Brother Juniper is a Catholic missionary whose greatest desire is to scientifically prove the existence of God. After the bridge collapse, he investigates the lives of the five victims in order to uncover some divine logic in their deaths. In doing so, Brother Juniper is attempting to support Catholic doctrine through logos. In fact, he says explicitly that he's trying to appeal to people's sense of logic or rationality, remarking that "it was high time for theology to take its place among the exact sciences." However, in one of the The Bridge of San Luis Rey's central ironies, all of Brother Juniper's experiments fail completely.
Brother Juniper's investigation of the bridge collapse yields no clear answers because all of the victims are extremely complex characters, neither bad enough to deserve a horrible death nor so exemplary as to be called to Heaven early. The failure of this central project, which gives the book its structure, is Wilder's way of demonstrating that faith cannot be justified by scientific means.
Later in the novel, Brother Juniper engages in even more foolhardy experiments. When the plague strikes the village of Native Americans for whom he is responsible, Brother Juniper abdicates his responsibility to care for the sick and instead spends his time rating the villagers on qualities like "piety" and "usefulness" in order to explain why God kills some and spares others. This project, too, yields no useful conclusions:
He added up the total for victims and compared it with the total for survivors, to discover that the dead were five times more worth saving. It almost looked as though the pestilence had been directed against the really valuable people in the village of Puerto.
Here, Brother Juniper's pseudo-scientific projects aren't just making him look silly. In treating people like statistics rather than seeing them as full humans, Brother Juniper is harming the villagers under his care and eroding his own humanity. In a final twist of irony, Brother Juniper himself falls victim to the Inquisition, which deems his experiments heretical. This is exactly the kind of pointless cruelty that Brother Juniper has been unsuccessfully trying to explain through theological reasoning; in that sense, his death suggests that religion shouldn't be used a kind of science that can be used to rationally explain earthly events. Rather, Wilder argues, people should use faith as an emotional guide that sustains them no matter what inexplicable tragedies occur.
