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Having just finished A Canticle for Leibowitz (hey, better late than never), I've been mulling some of the similarities between this book and Isaac Asimov's Foundation series (the original trilogy, at least), as well as the differences. Both series are episodic, of course, as they focus on certain moments in history following the fall of civilization – in Asimov's book, the fall was gradual; while in Leibowitz it's more instantaneous. Both books reveal a long-term plan to preserve human knowledge in the wake of the onset of a new Dark Age; and both use the ideals of an initial prophet to build the foundation that evolves over time.
Leibowitz, however, depends more upon faith and religious devotion as opposed to Foundation's ingenuity and endurance of humanity. It's interesting to note that the religious dogma followed in Leibowitz result in the group dedicated to the preservation of knowledge (the Albertian Order of Leibowitz) remaining modest and overlooked through the years; whereas the Seldon Foundation becomes the dominant force in the Galaxy through the execution of its own master plan.
Both books, in addition, base their histories on the working theme that history repeats itself, and that we are doomed to repeat the past. This theme is more subtle in Foundation, though; it is based on the concept of Hari Seldon's psychohistory, which predicts the behavior of large groups of human beings based upon their predictability. This predictability led to Seldon's ability to predict when certain crises of history would take place, based upon the tendency of humans to repeat their past mistakes…at least, until his predictions were negated by the presence of the unknown X-factor, the Mule. Then, the books focused on the attempts by the Second Foundation to pick up the pieces of their plan and return it to a pattern of predictability. (I won't get into Foundation's Edge, which IMHO negates a large part of Asimov's concept of human predictability.)
Foundation is more optimistic than A Canticle for Leibowitz, which by its final chapters is brow-beating the reader over the head with its message that mankind is doomed to repeat the past. What's interesting in Leibowitz is the way that science becomes more opposed to religion with each book in the story: in the first, science is an artifact to be kept hidden and preserved; in the second, newly-born science finds itself at odds with religion; and in the third book, science (and Mankind) has abandoned religion and considers it above religion, as exemplified by the argument over euthanasia in the last chapters. Miller is unquestionably in the pro-religion camp in this book, but if you accept this and just take his preaching as character storytelling, then it's still a good read.