The bonsai tree is mentioned when Mr. Chiba tries to persuade Pi that the story he has told them is scientifically impossible. How he does this is by citing the authority of his uncle who is a "bonsai master." This plan of his backfires, however, when Pi shows he does not know what a bonsai tree is. When Mr. Chiba explains and says they are tiny trees that are incredibly old and can be carried in your arms, Pi responds by saying:
Whoever heard of such trees? They're botanically impossible.
Pi ripostes the claim that the island where he stayed is a biological impossibility by insisting that he only believes what he sees. This should make the attentive reader think back to the two Mr. Kumars and the way that they challenge Pi's understanding of life and the universe by stressing the way in which we should be reliant on our own senses alone rather than other people's ideas of what is impossible or not.