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Everyone remembers when they discovered Pokémon eggs for the first time in Generation II. It simplified completing the Pokédex, allowed for the player to be involved in the quality of the Pokémon, and added new and more complex ways of obtaining Pokémon. Ultimately, the addition of Pokémon eggs was the largest and most important change that Generation II.
The biology that the Pokémon eggs are based on is something (obviously) mundane: real eggs themselves. Most people have consumed unfertilized chicken eggs in some form. The reproductive cycle of most non-mammals is well-known: the female lays eggs, the male fertilizes them, the eggs are then taken care of until they are hatched, when the offspring have the chance to develop into adults of their species.
[[File:Long-beakedEchidna.jpg|thumb|220px|left|An echidna, one of the few species of mammals that lay eggs]]
A decent fraction of the Pokémon are based on mammals, and this poses further problems: mammals do not lay eggs, or at least not in the context that Pokémon uses. While female mammals do have eggs, or "ovum," these
ovum are microscopic and are incubated within the mother's body, not externally. But again, Pokémon is rescued by the exception: the platypus and the echidna. Both of these mammals do lay eggs and incubate them externally. These mammals are strange: they lay leathery eggs, yet they possess mammary glands to produce milk to feed to their young. There is some debate as to whether this group of animals should be grouped together with mammals or if they should be separated and given their own group, separate from mammals, but at the moment the are a branch of mammals. Outside of these few, most mammals do not lay eggs, but the fact that Pokémon allows mammals to lay eggs has a few real-life mammals that back that theory.
Pokémon does recognize that the Pokémon that are based upon ideas that are non-organic cannot lay eggs
, it would be bizarre to see a Magnemite lay an egg, as it is based upon magnets. And again, to not allow the legendary Pokémon to reproduce is another time that Pokémon follows the rules of science: when there is only one animal left in a species, it cannot reproduce. But the most interesting Pokémon with respect to Pokémon eggs is Ditto. Most people have a ditto parked in the daycare as it can breed with any other Pokémon. This is where the series strays from science: ditto can change shape. And while there are real life animals that try something similar for camouflage, it is always an inherent characteristic of that animal. If we assume for a moment that shape-shifting is possible, then Ditto could successfully breed with any Pokémon. However, as real-life shape-shifting does not exist, this facet of Pokémon breeding is the most radical and strays the furthest from science.
[[File:132Ditto.png|thumb|right|180px|Ditto: the assembly line of Pokémon]]