TEMPO.CO, Jakarta - When the National Counterterrorism Agency (BNPT) declared that at least 19 pesantren (Islamic boarding schools) showed evidence of teaching radical thought, we realized just how critical the situation had become. Those 'radical' schools can be found in Jakarta, Cirebon, Ciamis, Cilacap, Solo, Lamongan, Aceh, Makassar, Poso and North Lombok.

Statistically, the figure is almost meaningless, given that some 28,000 pesantren can be found throughout the nation's 33 provinces, attended by about four million Islamic students. However, radicalism-particularly of the kind that has hardened and manifested itself in terrorism-is not just a matter of statistics. Its scope is difficult to grasp, particularly when it is most likely infused with flammable factors such as social injustice.

It is truly worrying when intolerance turns to violence, as it has over the past decade. Just last year alone, for example, authorities recorded 119 violations of freedom of religion and faith, a 23-percent increase over 2014. Radical elements forcibly dispersed a number of activities allowed under constitutional freedom-of-expression provisions-all under the noses of law enforcers.

Going to pesantren with the sole purpose of seeking out the roots of intolerance and radicalism would not be appropriate. The 19 pesantren suspected of teaching radicalism-if it is proven to be so-cannot be made a scapegoat for every act of violence and intolerance occurring in this country.

Take the Sidogiri Pesantren at Pasuruan, East Java, believed to be Indonesia's first Islamic boarding school. Since its establishment more than two centuries ago, it has never been dissociated from earthly issues, despite its dominant dedication to religious teaching. A number of studies on pesantren, which began to mushroom in the early 1970s, have shown how this school almost always, in one way or another, got involved in the ebb and flow of the country's politics, in particular during the struggle for independence and in ensuing conflicts.

As such, to hope for truly 'sterile' pesantren would be close to futile. Religious Affairs Minister Lukman Hakim Saifuddin reminded us last year of a pesantren somewhere in Java that taught the so-called 'Pesantren Trilogy': covering all aspects of education, religion and social studies.

The involvement of the pesantren in social dynamics in fact reinforces its position and role in the midst of the community. In reality, a tiny indigo blue point staining the sea of pesantren milk is just how the BNPT characterized them and how they need to be reviewed and studied again.

We can still find pesantren teaching the spirit of tolerance and religious diversity in every corner of the country, spreading the message of peace across the Muslim world and the need for a life of true togetherness.

Observe, for example, the Al-Mahrusiyah Pesantren at Lirboyo in Kediri, East Java. Established in 1910, today it is led by Kiai Haji Reza Ahmad Cahid, 36, a third-generation student. Reciting the Qur'an in serenity is the unique trait of this pesantren, located two kilometers from the western bank of the Brantas River.

About 1,000 students and scholars attend Al-Mahrusiyah, not taking into account hundreds of other students who are enrolled at the neighboring and like-minded Hidayatul Mubtadi'ein and Ar-Risalah Pesantren.

From the start, these three pesantren taught tolerance and the value of diversity. The founders easily made friends with all members of society, including non-Muslims. They organize events, often around Islamic holidays, which attract visitors from non-Muslim communities.

The religious affairs ministry has noted that besides Al-Mahrusiyah, there are other similar pesantren in West Java and East Nusa Tenggara that are also open to teaching tolerance and the importance of religious diversity. They see little threat to their existence from radical thought.

In other words, in the world of pesantren, the sky has yet to fall. Noble values of humanity and diversity will remain protected and fostered with serenity, not by threats or by violence. (*)

Read the full story in Tempo English Magazine Special Eid al-Fitr Edition