The first half of the Gospel is built up almost entirely of a series of signs and interpretative discourses. Theodore recognises the existence of this structure, but fails to do justice to its organic and theological character. He declares simply that it was Jesus' custom to follow his miracles with doctrinal instruction, because the greatness of his actions would serve as confirmation of his words. He shows no special understanding of or interest in the actual concept of the sign. This finds most adequate treatment in Origen's commentary. The word ‘sign’ is used of things which are indicative of something beyond the mere fact of their occurrence. Therefore a sign need not be miraculous, as Biblical usage bears out. In fact every Biblical miracle is also a sign, but this is an empirical and not a logical fact. The phrase ‘signs and wonders’ is not a mere tautology, because one can distinguish in thought between the symbolic and the marvellous aspect of any miracle. It is the fact that the miracles of the Fourth Gospel are so carefully and explicitly referred to as signs that shows unquestionably that they require a deeper, spiritual interpretation.

Two other passages from outside the commentary include relevant comments on the nature of a sign. In one passage Origen explains the words of Christ in John ii. 4 that his hour had not yet come to mean that the appropriate hour for his signs had not yet arrived. This, says Origen, is because signs are for unbelief, and unbelief can only be said to be present where there has already been preaching — a ministry on which Christ had not yet started at that time.