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As humans, we do get to choose what we eat, and when we choose to eat a plant, we are eating (i.e., harming) just that plant, plus indirectly whatever nutrients that plant consumed over its lifetime (and we are also harming whatever beings may have been living on that plant or who were injured or killed in the harvesting process). But when we eat an animal, we are eating not just that animal, but also indirectly all of the plants and other beings that that animal ate over its lifetime - those plants became the flesh that we eat.
