The usual reasons this is a flawed idea have been well covered in the media. However, the aggressive attempt to force prayer into the public arena makes legitimate the examination of the basic relationship between science and religion and the appraisal of prayer itself. Many people gloss over the profound and irreconcilable differences between science and religion.
Science is based on logic, systematic data collection, experiments and statistical analysis.
The results must be reproducible by other scientists. On the other hand, religious thinking is the antithesis of scientific thinking and embraces a supernatural way of looking at the universe. The basic tenets of religion are deeply held convictions based on faith as revealed in the revelations of some powerful, and often supernatural, entity. These beliefs become dogmatic, change very slowly, if at all, with time and are often not changeable by evidence or rational analysis. Therefore, the introduction of any aspect of religion into the public schools can only be detrimental to the teaching of critical and rational thinking.