The whales are Mr. B's babies. Bob let him create exactly one species, and, well, we think he did a pretty good job:
B began to picture a race of majestic sleek creatures with gently smiling faces and powerful tails that swept through the seas at wondrous speeds—yet breathed air and gave birth to live young. They lived underwater, but were not alien and cold-blooded like fish, and their voices were eloquent and haunting. And so he created the great whales, which even Bob had to admit were pretty nice. […] "How beautiful you are," he whispered to them, and they smiled back at him with their subtle smiles, happy to be admired. (6.11)
Mr. B is like a proud papa who is happy to see his babies growing up. That's why it's such a bummer to see them in danger—and a clue to who's really in charge around here. The whales are a symbol of Mr. B himself: powerful and majestic, but also subtle. Whales aren't in your face like lions or elephants. They stay hidden underwater, only occasionally surfacing to show off their awesomeness.
Unfortunately, the whales aren't just symbols of how Mr. B should really have been God. They're also a symbol of just how messed up the world is. Because Earth is messed up. Like, really messed up. Who thought it was a good idea for animals to eat each other? That's right, Bob. Earth was messed up from the very first time that a lion ate an antelope, and it's only gotten worse.
We're pretty used to hearing arguments about suffering and recycling, but instead of focusing on those arguments Rosoff puts whales at the center of these problems. Whenever Mr. B thinks about suffering, he thinks about his whales. Like here, when he just finished thinking about an Indian boy who might die:
Moving the Indian boy's file caused the whales' to slither out of the heap and onto the floor at his feet. In his head, Mr. B heard their desperate voices. Ninety-foot baleen whales had been sighted in unfeasibly warm seas, searching for krill that were searching for phytoplankton. Others turned up gasping on beaches, their sonar confused by hunger and illness and noise. (28.20)
But, by the end of the novel the whales have transformed from a symbol of despair to a symbol of hope. After all, the whales are the only creatures on Earth who know that there is someone up there that they can count on. As Mr. B says"
They were the only species with the intelligence to contact him directly, bypassing not only human intervention, but also Bob, for they (quite sensibly) did not believe in him. Their keen brains and their beauty touched him almost as deeply as their faith in his power to save them. (28.23)
In the last few chapters their faith is rewarded because they are saved:
The sky is crowded now, the faces of observers transfigured with ecstasy and fear. Mr. B feels as if he has returned to the enchantment of that first time, when Bob created all that the waters brought forth abundantly. Only this time, they are brought forth abundantly into the sky. Wherever the great whales have struggled against annihilation, they rise. They frolic in the sky. (46.21)
It's pretty majestic. And here's the cool thing: we're like Bob, right? Because he made us like him. Now, we can't make the whales fly—but maybe we can save them in a different way. Just Bob, we have the capacity for miraculous, goofily wondrous acts.
(Shh, no one mention air pollution.)