It took the U.S. Commission on Civil Rights three years to produce its report on religious freedom and non-discrimination. With 27 pages, more than 1000 days of work, and 200-some additional pages of commentary, the document essentially amounts to this: Legal scholars have no idea how to resolve the government’s conflicting obligations to allow free religious exercise and protect minority groups from discrimination. Ultimately, legal language is not sufficient to resolve ultimate conflicts over belief and identity. Legislatures and litigators will have to continue muddling through, finding an imperfect balance between competing cultural norms.

This issue, perhaps more than any other, has been a significant source of recent conflict within the court system. Supreme Court decisions on birth control and gay marriage have highlighted religious dissent on issues of sexuality and gender identity, but recent conflicts have covered everything from the conscience claims of ministers to sectarian town prayer to the rights of religious student groups. Created nearly 60 years ago, the USCCR exists to advise the United States government on civil-rights issues, even though it has no power to enact or enforce any of its findings. But even with a mandate to regularly investigate controversial issues, the Commission stalled out on religious liberty.

“Because the report raises a lot of controversial positions … it took a while for the Commission, as a bipartisan body, to reach any agreement,” said Brian Walch, a spokesman. “It’s a spine-y issue.”

The report is worth reading, if only because it shows how deeply divided the legal community is about religious liberty and civil rights. A majority of Commissioners ultimately found that “religious exemptions to the protections of civil rights based upon classifications such as race, color, national origin, sex, disability status, sexual orientation, and gender identity, when they are permissible, significantly infringe upon these civil rights.”

This is a broad finding, more of an orientation than a guiding legal principle. But it’s easy enough to guess what the commissioners may have had in mind: tax-exempt status for religious colleges and universities that don’t admit LGBT students. Laws that let bakers and other wedding vendors refuse to provide services for same-sex-wedding ceremonies. Court decisions about religious pharmacists who decline to stock certain kinds of birth control in their stores.

Federal and state laws often protect religious groups via these kinds of selective exemptions. But some see these carve-outs as an excuse for discrimination—the Commission’s chair, Martin Castro, argued as much.

“The phrases ‘religious liberty’ and ‘religious freedom’ will stand for nothing except hypocrisy so long as they remain code words for discrimination, intolerance, racism, sexism, homophobia, Islamophobia, Christian supremacy, or any form of intolerance,” he wrote.

The Commission is intentionally designed to be a microcosm of opposing political viewpoints, with four of the representatives appointed by the president, two by the speaker of the House, and two by the president pro tempore of the Senate. But the dissenting comments in the report go beyond mere partisan division.

“The conflict between religious liberty and nondiscrimination principles is profound,” wrote Commissioner Peter Kirsanow. “The passions involved may be fiercer than in any civil rights struggle since the 1960s.” He added that he found in favor of the report only because he “was concerned that a ‘no’ vote from me would be used as an excuse to further delay the report.”

Religious liberty is more fundamental to Constitutional principles than non-discrimination, Kirsanow argued. “Religious liberty is an undisputed constitutional right,” he wrote. “With the exception of racial nondiscrimination principles embedded in the Thirteenth, Fourteenth, and Fifteenth Amendments, nondiscrimination principles are statutory or judicially created constructs.”

Another dissenting commissioner, Gail Heriot, echoed something similar, but in harsher words: “People of faith should not allow themselves to become just another special interest that needs to be appeased,” she said.

“This debate will likely dominate civil-rights discourse for at least a generation.”

But conflicts over religious liberty and non-discrimination also involve two fundamentally different world views, Kirsanow argued.

“The first, which is secularism, holds an individual’s unfettered sexual self-expression as a preeminent concern because it is an aspect of their self-creation,” he wrote. The second, which he purposefully articulates in the language of Christianity, is that “individuals are not their own judge, but rather are subject to divine law and divine judgment. The morality of a person’s conduct does not ultimately depend upon whether he thinks it is right, or whether it accords with his desires, but whether it conforms to divine law.”

This is one, very specific way of framing secular and religious commitments. But his argument suggests that conflicting legal principles are only a small part of religious freedom and non-discrimination fights: Deeply held beliefs about the nature of morality, God, and identity are at stake. As cultural norms around those beliefs have shifted—as LGBT people have become much more accepted, for example—the legal system has struggled to keep up. This is evident in courts’ split over issues like gender identity.

But it’s also clear from the Commission’s recommendations. To summarize, very roughly, it found that “overly-broad religious exemptions” can create problems; that religious exemptions can’t limit the freedom of others; that courts should follow the Supreme Court precedent set in Employment Division v. Smith, which emphasized protection of religious beliefs over religious exercise; that the federal government should consider clarifying its Religious Freedom Restoration Act, the law that many religious groups use to seek exemptions from the law; and that states should clarify their versions of this law, too.

In theory, these are concrete suggestions to improve jurisprudence on religious-liberty conflicts. But in practice, they offer nothing to solve the fundamental challenge at stake in these cases. Sometimes, people’s religious beliefs teach opposition to certain identities.

Most recently, this has included everything from being lesbian, gay, bisexual, or transgender to having pre-marital sex. United States law holds that free expression of religion and identity are both important. There’s no easy formula for pre-determining when each should be given precedence, particularly when they clash in fundamental ways.

These conflicts will continue. As Kirsanow wrote, “This debate will likely dominate civil-rights discourse for at least a generation. And regardless of the outcome, we may emerge a very different country than the one we have been.” Specific cases will be judged against widely varying statutes and bodies of interpretation, and lawyers will continue to wage first-principle battles over the meaning of freedom. The system will remain confused, because the law is but clunky machinery for reconciling opposing world views.