The children in Letterfrack, Co Galway will go to school under the sea this week. As they take their little seats, the Baby and Senior Infants will see sea horses frolicking above their heads. Starfish will pirouette in the distance. Atlantic salmon will shimmer past on their way home from far-off Greenland and Canada and a gigantic Humpback whale will power its way towards the surface, writes Prof Tom Collins

And, as the children's eyes grow wider and wider to capture the mystery of it all, they will learn that, in the underwater silence, they are surrounded by a great orchestra of sound that their ears cannot detect, but by which all sea life manages itself.

These children will have visited Atlantis - a classroom with blacked-out windows, a sliver of light from a roof skylight, and a discarded fishing net draped under the ceiling, from which are suspended an eclectic range of sea-life creations. The teachers, parents and children in the school have created a new world which will unlock the children's imagination and transport them into a wondrous environment.

And when the children leave school in the evening and walk down to the Atlantic shoreline across the road from them, they will look at the sea and know that there is a whole world of life and energy underneath its surface. They will know that because they have been in that world.

These are fortunate children. Their first encounter with schooling will have been captivating and magical. They will have been transformed and enriched by this encounter. They will want to find out and explore more. They will be empowered and affirmed by the experience.

Will they continue to feel empowered and affirmed as they progress through the school system? In 2002 the National Council for Curriculum Assessment (NCCA) commissioned the Economic and Social Research Institute (ESRI) to engage in a longitudinal study of students' experiences of schooling.

To carry out this research, the ESRI accompanied a group of 900 students and their teachers in 12 different schools through their first three years in second-level schooling.

The first-year study, completed in 2003, looked at the experience of moving from primary to post-primary education. The research found that students became less positive about school over the course of their first year, particularly those students in lower streams in schools where streaming was used.

The study found that the second year was a pivotal one for many students. A chasm began to open up between two groups of students. On one side were those students who engaged more with the learning process. These were more likely to be girls, from professional backgrounds and with high academic ability.

On the other side of this divide was a minority of students who were drifting or were more actively disaffected and disengaged from school life. These were more likely to be male, from lower socio-economic backgrounds and often in the lower streams.

This divide crystallised more definitively in third year. While the majority of third-year students reported that they enjoyed school and got on well there, there was a decline in students' positive attitudes towards school over the course of the junior cycle. More than 20 per cent of the students strongly agreed that they did not look forward to going to school. One in 10 felt isolated in school; scared, alone, ignored or friendless.

There is a sense in which this study is merely confirming what every teacher already encounters on a daily basis in the classroom. It is not particularly surprising to find girls out-performing boys; to find working-class boys particularly disenchanted or to find lower streams less engaged in their schooling.

The real value of the study, however, lies in the way in which it casts light on the organisational and pedagogical process in the school which translates the predictable into the actual. The study shows that it is not inevitable that working-class boys, for instance, will under-perform in school. Rather, it draws attention to the kinds of intervention which can on the one hand result in such under-performance and on the other support and sustain student interest and engagement.

Student interest, for instance, is enhanced where teachers explain things clearly and employ a variety of teaching methods such as group work and class discussion, and where a positive, supportive classroom environment is created.

Subjects with a practical orientation are found to be the most interesting and least difficult - such as physical education, art, home economics, materials technology and computers. Subjects such as Irish, maths and modern European languages are most likely to be difficult and uninteresting.

The study draws attention to the overwhelming importance of the Junior Certificate in underpinning the deteriorating relationship to schooling in third year. As the examination looms, there is no longer time for fun. Teachers and students are more stressed as the need to "cover the course" becomes paramount. Coverage, not discovery, becomes the focus. Students having difficulty or struggling with difficult subjects gravitate towards ordinary-level papers rather than risk failing a higher-level paper.

This will in turn affect their Leaving Certificate choices - when it comes time to choose between pass or honours subjects, they will be more likely to choose the pass subjects.

In summary, it appears that there are four inter-related elements which are central to the quality of the school experience at second level, at least for the first three years. These are: the assessment system; the syllabus; school organisation and climate; and the pedagogical process.

While each of these is important, they are not all equally so.

Ultimately, assessment drives the broader curriculum. In third year, students are being taught to the test. No school or no teacher is free to ignore this, though each has significant discretion in how to approach or interpret it. It is a truism that the transformation of the schooling experience must begin with a transformation of the assessment process.

And while the majority of the school-going population cope reasonably well with the demands of the junior cycle, it is hardly acceptable that up to one quarter of them do not cope. As the disengagement of this minority intensifies in later years, as it almost certainly will, it will move from the classroom and the school into wider and more challenging public domains. It will be reflected in economic marginalisation, social disadvantage and a greater likelihood of drifting into anti-social and criminal behaviour.

We ignore the processes of disengagement in early-life schooling at our peril.