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In the very first draft, Lanyon was a lot more openly antagonistic towards the Lodgers, openly working against Jekyll to get the Society shut down because he believed they were dangerous weirdos who had dragged Jekyll into their dangerous weirdness. This conflict was severely toned down when he took on the role of co-founder alongside Jekyll and continued to be toned down further in subsequent drafts until that open animosity became a demure looking-the-other-way whenever the Lodgers did something Lanyon didn't like.
But there has always been a seed out doubt for him--first highlighted in the performance of The Mad Galvanist in Chapter Three, or even earlier in Bleeding Heart--that all this mad science business was a bad influence on Jekyll and would some day lead to tragedy.