I. The Specimen and the Interlocutor
The university studies Islam. It does not, as a rule, think with it.
There is a revealing asymmetry at the heart of the modern research university’s relationship with the Islamic intellectual tradition.
The distinction is not trivial. To study a tradition is to treat it as an object of inquiry: to place it under the lens, to analyse its structures, to situate it within comparative frameworks, and to produce knowledge about it that meets the standards of the institution conducting the study. To think with a tradition is something different. It means accepting the tradition as an intellectual interlocutor, a body of thought that might have something to say about the questions the institution itself is asking, including questions about the nature of knowledge, the purpose of education, and the relationship between understanding and the formation of character.
The modern research university is superbly equipped for the former. Its departments of Islamic studies, Middle Eastern studies, and religious studies produce scholarship of genuine quality. Its library systems preserve and make accessible an extraordinary archive of Islamic texts. Its graduate programmes train researchers who can navigate the classical sources with philological precision. None of this is in question.
What is in question is whether this institutional architecture can accommodate the Islamic tradition as a living intellectual enterprise rather than a historical deposit. The architecture of the modern university is not neutral. It encodes specific commitments about what knowledge is, how it is properly produced, and what its purpose consists in. Those commitments, forged in the specific historical experience of the European Enlightenment, include the separation of fact from value, the organisation of knowledge into autonomous disciplines, and the treatment of the researcher as a disinterested observer whose personal formation is irrelevant to the quality of the knowledge produced.
The Islamic intellectual tradition does not share these commitments. It holds that knowledge and ethics are inseparable, that the different branches of learning form a hierarchically ordered whole rather than a collection of autonomous disciplines, and that the character of the knower is constitutive of the quality of the knowledge produced. An institution built on the first set of commitments can study a tradition built on the second. It cannot think with it. The architecture does not permit it.
II. The Structural Problem: Why Inclusion Is Not Enough
The standard response to this asymmetry within the modern university is inclusion. Add more Islamic content to the curriculum. Hire more Muslim scholars. Fund more research on Islamic topics. Create centres and institutes devoted to the study of the Muslim world. The assumption is that the institution’s architecture is capacious enough to accommodate any intellectual tradition, provided sufficient resources are allocated to it.
This assumption is mistaken, and it is mistaken for structural rather than contingent reasons. The issue is not that the university devotes insufficient attention to Islamic thought. It is that the terms on which attention is granted are themselves the problem.
Consider the standard doctoral programme in Islamic philosophy at a leading Western university. The student will learn to read Arabic and Persian at a high level. She will acquire a detailed knowledge of the major philosophical texts. She will be trained in the methods of historical contextualisation, textual analysis, and comparative philosophy. She will produce a dissertation that makes an original contribution to the scholarly literature.
What she will not be expected to do is to take any of the philosophical positions she studies seriously as live options for her own thinking. She may write a brilliant study of Mulla Sadra’s theory of consciousness without ever being asked whether she thinks Sadra was right. She may produce a definitive analysis of al-Farabi’s account of the virtuous city without ever being asked whether that account has implications for how she thinks about political life in the present. The tradition is studied. It is not engaged as a source of answers to questions the scholar herself is asking.
This is not a failure of individual scholars, many of whom do take the traditions they study seriously as intellectual resources. It is a structural feature of the institution. The modern university’s assessment systems, promotion criteria, and methodological standards are designed to evaluate scholarly competence, not intellectual engagement with the truth claims of the traditions studied. A scholar who announced that she was not merely studying al-Farabi but reasoning from within the Farabian tradition would not be penalised for incompetence. She would be reclassified: from scholar to believer, from analyst to advocate, from the department of philosophy to the department of theology, or, more likely, to a confessional institution outside the university system entirely.
III. The Institutional Counterfactual: What Exists Beyond the Research University
The argument that the modern university cannot accommodate the Islamic tradition as a living enterprise is not a counsel of despair. It is an invitation to look at institutional forms that can.
The Muslim world possesses a remarkable diversity of educational institutions that operate on fundamentally different architectural principles from the research university. The most significant of these, for the purposes of this essay, is the pesantren tradition of Indonesia, and specifically the case of Ma’had Aly Lirboyo in East Java.
Ma’had Aly Lirboyo is a higher-level Islamic seminary within the pesantren system. It is worth attention not because it is perfect or because it should be replicated wholesale, but because it represents a functioning institutional model that does what the modern university structurally cannot: it thinks with the Islamic tradition rather than about it, and it has done so while achieving formal recognition within the Indonesian higher education system (Ubaidila, Sulaeman, and Khamim 2025).
The pesantren system, which educates millions of students across Indonesia, operates on principles that directly contradict the architectural assumptions of the modern research university. Knowledge is not separated from character formation. The relationship between teacher and student is not functional but formative: the teacher transmits not merely information but a way of knowing, and the student’s personal development is understood as integral to, not separate from, academic achievement. The curriculum is organised around classical texts rather than around disciplinary boundaries, and the method of instruction, including the practices of sorogan (individual recitation to the teacher) and bandongan (collective study of classical texts), preserves the chain of scholarly transmission that the Islamic tradition understands as the condition for genuine knowledge.
What makes Lirboyo particularly instructive is its response to the social and political crises of contemporary Indonesia. When sectarian tensions threatened to destabilise Indonesian society in the mid-2010s, Lirboyo did not import Western liberal theories of pluralism to address the crisis. It developed a curriculum of national jurisprudence, drawing on the classical tradition of Islamic legal reasoning to construct a framework for civic coexistence that was rooted in the tradition’s own resources rather than translated from external sources (Ubaidila, Sulaeman, and Khamim 2025). The tradition was not studied as a historical artefact. It was deployed as a living resource for addressing a contemporary problem.
The institutional evidence is suggestive. Between 2017 and 2024, Lirboyo’s student enrolment grew from approximately one thousand to over four thousand, and its faculty nearly doubled (Ubaidila, Sulaeman, and Khamim 2025). This growth occurred not because the institution adopted the metrics of the modern university but because it demonstrated a form of educational excellence that the modern university cannot replicate: the integration of intellectual formation with personal and ethical development, in a community that takes the Islamic tradition seriously as a source of answers to questions that matter.
IV. The Three Axes of Islamic Knowledge
To understand what the pesantren model preserves that the modern university has lost, it is necessary to describe the epistemological framework within which the Islamic tradition understands knowledge to operate. That framework can be characterised in terms of three axes of inquiry, each of which corresponds to a different mode of knowing and a different relationship between the knower and the known.
The first axis is textual: the disciplined study of the primary sources, including the Quran, the hadith literature, and the classical works of jurisprudence, theology, and philosophy. This is the dimension of knowledge that the modern university handles most competently, through its philological methods and its commitment to textual precision. But in the classical tradition, textual study is not an end in itself. It is the foundation upon which the other two axes depend.
The second axis is rational: the use of demonstrative reasoning, logical analysis, and systematic argumentation to extend the insights of the textual tradition into new domains. This is the mode of inquiry that produced the great philosophical and scientific achievements of Islamic civilisation, from al-Farabi’s political philosophy to Ibn al-Haytham’s optics. The modern university also handles this dimension competently, though it tends to evaluate the results of Islamic rational inquiry by the standards of Western philosophy rather than by the tradition’s own criteria of rigour.
The third axis is experiential: the dimension of knowledge that arises from the cultivation of the inner life, from spiritual discipline, and from the direct apprehension of realities that conceptual reasoning can point toward but cannot fully capture. This is the dimension that the modern university is structurally unable to accommodate, because it falls outside the boundaries of what the Enlightenment’s epistemological settlement recognises as knowledge. It is the dimension that the tradition of Sufi thought, the illuminationist philosophy of Suhrawardi, and the transcendent philosophy of Mulla Sadra all address with sustained rigour and, in the best cases, extraordinary sophistication.
The pesantren model integrates all three axes. The student’s engagement with classical texts is accompanied by rational training in the methods of jurisprudential and philosophical reasoning, and by practices of spiritual formation that are understood as conditions for genuine understanding rather than as extracurricular activities. The modern research university integrates the first two axes, with varying degrees of success, and excludes the third entirely.
The exclusion is not arbitrary. It follows necessarily from the institutional commitments described above: the separation of fact from value, the treatment of the researcher as a disinterested observer, and the reduction of knowledge to what can be publicly verified by methods indifferent to the character of the knower. Within these commitments, experiential knowledge is not knowledge at all. It is personal conviction, religious experience, or subjective preference: categories that the university may study but cannot participate in without violating its own foundational assumptions.
V. The Question of Scale
An obvious objection to the argument presented so far is the question of scale. The pesantren model, for all its merits, serves a specific cultural context. Can it be generalised? Can it produce the engineers, physicians, and policymakers that Muslim-majority societies need? Can it engage with the questions of artificial intelligence, environmental crisis, and global governance that define contemporary intellectual life?
