The university I lead has existed for more than four centuries and has witnessed the rise and fall of political orders. I have not, but I work every day in an institution that preserves those changes in its archives, statutes and culture of debate. The conditions that make knowledge trustworthy—including independent peer review, transparency about methods and data, and the ability to revise earlier research—are changing in ways that strike at the heart of the university’s purpose.

Academic freedom and independent research are under pressure in a growing number of countries. The familiar tools of quiet diplomacy, domestic negotiation and isolated warnings are no longer keeping pace with the changes. Over the past decade, governments have narrowed the space for independent evidence in several ways.

In the United States, changes to research-funding structures and programme priorities in areas such as climate science and gender studies, alongside the sidelining of environmental and public-health expertise, have shown how quickly political decisions can affect the systems that produce independent evidence (see below) go.nature.com/4hgg3ym and go.nature.com/4zzmtur). The European academic community has expressed concern in a public statement about pressures facing US science and international cooperation^1–2 (see also go.nature.com/4a3pn9s).

In Hungary, a legal campaign targeting foreign higher-education institutions led Central European University in Budapest to relocate to Vienna in 2019. In 2020, the Court of Justice of the European Union ruled that the legal changes were inconsistent with EU law.^4,5 Although Hungary’s political situation has changed since then, the legal instruments used—and the resulting damage to institutional autonomy and academic freedom—remain.

Elsewhere, grant language is being rewritten to direct funding towards favoured themes such as economic competitiveness, innovation and national security. Access to public data in sensitive areas such as climate and health is decreasing. Researchers are adjusting their proposals accordingly, sometimes avoiding or adding particular topics and terms to improve their chances in the next funding round.

Although the details vary, this pattern is familiar to many people working in universities. When governments and funders intervene in universities, do they strengthen or weaken the safeguards that make knowledge trustworthy?

Others have already warned independent investigators about these threats^1,2,6. Here, I translate these concerns into principles that can guide practical decisions in the difficult situations academics face. They can be used to assess measures affecting universities and apply equally to governments, funders and university leaders.

These principles are intended for people who must decide, often under time pressure, where the legitimate operation of publicly funded systems ends and interference with independent knowledge begins. They concern both the freedom of academics to pursue questions wherever the evidence leads and the ability of universities to protect research from undue influence. Although these are separate responsibilities, they are connected: pressure on one often weakens the other.

The first three principles explain why independent inquiry must be protected and how that protection is rooted in the core mission of universities. The final three indicate when that protection should be balanced against other legitimate concerns.

1. Protect academic freedom to produce reliable knowledge

Universities have a responsibility to produce reliable knowledge of lasting public value and to teach students how to think with that knowledge—including those who will never enter a lecture hall. Academic freedom is the working condition that makes this possible.

I learned this from supervisors who allowed me to ask awkward questions and from students who challenged me in seminars. Universities are primarily responsible for the quality and integrity of the knowledge they produce and teach. Academic freedom is one way they fulfil that responsibility.

Discussions about academic freedom often begin with rights and then describe responsibilities as limitations. I prefer to reverse that order. Universities are primarily responsible for the quality of the knowledge they create and communicate. Academic freedom and institutional autonomy are conditions for doing this properly.

When research is influenced by political or commercial pressure, those pressures affect the questions asked, the methods selected and the results presented.^7,8 Education that foregrounds political directives trains students to adapt their thinking to approved answers rather than testing arguments against disciplinary standards (see go.nature.com/4a3pn9s).

External direction that determines in advance which questions may be asked or which answers are acceptable reduces the scope for questioning assumptions and correcting mistakes. When the people who produce and teach knowledge can no longer work independently, their ability to correct one another—and to challenge those in power—gradually disappears.

Quality is often cited as the main reason to protect academic freedom. It is also frequently used to justify restrictions. Some governments have reduced universities’ independent research capacity in the name of quality, integrity, balance or public safety, presenting intervention as a way to protect academic standards. What matters is how knowledge is actually produced, whether others can see and test the work, and whether it remains reliable over decades.

Measures that genuinely improve knowledge make it easier to confirm and challenge methods and results. By contrast, changing grant applications to favour certain answers, screening researchers for their opinions and taking uncomfortable data offline weakens scrutiny and limits what society can learn from existing research. The test is whether a measure strengthens independent oversight and, as a result, universities’ ability to fulfil their responsibilities to society.

2. Protect valuable research questions that cannot be predicted in advance

Curiosity-driven research often leads to applications that nobody could have predicted. If we limit the questions researchers may pursue in advance, we also limit the future that science can open up.

Many applications began with research whose value was not immediately apparent. Research into how bacteria protect themselves from viruses led to CRISPR gene editing, which is now the basis of treatments for sickle-cell disease. Research in linguistics and digital humanities helped build translation tools and search systems. Longitudinal epidemiological cohort studies underpin public-health guidance on smoking, diet, workplace safety and environmental exposures. Decades of research into messenger-RNA delivery and lipid nanoparticles became the platform for a COVID-19 vaccine when the world needed one. None of these projects would necessarily have scored highly against narrow definitions of immediate social relevance.

Major U.S. scientific committees are being abolished and others are becoming less open

Research needs to address societal challenges, but funding systems must also leave room for questions whose value cannot yet be identified. Narrow relevance criteria tend to reward safe, incremental projects and steer researchers towards lower-risk investigations. Open-ended research matters because scientists cannot know in advance which questions will become important.

Governments that want to base policy on solid knowledge depend on research systems that can independently generate and test that knowledge. Cutting public investment in basic research may reduce spending in the short term, but it transfers costs into the future through missed treatments, weaker prevention, lost innovation and a reduced ability to respond when the next crisis arrives. The test is whether a measure unduly narrows the range of questions that researchers can still ask.

3. Treat universities as democratic infrastructure

Universities decentralize power by training experts who can question official decisions, providing analysis that challenges government and corporate claims, and placing independent expertise in courts, the media and public forums. Together with the executive, legislative and judicial branches, a free press and civil society, universities form part of the infrastructure of democracy, human rights and the rule of law. When that broader structure is weakened, universities are usually affected as well.

Hungary illustrates how this can happen. From 2017 to 2019, Viktor Orbán’s government reduced the independence of universities and research institutes by transferring control of research funding from the National Academy of Sciences to a new research network. Its board of directors is chaired by a government-appointed ministerial nominee. The government used the Higher Education Act to force Central European University abroad and, through parallel legal reforms, brought courts, the press and civil society under tighter political control.⁴

Elsewhere, earmarked funds, new laws governing cooperation, politicized board appointments and sustained public attacks on expertise point in a similar direction. Academic-freedom watchdogs and national reports across the world and the European Union document examples of these trends.^9–11

Even when dramatic events occur overseas, academic freedom is not automatically secure at home. In the Netherlands, the National Academies warned in 2025 that deep budget cuts would increase pressure to shift from independent research to contract research. They also warned that proposed knowledge-security review laws could limit researchers’ freedom to choose collaboration partners. Researchers documented self-censorship after being threatened in public forums.¹² That year, Dutch university presidents also warned of a growing political tendency to guide scientific debate and educational content (see go.nature.com/3v3ktjj).

Institutional autonomy means being accountable to the public for the quality and integrity of knowledge, rather than being accountable to governments for the political acceptability of conclusions. The framework of rules and responsibilities is not itself the problem. Many rules protect people, ensure workplace safety and safeguard public funds. Problems arise when control shifts from universities to ministries through the cumulative effects of funding conditions, reporting requirements and rules governing collaboration. One form of accountability strengthens independent knowledge. The other replaces it with political acceptability.

4. Treat research security and academic openness as connected responsibilities

Claims about academic freedom are closely linked to concerns about research security. The risks of espionage, intellectual-property loss and the harmful use of confidential knowledge are real, and universities cannot ignore them.

At the same time, security measures designed without considering academic freedom can unintentionally narrow independent investigation. They can also place greater control in the hands of those who control access to data, infrastructure and international cooperation.

Scientists fight back against far-right plan to restrict academic freedom in Germany