Symbolism, Imagery, Allegory
In a way, Silence uses a series of plant-based metaphors to create its own theory of evolution. Instead of studying how biological organisms adapt to their environment, however, we'll be looking at the evolution of religious faith.
Throughout the novel, missionary work is likened to planting a seed in a garden. Rodrigues believes that this is a good thing, for obvious reasons.Ferreira, on the other hand, has a different opinion, stating that "a tree which flourishes in one kind of soil may wither if the soil is changed" (6.49). In other words, you can't merely plop Christianity into Japan and expect it to function just as it does in the West.
This metaphor is deepened by Ferreira's assertion that Japan "is a more terrible swamp than you can imagine" (7.220). Think about that one for a second. Swamps are known for their dense, messy vegetation, with plants of all shapes and sizes growing in every direction. Just as a plant from the mountains might go through some serious changes (or die altogether) when planted in a swamp, "the Christianity [...] brought to Japan has changed it forms and has become a strange thing" (10.55).
In the end, these metaphors serve to emphasize the cultural aspect of religion. Japanese Christianity certainly seems to be a unique beast: a full-bodied blend of Christianity, Buddhism, and Shinto. You can find similar examples of this kind of belief-blending—if you want to be all fancy, you can call it syncretism—from all over the world, whether you're talking Voodoo or Rastafarianism. As with Japanese Christianity, these religions were bred by the natural blending of Christianity and local belief systems.