Now that we have established the cultural significances of various Pokémon, it is time to wrap our minds around the science of Pokémon-- namely, the creatures themselves. This essay will come in two parts, namely due to the fact that researching the more exotic creatures is taking a little more time. For now, we will be discussing the "usual" Pokémon found in the Pokémon world. However, you may notice that Bug types, Normal types and Flying types are omitted; this is due to the fact that readers should understand what a bug is and what makes a bird fly. The only thing to say regarding each, since they seem to be somewhat larger than our world’s counterparts, is that early in the history of the animal world, there can be found in the fossil record large versions of any possible creature. Dragonflies the size of small radio-controlled toy planes, flightless hawks the size of (or maybe greater than) ostriches-- ecological diversity could once again create giant-sized insects, arthropods, etc. The Pokémon that concern us for the moment are the ones not so easily explained, the ones that are the favorites of those who despise the franchise, saying Pokémon are evil spirits simply because they do not understand what their own world can accomplish.
We begin with Pokémon such as Charmander, Slugma, Cyndaquil, Growlithe, Ponyta, Torchic, Numel, etc. How is it possible to breathe fire? It has been seen as a Vegas magic trick, where the magician spews out alcohol in front of an open flame to create the effect, however, Pokémon do not seem to create fire like this. The flame seems to come from within. We do not wish to use "magic" in our explanations-- that defeats the purpose of the essay. Thus, we must come up with suitable explanations that seem scientifically reasonable. The only concept that seems to work is the combustion of compost. The online journal BioCycle discusses the capacity of compost heaps to create fire:
Microbially generated heat - or what I call a "Biological Fire" - is the match that can lead to spontaneous combustion, a chemical fire with smoking embers, and at worst, flames. While surface fires nearly always are caused by human or external situations, spontaneous combustion is the result of failing to control the internal pile temperature. In both cases, the source of this energy is oxidation of organic matter, or volatile solids. Water, carbon dioxide, energy and other gases are given off, leaving a residue. In the case of the composting process, waste energy is generated as heat, and the residue is compost.
For spontaneous combustion to occur, heat from both biological oxidation and chemical oxidation are needed. The biology of the process can bring the temperature up through 55°C to assure pathogen kill, but will continue to rise into the 70°C to 80°C range, where chemical oxidation takes over as the predominant energy source and biological death occurs. Unless immediate action reduces this temperature, a compost fire is very likely. In short, both biological and chemical oxidation - combined with retention of the heat in a pile - are required for spontaneous combustion.
The diet of the Pokémon would have to include items similar to those found in compost piles. Indeed, the Pokémon are generally assumed to be herbivorous or at least omnivorous, so one can imagine a Charmander or a Ponyta storing undigested plant pulp in a special stomach used for fire generation. Also, there would have to be special pores in their hides to facilitate oxidation of the compost heap. Based on looking at pictures of Pokémon, Magmar and Charmander seem to concentrate these pores in the tail; Ponyta and Cyndaquil have them primarily on their backs. Slugma and Numels seem to possess large openings on their backs for this purpose. These pores or openings not only serve to oxidize the fires within, but they also permit the means of venting the flames so the animal does not die of overheating, which may be possible if the temperatures rise high enough to kill the microbes inside the Pokémon guts that create the flammable gases.
These openings might also be the key when musing about the peculiar fate of the Charmander family line when they are immersed in water. This is not mentioned (to the best of my knowledge) about any other Pokémon, but Charmander are said to die when their tail flames go out. It may not be just that water weakens them-- when the pores are submerged, the flames inside the body can no longer acquire enough oxygen and also the core body temperature would decrease substantially. It is reasonable to assume, then, that these reptilian, assumedly cold-blooded creatures (ironically enough) cannot withstand the sudden drop in temperature in their digestive furnaces as their bodies would go into shock. Other Pokémon, such as Growlithe, Houndour, Vulpix and Torchic, do not seem to have this problem. Indeed, they seem to have no visible flame on them at all. Perhaps because they are based on warm-blooded creatures, temperature regulation may not be as important an issue as it is with the Charmander line. Fire generation does not appear to be as vital to their biology as it does with the Kantonian starter.
But how can these creatures survive such extreme temperatures? Wouldn't the constant high heat, not to mention the powerful flame attacks they must sometimes generate, burn their poor bodies to cinders? The authors suspect that it is possible that there is a tremendous amount of symbiosis occurring between the Pokémon and thermophilic microbes. According to Microbe.org, thermophiles have special enzymes to keep their cellular structure together during high heat. If Pokémon were somehow able to acquire these same abilities, then they might very well survive such extreme temperatures.
The primary mystery of water Pokémon such as Poliwag, Squirtle, Krabby, Totodile, Mudkip, Surskit and Spheal is their ability to expel copious amounts of water, especially during attacks like Hydro Pump, when the Pokémon themselves are neither near water nor do their bodies match the volume of the expelled water. This does not seem to be a problem when the Pokémon are battling in the water, since the more cephalopoid pokemon (Omanyte, Octillery) and mollusk Pokémon (Shellder, Clamperl) can mimic their real-world counterparts and jettison water for both propulsion, attack and play (see here for examples of real "water gun" attacks and their uses). Perhaps the problem is trying to attach the same modus operandi to all water Pokémon. It might be more useful to use a variety of explanations since the animal families they are based upon vary so widely. Two ways immediately spring to mind: 1) adaptation of swim bladders and 2) something biologically similar to fuel cell technology. Imagine a fish needs to cross a short distance of land in order to reach another pond nearby for whatever reason (mating, food, etc). Unable to breathe in such a scenario, it fills its swim bladder (the organ that usually holds air to help with buoyancy) with water and creates the opposite of a diver's air tank, allowing it to cross the land and breathe its watery reserves. Now, imagine a Squirtle or some other air-breather who could also contain such swim bladders. They would adapt so that instead of breathing that water, they store it instead to use it for attacks. It's a stretch, true, but it could be feasible. The other method would be to create a physiology that permits the intake of hydrogen and oxygen and combining them to create water. This may not be the most efficient method, but at least with this method, one does not need to store gallons of water in an extremely strained swim bladder to sustain one single attack, not to mention multiple attacks.
There appear to be two types of grass Pokémon: the animal types, and the plant types. Pokémon such as Bulbasaur, Chikorita, Treecko, Celebi, Lotad and Tropius appear to be animals with symbiotic relationships with plant cells, supplementing their herbivorous diet with energy from photosynthesis. Others, such as Oddish, Sunkern, Bellsprout, Hoppip, Cacnea and Roselia, on the other hand, appear to be plants with faces. