Discussions surrounding what counts as “scientific” are often treated as if they were already settled. In the prevailing imagination—particularly in the wake of what is commonly referred to as the Scientific Revolution—knowledge is equated with objectivity, neutrality, and a presumed detachment from ideological or religious commitments. Within such a framework, an educational institution is deemed “scientific” to the extent that it maintains distance from doctrine, authority, and specific normative orientations.
I recall, during my graduate studies in Philosophy of Religion and Islamic Studies at UIN Sunan Kalijaga, engaging with foundational discussions in philosophy and philosophy of science. I had the privilege of learning from figures such as Prof. Kuntowibisono (UGM), Prof. Mukti Ali—particularly his notion of scientific cum doctrinaire—as well as Dr. Haryatmoko, Prof. Amin Abdullah, Prof. Machasin, Prof. Komaruddin Hidayat, and Prof. Franz Magnis-Suseno.
Yet, when one turns to developments in contemporary philosophy of science, the notion of the “scientific” appears far less straightforward. Thomas Kuhn, for instance, persuasively argues that science never operates in a vacuum; rather, it develops within paradigms—configurations of assumptions, values, methods, and practices shared by particular scientific communities. This insight resonates with Karl Mannheim’s sociology of knowledge, which underscores that all forms of knowledge production—including religious interpretation—are socially and historically situated, and often entangled with ideological and even political interests. From this perspective, it becomes crucial to discern the interplay between ideological, utopian, and contextual dimensions within knowledge claims.
Karl Popper, through his theory of falsification, foregrounds the centrality of critique and refutability, yet he does not require scientists to be entirely detached from their background commitments. Paul Feyerabend goes even further, challenging the very idea of a single, universal standard of scientific method.
These perspectives collectively suggest that the “scientific” cannot be understood as a context-free or value-neutral category. Rather, it is always embedded within historical trajectories, intellectual traditions, and, to a certain extent, systems of value and belief.
Against this backdrop, it becomes both relevant and necessary to reconsider the epistemic status of pesantren (Islamic boarding schools). They are often perceived—whether traditional or modern—primarily as sites of religious transmission or guardians of inherited traditions, rather than as loci of knowledge production in the modern academic sense. The underlying assumption tends to be that their commitment to particular doctrinal frameworks renders them less capable of meeting the criteria of “scientific” inquiry, especially those associated with neutrality and openness to critique.
Such a view is not entirely unfounded. Historically, pesantren have indeed functioned as custodians of the Islamic intellectual heritage (turāth), particularly in theology and jurisprudence. The relationship between kiai (scholars) and santri (students) is often structured around ethical discipline, reverence, and trust. In certain instances, this configuration may limit the development of open, egalitarian spaces for critique, as typically idealized within modern academic discourse.
Nevertheless, to conclude that pesantren are inherently “unscientific,” or have never been part of a scientific enterprise, would be an unwarranted simplification.
Several considerations are in order.
First, pesantren are far from monolithic; they represent a broad and dynamic spectrum. At one end are salaf pesantren, deeply rooted in the study of classical texts, and at the other are modern institutions that have incorporated formal academic curricula, research methodologies, and even scholarly publication. Some have gone further by integrating religious learning with the natural sciences—such as Trensains in Jombang. Coincidentally—or, to borrow a more theological expression, qadarullah, which may not always sit comfortably within conventional scientific language—my own child studies there.
The emergence of such institutions reflects a conscious effort to bridge theological-ethical commitments with scientific inquiry within the pesantren milieu. In recent decades, many pesantren have actively engaged with contemporary intellectual discourses, both through collaborations with universities and through the development of interdisciplinary approaches.
Second, intellectual life within pesantren is not devoid of critical engagement. Traditions such as bahtsul masā’il exemplify processes of deliberation, argumentation, and even contestation among scholars and students. While these practices may differ in form from modern academic discourse, they nonetheless embody a recognizable mode of rational inquiry.
Third, insights from contemporary philosophy of science invite us to reconsider the long-standing assumption that knowledge must be entirely value-free. Muslim thinkers such as Syed Muhammad Naquib al-Attas, Kuntowijoyo, and Amin Abdullah, among others, have proposed integrative frameworks that seek to reconcile knowledge with ethical and spiritual values. Within such perspectives, a commitment to particular values does not inherently undermine scientific validity, provided that rigorous epistemological and methodological standards are upheld.
In light of these reflections, it may be more fruitful not to position “the scientific” and “pesantren” in binary opposition, but rather to revisit the very meaning of the “scientific” itself.
Must scientific inquiry always be value-neutral?
Does rootedness in tradition necessarily preclude innovation?
Or might it be possible to envision a more dialogical and dialectical model of knowledge—one that remains open to critique while still grounded in ethical and cultural traditions?
From this vantage point, pesantren can be understood not merely as sites of indoctrination, but as living traditions—or, in Talal Asad’s terms, discursive traditions—that continue to evolve through ongoing interpretation and engagement. The challenges are evident: expanding spaces for critical inquiry, strengthening methodological rigor, and fostering dialogue across disciplines. Yet it must also be acknowledged that modern academic institutions themselves are not entirely free from bias, interest, or limitation.
Ultimately, this discussion reminds us that the “scientific” is not a fixed or static label—not mabnī ‘alā al-sukūn, to borrow from Arabic grammatical terminology—but rather something dynamic and inflected, mu‘rab, continually negotiated and rearticulated. Pesantren, in all their diversity, are part of this ongoing process—sometimes positioned at a distance, sometimes intersecting, and often offering possibilities for synthesis that remain underexplored.
In closing, one is reminded of the classical scholarly expression, “wa Allāhu a‘lam bi al-ṣawāb” (God knows best what is correct). This phrase reflects not only epistemic humility but also a critical ethical awareness: an acknowledgment of the possibility of error, alongside an openness to revision, validation, and even falsification in light of new evidence and evolving contexts.
Wa Allāhu a‘lam bi al-ṣawāb.