Last fall, emails revealed that scientists at the Climatic Research Unit at the University of East Anglia in England and colleagues in the U.S. and around the globe deliberately distorted data to support dire global warming scenarios and sought to block scholars with a different view from getting published. What does this scandal say generally about the intellectual habits and norms at our universities?

This is a legitimate question, because our universities, which above all should be cultivating intellectual virtue, are in their day-to-day operations fostering the opposite. Fashionable ideas, the convenience of professors, and the bureaucratic structures of academic life combine to encourage students and faculty alike to defend arguments for which they lack vital information. They pretend to knowledge they don't possess and invoke the authority of rank and status instead of reasoned debate.

Consider the undergraduate curriculum. Over the last several decades, departments have watered down the requirements needed to complete a major, while core curricula have been hollowed out or abandoned. Only a handful of the nation's leading universities—Columbia and the University of Chicago at the forefront—insist that all undergraduates must read a common set of books and become conversant with the main ideas and events that shaped Western history and the larger world.

There are no good pedagogical reasons for abandoning the core. Professors and administrators argue that students need and deserve the freedom to shape their own course of study. But how can students who do not know the basics make intelligent decisions about the books they should read and the perspectives they should master?

The real reasons for releasing students from rigorous departmental requirements and fixed core courses are quite different. One is that professors prefer to teach boutique classes focusing on their narrow areas of specialization. In addition, they believe that dropping requirements will lure more students to their departments, which translates into more faculty slots for like-minded colleagues. By far, though, the most important reason is that faculty generally reject the common sense idea that there is a basic body of knowledge that all students should learn. This is consistent with the popular campus dogma that all morals and cultures are relative and that objective knowledge is impossible.

The deplorable but predictable result is that professors constantly call upon students to engage in discussions and write papers in the absence of fundamental background knowledge. Good students quickly absorb the curriculum's unwritten lesson—cutting corners and vigorously pressing strong but unsubstantiated opinions is the path to intellectual achievement.

The production of scholarship also fosters intellectual vice. Take the peer review process, which because of its supposed impartiality and objectivity is intended to distinguish the work of scholars from that of journalists and commercial authors.

Academic journals typically adopt a double blind system, concealing the names of both authors and reviewers. But any competent scholar can determine an article's approach or analytical framework within the first few paragraphs. Scholars are likely to have colleagues and graduate students they support and whose careers they wish to advance. A few may even have colleagues whose careers, along with those of their graduate students, they would like to tarnish or destroy. There is no check to prevent them from benefiting their friends by providing preferential treatment for their orientation and similarly punishing their enemies.

That's because the peer review process violates a fundamental principle of fairness. We don't allow judges to be parties to a controversy they are adjudicating, and don't permit athletes to umpire games in which they are playing. In both cases the concern is that their interest in the outcome will bias their judgment and corrupt their integrity. So why should we expect scholars, especially operating under the cloak of anonymity, to fairly and honorably evaluate the work of allies and rivals?

Some university presses exacerbate the problem. Harvard University Press tells a reviewer the name of a book manuscript's author but withholds the reviewer's identity from the author. It would be hard to design a system that provided reviewers more opportunity to reward friends and punish enemies.

Harvard Press assumes that its editors will detect and avoid conflicts of interest. But if reviewers are in the same scholarly field as, or in a field related to that of, the author—and why would they be asked for an evaluation if they weren't?—then the reviewer will always have a conflict of interest.

Then there is the abuse of confidentiality and the overreliance on arguments from authority in hiring, promotion and tenure decisions. Owing to the premium the academy places on specialization, most university departments today contain several fields, and within them several subfields. Thus departmental colleagues are regularly asked to evaluate scholarly work in which they have little more expertise than the man or woman on the street.

Often unable to form independent professional judgments—but unwilling to recuse themselves from important personnel decisions—faculty members routinely rely on confidential letters of evaluation from scholars at other universities. Once again, these letters are written—and solicited—by scholars who are irreducibly interested parties.

There are no easy fixes to this state of affairs. Worse, our universities don't recognize they have a problem. Instead, professors and university administrators are inclined to indignantly dismiss concerns about the curriculum, peer review, and hiring, promotion and tenure decisions as cynically calling into question their good character. But these concerns are actually rooted in the democratic conviction that professors and university administrators are not cut from finer cloth than their fellow citizens.

Our universities shape young men's and women's sensibilities, and our professors are supposed to serve as guardians of authoritative knowledge and exemplars of serious and systematic inquiry. Yet our campuses are home today to a toxic confluence of fashionable ideas that undermine the very notion of intellectual virtue, and to flawed educational practices and procedures that give intellectual vice ample room to flourish.

Just look at Climategate.

Mr. Berkowitz is a senior fellow at Stanford University's Hoover Institution.