These are legitimate questions, and they deserve serious rather than dismissive answers.
The answer is not that the pesantren model should replace the modern university. It is that the pesantren model demonstrates an architectural principle that the modern university has lost and that any institution aspiring to think with the Islamic tradition, rather than merely about it, must recover: the principle that knowledge, character, and purpose are not three separate things but aspects of a single formative process.
This principle can be instantiated in many different institutional forms. A medical school that teaches anatomy and pharmacology with the same rigour as any Western institution, but that embeds clinical training within a framework of ethical formation rooted in the Islamic tradition’s account of the sanctity of life and the responsibilities of the healer, would be thinking with the tradition. A law faculty that teaches comparative jurisprudence and international law with full technical competence, but that grounds its curriculum in the tradition’s understanding of justice as a cosmic rather than merely procedural value, would be thinking with the tradition. A programme in artificial intelligence that develops technical capacity at the highest level, but that situates that capacity within the tradition’s sustained reflection on the nature of the intellect and its relationship to consciousness, would be thinking with the tradition.
In each case, the integration is not a matter of adding Islamic content to a secular curriculum. It is a matter of reorganising the curriculum around a different set of architectural principles: principles that hold knowledge and formation together rather than treating them as separate domains.
VI. From Sovereignty to Practice
The concept of epistemic sovereignty, invoked frequently in contemporary discussions of decolonisation, is useful but insufficient. Sovereignty implies autonomy: the capacity of a tradition to generate knowledge from within its own resources rather than waiting for external validation. But sovereignty without practice is a slogan. The question is not whether the Islamic intellectual tradition deserves epistemic sovereignty. Of course it does. The question is what epistemic sovereignty looks like when it is actually practised, in institutions, with students, on a Tuesday afternoon.
The pesantren tradition offers one answer. The hawza system of Shi’i seminary education offers another. The surviving networks of traditional scholarship in West Africa, in the Indo-Pakistani subcontinent, and in Central Asia offer still others. These institutions are not perfect. Many struggle with inadequate funding, institutional rigidity, and insufficient engagement with contemporary intellectual questions. But they possess something that the modern university, for all its resources, does not: an architecture that holds knowledge and formation together, and a living tradition of teacher-student transmission that cannot be replicated by any technology, however sophisticated.
The task for the present generation of Muslim scholars and institution-builders is not to choose between these models and the modern university. It is to learn from both. The modern university’s commitment to textual precision, methodological rigour, and open inquiry is genuinely valuable, and any institution that abandons it in the name of tradition will produce not wisdom but obscurantism. The traditional institution’s commitment to the integration of knowledge and character, to the formative relationship between teacher and student, and to a conception of knowledge that is oriented toward purposes larger than individual career advancement is equally valuable, and any institution that abandons it in the name of modernity will produce not scholars but technicians.
The university unbound is not the university destroyed. It is the university liberated from the assumption that its current architectural form is the only possible one, and opened to the possibility that a tradition which has been thinking about knowledge, its nature, its purpose, and its relationship to the human person for fourteen centuries might have something to contribute to the question of how institutions of learning should be designed.
That contribution will not be made by studying the tradition from outside. It will be made by thinking with it from within.
Bibliography
al-Attas, Syed Muhammad Naquib. 1980. The Concept of Education in Islam: A Framework for an Islamic Philosophy of Education. Kuala Lumpur: Muslim Youth Movement of Malaysia.
Alatas, Syed Farid. 2024. “The Coloniality of Knowledge and the Autonomous Knowledge Tradition.” Sociology Compass 18, no. 8. https://doi.org/10.1111/soc4.13256.
Lumbard, Joseph E. B. 2024. “Islam and the Challenge of Epistemic Sovereignty.” Religions 15, no. 4: 406. https://doi.org/10.3390/rel15040406.
MacIntyre, Alasdair. 2009. God, Philosophy, Universities: A Selective History of the Catholic Philosophical Tradition. Lanham: Rowman and Littlefield.
Ubaidila, Sulaeman, and Khamim. 2025. “Decolonization of Islamic Education and Efforts to Achieve Academic Independence: A Case Study of Ma’had Aly Lirboyo.” Tribakti: Jurnal Pemikiran Keislaman 36, no. 1.
Woodward, Mark. 2025. “Paradigms, Models, and Counterfactuals: Decolonializing the Study of Islam in Indonesia.” Studia Islamika 32, no. 1: 101–135. https://doi.org/10.36712/sdi.v32i1.46005.