Master and Commander: Where Did God Go?

Lately my “fun” reading has been in Patrick O’ Brian’s Aubrey–Maturin series.  I read Master and Commander and couldn’t put it down.  The series is set during and around the Napoleonic Wars (beginning of the nineteenth century) and revolve around a Captain in the Royal Navy (Aubery) and his best friend and ship’s surgeon (Maturin).  
I have been reading so much nineteenth century British literature over the past fifteen years or so, that I was somewhat surprised by the explicit immorality referred to in the novel.  The references are subdued by twenty-first century standards, but by nineteenth century standards, they would be shocking indeed, perhaps unpublishable.  
I am not naive regarding Victorian era morality.  Just because talk about sexual immorality was not explicit, does not mean that it did not happen.  Nevertheless, there was a high standard.  And while deviation from that standard may have been common, it was understood as deviation, perversion.
O’ Brian wrote the Aubrey–Maturin series between 1970 and 1999.  The new sexual morality of the twentieth century certainly colored how he portrayed the early nineteenth.  However, there is another factor.  O’ Brian’s characters are largely a-religious.  Maturin is a Catholic, but doesn’t seem to practice.  Aubrey is Protestant enough to hate Catholics generally, but not specifically, unless it is convenient.  Mostly, references to God or the “Transcendent” or religion (except in political contexts) are absent.
Why is this?
In an essay on Patrick O’ Brian by William Waldegrave attached to the end of the current text I am reading, I got my clue.  Waldegrave refers to a particular navel incident that O’ Brian describes, an incident that Waldegrave’s own great grandfather participated in and described in an unpublished manuscript.  Waldegrave commends O’ Brian’s historical accuracy—”though happily Aubrey shows none of my forebear’s tedious commitment to the exposition of the scriptures.”
O’ Brian brings a late twentieth century religious sensibility to his retelling of the early nineteenth.  Waldegrave in the late twentieth century finds his great grandfather’s regular reference to scripture to be “tedious.”  And while I’m sure levels of religious commitment varied among sailors (not everyone had a “commitment to the exposition of the scriptures”), certainly religious reference was much more common in the early nineteenth century than one notices in O’ Brian’s novels.
This is not a criticism of O’ Brian’s novels.  He wrote for a late twentieth century audience.  Contemporary readers would probably find a historically accurate reflection of the religious feelings, thoughts and references of the time to be “tedious.”  I merely wanted to explain to myself what was missing.  O’ Brian’s portrayal of the naval life in the early nineteenth century seems to be praised by everyone for its accuracy.  
No one even notices that God is missing.

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