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On April 18, the Vatican Congregation for the Doctrine of the Faith—the modern-day vestige of the Holy Office of the Inquisition—released the conclusions of an investigation begun in 2008 into the sins of our sisters. The congregation issued what amounted to a takeover decree to the Leadership Conference of Women Religious, a move that “stunned” the organization. With over 1,500 members, all heads of religious congregations, LCWR leans liberal and represents 80 percent of America’s 57,000 nuns. Ad Policy

After giving an obligatory nod to the sisters’ good works in schools, hospitals and social service agencies, the CDF devoted the remainder of its Doctrinal Assessment to attacking the sisters for failing to provide “allegiance of mind and heart to the Magisterium of the Bishops”; focusing on the “exercise of charity” instead of lambasting lesbians, gays, and women who use birth control or have an abortion; refusing to accept the ban on women’s ordination; allowing “dialogue” on contentious subjects; and tampering with the notion of God the “Father” while promulgating other “radical feminist” theological interpretations. The CDF’s solution: send in three men, an archbishop and two other bishops, to take control of LCWR for five years. Related Article Angela Bonavoglia: The Vatican Is Targeting America’s Nuns With a ‘Takeover Decree’ The Nation

This led to an enormous outpouring of support to the sisters. But to anyone who has been watching the nuns closely, an unsettling observation emerges: these charges appear, in some measure, to be true. But that is not because, as the Assessment insists, LCWR has rejected “communion” with the church. Instead, it is evidence of a theological conflict that is raging in the Catholic Church, a conflict that most of us only notice when it spills over into American politics.

Liberal voices in the Church have been under attack ever since Vatican II. A number of vocal Catholic women, including nuns, have been among the most persistent and influential leaders of the fight to save the church from what they see as soul-crushing conservatism. This has galled the hierarchy, which has responded with silencings, firings, excommunications and public denunciations. Seeing that picking their targets off one by one wasn’t working, the Vatican, in taking on LCWR, decided to go for broke.

To understand what is behind the Vatican’s crackdown, go back to the 1970s, when feminism was seeping into the bones of American nuns. In 1971, the vast majority of the nuns who belonged to the Conference of Major Superiors of Women, which had been founded at the Vatican’s behest in the 1950s, moved to change the name of their organization to the Leadership Conference of Women Religious to reflect a commitment to women’s leadership and a more democratic spirit. Nuns were major participants in the first women’s ordination conference in 1975, and in the second, even larger one, three years later. By 1979, LCWR had become so spirited that its president, Sister Theresa Kane, challenged Pope John Paul II from the podium at Washington, DC’s Shrine of the Immaculate Conception to include women “in all ministries of our Church.” She did this while nearly fifty sisters wearing blue armbands, symbolizing women’s ordination, stood in silent protest.

Sister Elizabeth Johnson, who attended the second women’s ordination conference and whose order belongs to LCWR, found feminism too, but she also found theology, becoming the first woman to earn a PhD at Catholic University’s Department of Theology, which had previously granted degrees only to priests. (Catholic University is the only US university under Vatican control.) Upon graduation, Johnson became the first woman to join Catholic University’s theology faculty. She slipped the occasional feminist reading into her course on Christology, inviting forty male seminaries to wrestle with the question of whether a male savior could save women, originally posed by the grandmother of Catholic feminist theology, Rosemary Radford Ruether. In time Johnson became the first woman eligible for tenure in CUA’s theology department. But that’s when her meteoric rise ended. In 1986, her bruising tenure battle began.

In addition to being female and not ordained, Johnson faced opposition for having publicly supported Father Charles Curran, who was eventually fired from Catholic University for defending birth control, and having authored a single article on Jesus’ mother, Mary, in which Johnson quoted “some pretty vicious things” said about Mary by feminists—that she was sexless, passive and not a good role model. While Johnson understood the criticisms, she attempted to counter them. “If we went back to Scripture, you wouldn’t see her that way,” she told me when I interviewed her for my book Good Catholic Girls. “I was trying to defend Mary! I was on the good side, but they couldn’t see that.”

