So the ship uses naval ranks like captain and the marines use ranks like sergeant, why is Anya a major? if all the pilots are marine fliers that makes sense but if she's a navy pilot she should be a commander or something like that. I'm using human ranks because since everything is from a human perspective I assume that's what he hears
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Using Sheol for a standard on military ships would be a mistake. A lot of the women stationed there caught that post as a punishment and both Anya and Beth are likely from the Union Europa (UE) sector, whereas Captain Mari was from the United American Federation (UAF), and the three supra-governments generally don't intermix.
As a general template for the Alliant space fleet however, the forces that engage the enemy directly will roughly follow Marine rank structure while the operators of the ships themselves roughly follow Naval ranks. There are a number of adaptations the alien races have "borrowed" from watching humanity develop over the past several millennia, and that includes certain military doctrines. Earth was the highest rated reality show on Comnet for several centuries before the humans made it to space and found their system transit wormhole, and by far the largest disseminator of entertainment media during that time period was the U.S., so it makes sense they'd have the biggest cultural footprint in Bedlam.
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On the authoring side, some things you just do for clarity's sake so the reader can move through the story unimpeded. I've done things like playing with common linguistic structures, vowel usage, alien time systems, and planets that have different day/month/year lengths and whatnot in other books and generally speaking it just bogs the reader down. So unless it's really important to the story, I usually throw an archetype like "Earth Standard" in so the story can move along at a good pace. It works well in the setting since, if you have AI and a way for it to interact with your senses, you can have bespoke versions of everything in any language you please all the time, anyway.