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I think that the reader gets to follow Jim through his adventure as well as through his maturation. Jim goes from a timid and scared boy to a responsible self-aware young man. Jim is a likable protagonist who embarks on a boy's adventure and returns a young man. I do not think that the reader would have been emotionally invested as much if Jim were not a boy.
I believe that since this book was originally written for his grandson in the 1800's that he wanted his grandson to be able to relate towards the character more and at the time it wasn't common for females to be apart of a ship crew.
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