An opponent of her tenure, then-Chancellor James Hickey sent Johnson’s case to the CDF, the same group that is now disciplining the nuns. At the time, the CDF was headed by Cardinal Joseph Ratzinger, now Pope Benedict XVI. The CDF required Johnson to respond to forty “dubia” (doubtful things) regarding her beliefs about Mary. When her answers failed to allay their fears, they ordered Johnson to appear before the six American cardinals to be interrogated about her theology. As that tense session drew to a close, an angry Boston Cardinal Bernard Law, who would later resign in disgrace for having failed to protect children from pedophile priests, slammed shut the binder before him that contained Johnson’s sixteen articles. “Well, you mostly write in Christology,” he snapped. “You’re not going to do any of that feminist stuff anyway.”

“Oh,” thought Johnson, “you wait and see.”

Johnson got tenure, but she soon left Catholic University for Fordham. She went on to write a blockbuster, theologically speaking; She Who Is is a brilliant, moving and utterly convincing exploration of the Biblical evidence for a female face of God.

Johnson’s next confrontation came in 1995, when she was incoming president of the Catholic Theological Society of America. She and the Society battled Cardinal Ratzinger and the Congregation for the Doctrine of the Faith over just how definitive Pope John Paul II’s 1994 teaching against women’s ordination was. Observing the resistance of many Catholics to the teaching, the CDF issued a document declaring that the teaching was infallible—despite the fact that the pope himself had not used that crucial word.

“The head of the Congregation for the Doctrine of the Faith had never come out before and said ‘I’m declaring this to be infallible,’ ” Johnson told me. Reflecting a growing fear among Catholic theologians of “creeping infallibility,” the society publicly refuted the CDF’s contention. “There are serious doubts regarding the nature of the authority of this teaching and its grounds in tradition, [and] widespread disagreement…not only among theologians, but also within the larger community of the Church,” their statement read. It added that not all traditions are “legitimate,” particularly those based on women’s “inferiority” and “divinely intended” subordination. They called for study, discussion and prayer “by all the members of the Church.”

The American bishops were irate. That anger colors the Doctrinal Assessment, in which the CDF chastises LCWR for daring to “contradict or ignore magisterial teaching” and for failing to recognize the bishops as the “Church’s authentic teachers of faith and morals.”

Yet in their claim to absolute power to serve as the church’s teachers of faith and morals, the hierarchy of cardinals and bishops disregard the cherished Vatican II concept of the sensus fidelium (sense of the faithful). It says that church teachings must be accepted by the faithful to be legitimate. That means that the voices of theologians, women religious and other lay Catholics carry significant weight.

The fundamental tension between the bishop’s claim to unchallenged power and the voice of lay Catholics was on full display in 2010, when the US Conference of Catholic Bishops opposed President Obama’s healthcare reform law. That law passed narrowly, a result of support provided by LCWR; NETWORK, a Catholic social justice lobby; and Sister Carol Keehan, president of the Catholic Health Association.

NETWORK—founded by sisters, including members of LCWR, with whom it works closely—originated a petition supporting healthcare reform, which LCWR signed. Unlike LCWR, NETWORK is not under the Vatican’s control. The Assessment allowed the Vatican to go after NETWORK indirectly, criticizing LCWR’s association with the organization and their failure to promote an anti-abortion agenda.

According to the National Catholic Reporter, LCWR made it clear, in meetings with Vatican officials in 2010, that LCWR was not in favor of abortion, but disagreed with the bishops that the healthcare reform law would allow federal funding for abortion and felt they had a “moral imperative” to support a law that would give 30 million previously uninsured people health insurance.

This same tension played out when Sister Carol Keehan backed the Obama compromise to enable women working in religiously affiliated organizations to access birth control without a co-pay, and the bishops opposed it. And it is playing out right now, as Cardinal Timothy Dolan, head of the US Conference of Catholic Bishops, says he finds Obama’s support for same-sex marriage “deeply saddening”—while some leading Catholic theologians and 51 percent of lay Catholics disagree. They are following in the footsteps of Sister Jeannine Gramick, co-founder of New Ways Ministry, who refused decades ago to see homosexual acts as “intrinsically disordered,” as the church proclaims, and rejected Cardinal Ratzinger’s decree that she end her ministry, a CDF order publicly decried by LCWR.

Much work by Catholic feminist theologians has undermined the hierarchy’s claim to absolute authority in matters of faith and morals. Feminist theologians have re-envisioned God. They reject the one-time, one-place, men-only view of revelation. Like Johnson, they see Mary as assertive, autonomous, and strong, her decision to bear the Messiah between her and God. They claim Eve as human, not evil, and hold Adam responsible for his own Fall. They demand an inclusive church and liturgy. They work across faith lines toward a truly ecumenical world.

