Mary-wa [[[John-ga [[ [e] atarasii kasetu-o teiansi-ta] gakuse]-o homete-ita] sono atarasii kasetu]-no kekkan]-o siteki-si-ta .
Mary.TOP John.NOM  new hypothesis.ACC propose.PAST student.ACC praise-had that hypothesis.GEN defect.ACC point.out-do.PAST
literally: ‘Mary pointed out a defect in that new hypothesis [that John praised the student who proposed a new hypothesis].