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In Phineas & Ferb Universe apparently exist two types of animals (not including humans), animals that work in O.W.C.A and "normal" ones.

What I don't understand is, how animals that work in O.W.C.A became what they are. They can understand human language, they can fight and just overall more intelligent, than other animals. Not to mention that they also can grab stuff with their hands and stand upright.

For example, there was an episode where Phineas and Ferb invented animal language translator. Normal animals can not understand human language without it, but special ones like Perry, can.

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Because they are special animals - ones that are anthropomorphic (have human-like skills). Working in special forces requires quite a bit of intelligence after all!

It seems that in the Phineas universe it is rare but not unheard of - when Stacy finds the truth about Pery she is surprised, but not shocked.

Out of universe: it is quite common that in cartoons that have anthropomorphic animals, they would be presented as a main characters in contrast to the majority of regular animals (Brian from "Family Guy" is a good example).

Pearls before the swine shown this in this strip:

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