Is "by" necessary from the sentence "Is by using gravity?"
Yes, it is necessary. The speaker means to say that gravity is a method that can be used, so the preposition "by" (or "through") is needed here. This is because it is the agent performing the action, so "by" is used to signify that. Ex: You can commute to school or work by taking the subway or bus. Ex: You can improve your job prospects by taking online courses or learning new skills.