Most members of the educated public probably think of America’s greatest universities in terms of undergraduate and professional education—in terms of teaching and the transmission of knowledge rather than the creation of new knowledge. This point of view is completely understandable. They are concerned about the education of their children and grandchildren or relate to their own educational experience.

But what has made American research universities the greatest in the world has not been the quality of their undergraduate education or their ability to transmit knowledge, as important as that is. Instead, it’s been their ability to fulfill one of the other central missions of great universities: the production of new knowledge through discoveries that change our lives and the world.

The teaching of undergraduate and graduate students is critically important and an integral part of the mission of great universities; some do this very well, others in a less distinguished manner. In many ways, such teaching is the faculty member’s first calling. At least at the graduate level, many of the great research discoveries are produced through a collaboration between a faculty member and her students. At the undergraduate level, there is, in fact, contrary to popular belief, a modest positive association between the quality of a professor’s research and the assessed quality of her teaching. But, the fulfillment of the undergraduate teaching mission is not what has made America’s universities the best in the world.

When educated Americans think of their best universities, they probably don’t think that lasers, FM radio, magnetic resonance imaging, global positioning systems, bar codes, the algorithm for Google, the fetal monitor, the nicotine patch, antibiotics, the Richter Scale, Buckyballs and nanotechnology, the discovery of the insulin gene, the origin of computers, of bioengineering through the discovery of recombinant DNA, transistors, improved weather forecasting, cures for childhood leukemia, the pap smear, scientific agriculture, methods for surveying public opinion, the concept of congestion pricing, human capital, or “the self-fulfilling prophecy” all had their origins in the country’s research universities. Even the electric toothbrush, Gatorade, the Heimlich maneuver, and Viagra had their origins at these great universities. These institutions have become the engines of innovation and discovery that now drive a large part of the economic growth and social change in the United States.

Of course, there are other great universities in Europe and Asia, but there is arguably no system of higher learning that matches that in the U.S.—as determined by the number of Nobel Prize winners it’s produced (350-plus), the impact of its discoveries, the multiple international rankings that have American research universities at about 75 percent of the top 50 institutions and about 60 percent of the top 100. What, then, has made these universities the envy of the world? And how, in less than 75 years, have they become the preeminent backbone of higher education internationally—the place where many of the brightest and most able young people want to attend and work?

The American research university was born a century after the American Revolution, when Johns Hopkins University opened its doors in 1876. It was an amalgam of the British Oxbridge undergraduate system and the German emphasis on research; Hopkins’s focus on inquiry and experimentation drew the attention of some of the late 19th century’s great academic minds—people like Henry A. Rowland, who became the first president of the American Physical Society. America’s research universities, even in their early years, were far more open and democratic than their European counterparts.

Perhaps more importantly, the system was, from the beginning, fiercely competitive. Even in its neonatal state it represented the beginning of academic free agency; it was always competing with other institutions to be the best. The renowned Columbia University physicist I.I. Rabi in the 1930s said that the United States had young people as talented as any in the world, but that it lacked the established leadership found at great German, English, and French universities. As it turned out, the nightmare that was created by Hitler’s National Socialism represented, ironically, a boom for American research universities. The migration of Jews and others at risk in Europe—including intellectuals in virtually all fields—propelled the American higher-education system forward.

When this talent was combined with the internalization of the extraordinary value system that derived from the science revolutions of 17th-century England, the United States created the foundation on which great research universities could be built. Those core values included meritocracy; organized skepticism (the willingness to entertain the most radical of ideas, but subject the claims to truth and fact to the most rigorous scrutiny); the creation of new knowledge; the belief that discoveries should be available to everyone and that those that make discoveries should not profit from them; the peer-review system that relies on experts to judge the quality of proposed research that’s seeking funding; and academic freedom and free inquiry, without which no great university can be established. These values became part of the culture of America’s great research universities.

To be sure, these were ideals that have yet to be reached. Some of these values have, in fact, eroded over the past 25 years with the increased commodification of the university and the desire by universities and their faculty members to gain income from things like patented discoveries and from contracts with business that want to be associated with a university’s football or basketball team. But essentially, these values have represented the foundation on which these universities have been built.

Add to these values the implementation after World War II of the most enlightened federal science policy that the world has ever produced—one that used taxpayer money to fund research; that outsourced the work to the great universities on a competitive basis; that linked research and teaching by concentrating the training of advanced students with laboratory work with a leading professor; that produced funding for veterans to return to school and to those who could not afford college without financial aid; and that granted great autonomy to universities in exchange for the production of new discoveries, increased human capital, and more enlightened citizens—then you have some of the conditions that led to the international preeminence of the American research-university system.

Looking at the people who live in this community of scholars offers perhaps the best way to convey how research, combined with teaching, is the principal determinant of a university’s greatness. Take Bonnie Bassler, a molecular biology professor working with students from around the world who’s doing fundamental science at an extremely high level in her laboratory at Princeton University. She is charismatic and has won almost every prestigious award a scientist can hope for. Bassler works with bacteria that can cause lethal diseases such as anthrax, and her goal, of course, is to make fundamental discoveries that will lead to cures or treatments for these diseases.

She wants to develop molecules that will act as antimicrobial drugs aimed at bacteria that can cause lethal diseases. It turns out that these lethal bacteria are impotent against the human immune system when they attack it alone—but they have the ability to talk to each other (chemically), to strategize, and to attack the immune system at its weakest point. When they attack in great numbers, they can overwhelm a human’s immune system; Bassler and her students and colleagues want to find a way to stop the bacterial from “talking.”

Bassler is, of course, only one of thousands of extraordinarily talented scientists in America’s research universities who train a multinational group of students—who effectively become their extended family members—in how to conduct the research necessary to make profound discoveries. She and other world-class scientists and engineers and humanists show just how deeply embedded teaching is in the research function of America’s great universities. Postdoctoral fellows, graduate students, and occasionally undergraduates are learning through doing—they are rubbing minds with some of the most original thinkers of the era. Even if this is not the teaching that the public hears most about, it is going on in abundance at the country’s major universities, and accounts for the research discoveries and innovations that they’re spearheading. Moreover, these research communities have become even more important amid the demise of so many prominent industrial research laboratories, such as the Bell Labs or Xerox laboratories.

Yet all of this research potential is now at risk. Academic freedom and free inquiry are under attack from many political leaders who endorse anti-science positions and who interfere with the relative autonomy of these institutions. The compact between the federal government and the universities is frayed, with weakening trust on both sides leading to thousands of federal government regulations, the stagnation of research budgets, unnecessary controls on research,  false claims that the universities are bilking the taxpayer, and, ultimately, the loss of American supremacy in some important research areas.

The universities, looking for new sources of revenue while competing for students and faculty, are increasingly becoming commodities—businesses to be run. Visa policies are far too restrictive—preventing unusual and creative talent from staying in the United States and working at its distinguished postsecondary institutions. There are few great, outspoken, and courageous higher-education leaders who have a vision for the future and the capacity to introduce significant change at their institutions. There are even fewer leaders who have “quitting issues”— who would be willing to resign when others undermine his or her core values. These threats represent real challenges for American universities’ continued preeminence and to the character of these great institutions of higher learning.