In The City of Ember, Clary and Lina were looking at a bean in the greenhouse. What does the bean symbolize?"It looked like a neck, as if a creature in the bean were trying to escape."
Great question! This is actually rather a clever use of symbolism by the author. To unlock the symbol of the bean in the greenhouse, compare the situation that the inhabitants of Ember face with the situation that the bean finds itself in. We know that the inhabitants of Ember seem to be trapped in this cave-like existence with, worryingly, ever lengthier blackout times as the generators fail. Their existence and future as a people seems to be extremely questionable. We can therefore see a rather disturbing parallel between the bean and the way that it is trapped but trying to work out how to free itself from its predicament.
The symbolism thus highlights the plight of the people in the city of Ember. It is clear that their time is limited, but they remain trapped in their situation without any hope of escape or any knowledge of a potential life outside of Ember. Nevertheless, the struggles of the bean in this powerful image show the way that some brave citizens, namely Lina, Doon and Clary, seek to not only fight their situation but also the state of ignorance that they have been kept in.