The universe contracted; at its exact geometric center floated that sandy tidbit of dark bread and pale cheese. A demon commanded the muscles of his left leg to move his left foot half a yard forward. (1.28)
Our first example of religion comes in the form of Brother Francis, and he demonstrates how the novel won't make this theme easy on us. On the one hand, Francis's beliefs have made him a wonderfully honest, innocent guy. On the other hand, the whole idea of a demon seizing control of Francis for a snack is meant to show religion's more ridiculous side.
The Memorabilia was there, and it was given to them by duty to preserve, and preserve it they would if the darkness in the world lasted ten more centuries, or even ten thousand years, for they, though born in that darkest of ages, were still the very bookleggers and memorizers of the Beatus Leibowitz. (6.21)
The church protects the knowledge of the Memorabilia even though it doesn't know what to do with it or what it does. In a way, the church has faith in the Memorabilia, even though its origins are earthly, not heavenly.
Even the idiot which seems less gifted than a dog, or a pig, or a goat, shall, if born of woman, be called an immortal soul, thundered the magisterium, and thundered it again and again. After several such pronouncements, aimed at curbing infanticide, had issued from New Rome, the luckless misborn had come to be called the "Pope's nephews," or the "Pope's children," by some. (10.3)
Here we see the first major instance in the book of the Church not changing its beliefs to meet the challenges of an ever-changing world. In this case, things don't end very well for Francis. As the novel continues, these instances extend beyond lone street travelers to affect the whole world.
For the first time, [Francis] noticed a moth-hole in the Pope's cassock. The cassock itself was almost threadbare. The carpet in the audience room was worn through in spots. Plaster had fallen from the ceiling in several places. But dignity had overshadowed poverty. Only for a moment after the wink did Brother Francis notice hints of poverty at all. The distraction was transient. (11.46)
Francis notices the dual nature of the Church. It's stuck on earth like the rest of us, and subject to the laws of wear and tear. But for Francis, it manages to extend itself beyond those earthy binds, achieving an almost supernatural status.
[Thon Taddeo] huffed impatiently. "The incongruity. Men as you can observe them through any window, and men as historians would have us believe men once were. I can't accept it. How can a great and wise civilization have destroyed itself so completely?"
"Perhaps," said Apollo, "by being materially great and materially wise, and nothing else." (12.78-79)
As we enter the next generation, society tries to obtain its long-lost glory. But the Church—represented here by Marcus Apollo—sees itself as the barrier between the future and those long-lost catastrophes. Apollo's warnings are directed toward the society Thon Taddeo represents, not just Taddeo himself.
There was objective meaning in the world, to be sure: the nonmoral logos or design of the Creator; but such meanings were God's and not Man's, until they found an imperfect incarnation, a dark reflection, within the mind and speech and culture of a given human society, which might ascribe values to the meanings so that they become valid in a human sense within the culture. (14.2)
Dom Paulo believes that the knowledge of science is a "dark reflection" of God's design. Paulo's idea is very similar to Plato's "Theory of Forms," and is Paulo's attempt to marry religion and science.
"But you promise to begin restoring Man's control over Nature. But who will govern the use of the power to control natural forces? Who will use it? To what end? How will you hold him in check? Such decisions can still be made. But if you and your group don't make them now, others will soon make them for you. Mankind will profit, you say. By whose sufferance? (21.64)
Dom Paulo questions who will control scientific knowledge if it's returned to the world. The key question in this quote seems to be, "How will you hold him in check?" Could Dom Paulo be suggesting that religion is that how?
The Order conformed to the times, to an age of uranium and steel and flaring rocketry, amid the growl of heavy industry and the high thin whine of star drive converters. The Order conformed—at least in superficial ways. (25.139)
The technology might change, the building might finally be up to code, but this is the same old abbey as we saw in Francis's day. Zerchi seems to find comfort in the everlasting nature of the abbey, but should the reader also find comfort in it?
"We shouted it loudly enough—God's to be obeyed by nations as by men. Caesar's to be God's policeman, not His plenipotentiary successor, nor His heir. (26.13)
The problems Dom Paulo saw for his religion have come to pass. The Church is no longer able to keep either scientific or political forces in check. It has lost the power to alter the course of humanity. Luckily for Dom Paulo, the abbey is Zerchi's problem now.
Listen, my dear Cors, why don't you forgive God for allowing pain? If He didn't allow it, human courage, bravery, nobility, and self-sacrifice would all be meaningless things. Besides, you'd be out of a job, Cors. (29.35)
This is Zerchi's personal attempt to bridge the gap between his and Dr. Cors's worldviews. It's his attempt at theodicy, or an answer to the problem of evil in the world. And it's a little late, given that the world is ending and whatnot.