I've always wonderd what happens to Pokemon's bodies when they use moves, when their abilities active or when they evole, i.e when a Primeape's anger point actives does a huge surge of testosterone? When a Pokemon learns a new move does it grow a new body part? i.e Slowbro using Fire blast. When a Pokemon evoles does it emite some kind of radiation?
When Swift swim or Chlorophyll actives does it make the pokemon's body more felxible so it can move faster? ect.
Well DUH. XD Of course pokemon have different hormones than us humans, after all they need them considering if they're going to use moves; escpecially those of phenomenal power. They're mythical, not nautral but are creatured that most of us want to be actually living and breathing beside us.
I've always thought that there was some kind of mystical aura of power - similar to QI. The aura is unique to each species of Pokémon and that might be what determines their type and which kind of moves they make. It is quite hard to make sense from some aspects of Pokémon and this certainly is one of those aspects.
Oh, I love biology...you asked for science, you will have it...
WARNING: HIGH LEVEL OF SCIENCE AHEAD:
Spoiler:
Don't worry I will not say anything complicate (I hope). First of all, it's useless discuss how things work in the fictional word of the game, so I'll say how they would work "if pokemon were real". First of all pokemon evolution wouldn't exist, since it's more a growth, and growth is "analogic" so it would be like a baby becoming an adult, with gradual transformation: imagine bulbasaur slowly growing bigger and is bulb blooming...naturally this could be training based (to simulate exp) so only if its body is stimulated from battle (or gyms, the real word ones) it grows: so a pokemon could end its life withouth growing. On the matter of attacks and types I would say that pokemon could use a hormon-nervous system similiar to animals one; the types are already present in nature (think of plants with vines or the fish capable of electric attack or sprout water) but would be a bit different: ground and rock would be unite, the majority of stell pokemon would need an artificial creation, fire pokemon could use natural bacteria proces to create flammable gas, dragon could use a similiar process to create hydrogen, that's more reactive and burn with blue light...psy pokemon would be very hard to do,(maybe utilising trick like dark pokemon, but that would be "wrong") and ghost would remain impossible, or be merged in dark category. We wouldn't have pokeball, at least for a long time, and I do NOT WANT to think of pokemon sex (to avoid disturbing thougth during play:P).
I like to think that some things just barely edge into the supernatural. Makes it easier to get away with teleportation and enough water to fill a reservoir in creatures two feet tall.
I like the idea of Dragon types using hydrogen or something close. It reminds me of Flare vs. Firaga in FF games...
Step one, I think, is that psychics and ghosts and (pseudo?)spiritual life force are confirmed fact in the Pokemon world.