They claim women’s moral authority, clinging to the fundamental belief in the primacy of conscience. “God gave us free will,” explained the late Sister Margaret Ellen Traxler, a signer of Catholics for a Free Choice’s 1984 petition, published in the New York Times, calling for dialogue in the church on abortion. “Free will is guided by conscience…. A woman will answer to God for one thing: Has she followed her conscience?… It’s nobody’s right to tell her what her conscience said to her.”

How many of the women affiliated with LCWR, NETWORK or the Catholic Health Association accept these and other tenets of feminist theology is unknown. But the groups’ joint efforts to push policies that they believe represent Catholic social teaching, as well as their individual interactions, indicate mutual respect. LCWR gave Keehan their 2011 Outstanding Leadership Award for her “significant role in working for US healthcare reform.” They gave the same award in 2007 to one of the world’s leading Catholic feminist authors, former LCWR president Sister Joan Chittister, who, in 2001, with the support of Benedictine sisters nationwide, refused a Vatican order not to speak at the first international conference on women’s ordination. Sister Elizabeth Johnson spoke at an LCWR event in 2008, a year after she published Quest for the Living God, a book the US bishops last year publicly denounced.

It is no accident that the women condemned for their failures in the Assessment are “especially those involved in theological research, teaching, publishing, catechesis and the use of the means of social communication.” And it’s no surprise that the LCWR speaker singled out by the CDF as a purveyor of “serious theological, even doctrinal errors”—Sister Laurie Brink, an assistant professor at Chicago’s Catholic Theological Union—ventured into what some Christians, perhaps many, see as the most frightening frontier of feminist theology.

In exploring the divergent paths being taken by women religious, Brink in her 2007 LCWR keynote address described the “sojourning congregation,” which “has grown beyond the bounds of institutional religion.” She noted, “The Jesus narrative is not the only or the most important narrative for these women,” and that while “they still hold up and reverence the values of the Gospel,” they also recognize that those values are not the sole province of Christianity. Seeing these women as both courageous and potentially prescient, Brink wonders if they are providing “a glimpse into the new thing that God is bringing about in our midst.” Most provocatively, she asks: “ Who’s to say that the movement beyond Christ is not, in reality, a movement into the very heart of God?”

The CDF took those observations as a “cry for help”—specifically, from an all-male cadre of hierarchs who still cannot summon the leadership to condemn the real sinners in their midst and who failed miserably to protect the children in their care from sodomy, rape and their own indifference.

Observing the work of feminist theologians, Peter Steinfels, co-director of Fordham’s Center on Religion and Culture, came to a very different conclusion. “[O]ver the long run, nothing in Catholic Christianity, like nothing in other forms of Christianity—or in Judaism, Islam, Buddhism, and even Hinduism…will remain untouched by the passage from a patriarchal era to one of female equality,” he wrote in A People Adrift. “[N]o one should be confident about predicting which elements in the great religions will be radically revised, which will be reconfigured, which will remain relatively intact.”

The church fathers are so desperate that they have ordered the archbishop and his two assistant bishops to take over everything from LCWR—revising the community’s rules, planning events, approving speakers, withdrawing unsuitable materials. Chittister minced no words in assessing the Assessment. She told the National Catholic Reporter that it was “immoral,” “demeaning,” and nothing more than an attempt “to control people for one thing and one thing only…for thinking.” She sees rejecting Vatican control and forming an independent organization as the only real option for LCWR.

The organization has given no indication of what it will do next. The board plans to meet from May 29 to June 1. While a spokeswoman told me she highly doubted that any decision will be made at that meeting, they expect to make public statements after the board meets.

That can’t make the hierarchy too happy—any institution that behaves autocratically counts on silence to keep its power. Social change begins with voice. In the church today, those voices for change are loud and unrelenting. And they are everywhere—in the pews, in the public square, and deep in the hearts of the sojourners among us.

There is nothing the hierarchy can do about that: you can’t stop an echo.

Editor’s Note: An earlier version of this piece incorrectly stated that Sister Elizabeth Johnson was the first woman to earn a PhD at Catholic University. In fact, she was the first woman to earn a PhD in the Department of Theology. The correction has been made above.