I just found this Encytemedia post on Prototype inheratance that’s totally worth the read. Additionally, at the end he (Justin Palmer) points to Dean Edward’s Base script that provides an interesting alternative.

…All that has since changed. Thanks to the persuasion of The Javascript MacGyver, Sam replaced the Object.prototype bits in favor of Object.extend and Object.inspect. With this decision, however Prototype’s inheritance scheme can be messy, and it’s certainly hard to read if you don’t spend time trying to really figure out what’s going on.

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