Certainly Chapter 1 when David befriends Sophie and catches a glimpse of her feet causes the child David to find a discrepancy between what he has been taught and the truth as he experiences it. Consider how he thinks about it at the end of Chapter 1:
Clearly there must be a mistake somewhere. Surely having one very small toe extra - well, two very small toes, becuase I supposed there would be one to match on the other foot - surely that couldn't be enough to make her "hateful in the sight of God...?"
The ways of the world were very puzzling.
David begins to question and secretly doubt the rules and culture of his world. Of course, his befriending of Sophie and the discovery of her genetic "deviation" foreshadows his own discovery.
Chapter 4, with Uncle Axel's stern insistence that David and the others promise never to talk about their "gift" to others represents another milestone in David's development:
There had been no acknowledged, co-operative policy among us. It was simply as individuals that we had all taken the same self-protective secretive course. But now, out of Uncle Axel's anxious insistence on my promise, the feeling of a threat was strengthened. It was still shapeless to us, but it was more real.
As David goes on to comment, this decision they make together was what began their collective consciousness as a group - "it made us into a group." From this point on, the group thinks and acts as a group, working together (except of course when one of them chooses to marry outside of the group).
The discovery of Sophie and her fleeing and capture, combined with the suicide of David's Aunt Harriet and presumably the death of her baby in Chapter 7 equally serves to reveal to David what is at stake if their "gift" becomes known. As he comments, "And I went on being very frightened." David even prays to be "normal".
When Anne chooses to marry outside of the group and in Chapter 10 is found hung after the death of her husband, it is clear that this fear they have of discovery is heightened. It was just by chance that Rachel managed to obtain Anne's note of confession and thus saved the group from discovery. The group live in a dangerous world where at any moment they could be found out with horrifying consequences, as displayed by Sophie and Aunt Harriet. These really are the key events that form David Storm and prepare us for the group's discovery of Petra, which of course equally destroys the group and gives some of them hope for the future.