One theme I've found throughout the Holmes stories is the critique on reasoning that Doyle employs. At this time in history, most trains of thought were based around an "inductive" style of reasoning - that is, "clues" or "evidence" was sorted into categories, and based on the category a response was chosen. Even Watson, a doctor, was prone to this. Just like other doctors at the time, Watson would see clues for a case much like he would symptoms in an illness. Based on what illness the symptoms seemed to indicate, he had a regimented treatment for that illness.
Holmes takes another approach. While at first seeming similar in that both characters use evidence to support their conclusions, Holmes' utilization of deduction, while potentially open-ended and inconclusive, proves to be a much more valid method in many cases. He takes the clues for what they are and pieces them together, without a regard for what convention may suggest the clues indicate.
I feel that Watson would say, "If it looks like a duck, walks like a duck, and quacks like a duck, then it's a duck and we should feed it bread." However I see Holmes as saying something more like, "If it looks like a duck, walks like a duck, and quacks like a duck, then we've only proven it to be like a duck."
As a side note, the deductive style of reasoning is more common in medicine today, I think. Rather than having one approach to an illness, doctors more and more often develop individualized plans of treatment. While they can't defenestrate convention's suggestions as easily as Holmes seemed to, it is a marked change.
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