalist, am comfortable with. I’m for information.”

“But,” she added, “If they are coming at it from a particular angle—only carbon limits, or doing away with dirty coal—it’s not that simple. Does the nature of their imperative mean that their reporting will be skewed? If it means that, then don’t enter into a partnership.”

In his final column at the Times, Keller wrote, “There is reason to hope that [Obama] will feel less constrained, that the eight commutations were not just a pittance but, as he put it, ‘a first step,’ that [Attorney General Eric] Holder’s mounting enthusiasm for saner sentencing is not just talk, but prelude, that the president will use his great pulpit to prick our conscience.”

Earlier this month, Obama commuted the sentences of 46 drug offenders and became the first president to visit a federal prison. Times have changed dramatically in the year since Ferguson—how, then, does The Marshall Project’s role change with it? The Rikers story offered a vivid look inside that prison, but so did preceding pieces from the New Yorker and the Times. The mission was to fill a reporting void. As criminal justice becomes a coverage trend, does that imperative weaken?

“I think it was cause for celebration when the Times sent two great investigative reporters to Rikers Island,” Keller said, “to write about a place that is just a shameful blight on the national conscience. It got our competitive juices flowing a little bit, too. But I’ve never seen our mission as just creating a sense of urgency about this issue, but to sustain it. I think it matters a lot that when others leave the field, we’ll still be here.”

It wasn’t initially clear whether The Marshall Project sought to be a short-term operation or a media mainstay. “I aspire for the Marshall Project to be around forever, sure,” Barsky said. “But I think you’re giving us a little too much credit for planning.” What is clear is that the desire for “impact” is far from satisfied.

As cross-publishing partnerships become more common, few editors seem particularly concerned. “I don’t think that having a substantive focus means you have to be an advocate,” ProPublica’s Tofel said. “So, CNN starts all-news television. Then, some years later, along comes Roger Ailes and Rupert Murdoch, and they decide we can do a politically motivated, ideological version of all-news television. Okay. You can do a politically motivated, ideological version of almost anything if you want to.”

Tofel is right: some single-subject nonprofit news organizations operate no differently than newspapers covering the same beat. Others, such as The Marshall Project or InsideClimate News, are created with a purpose. InsideClimate News won a Pulitzer for National Reporting in 2013. Maybe The Marshall Project will win one someday for its exceptional reporting. But some conceptual distinctions need clarifying.

“Advocates seek impact based on their opinion of societal needs,” Tofel writes in his analysis of impact. “[J]ournalists may identify possible steps toward reform, but should do so only from facts they have established.” Yet advocates, in their minds, are proceeding from established facts, and investigative reporters require an opinion of societal needs in order to know which facts to pursue. One form of advocacy, as seen in documentary films, presents just the facts, but with a clear suggestion of what conclusions should follow.

If “The Snowden Project” were created to do nonprofit investigative reporting on government surveillance, some might see that as no different than the work commonly done by national outlets. Others would suspect a political agenda. In his letter in the “About” section of The Marshall Project website, Keller writes, “We are not here to promote any particular agenda or ideology.” Unless “promote” is interpreted as to include only overt political instruction, that statement is not quite true. The Marshall Project exists to promote the agenda of criminal justice reform, which is inspired by an ideology that values human decency, racial justice, and the possibility of redemption after committing a crime. Those are easily endorsable morals, but morals no less.

“I worry and suspect that we’re in a kind of bubble of interest that’s brought about by a confluence of trends and events, the coming to adulthood of a generation that did not grow up with the crack panic and urban riots, and therefore does not list crime in the top 10 issues they care about,” Keller said.

That bubble arises in part from the absence of deep understanding, when shock over prison overpopulation or police misconduct isn’t accompanied by an awareness of forces that create those conditions, and by evolved moral priorities for criminal justice. Maybe connecting those dots does require advocacy. Barsky, after all, was moved to embrace the cause of criminal justice with the help of book authors who boldly addressed those questions.

“I found that I was lying awake at night thinking about how I could do this,” Keller told the Times last February when asked about his decision to join The Marshall Project. In under a year, Keller’s organization has succeeded in drawing considerable attention to abuses in criminal justice. But the broader question of whether cause-driven journalism is reliable—in different hands, for different ends—has hardly been put to rest.

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Danny Funt is a former CJR Delacorte Fellow. Follow him on Twitter at @dannyfunt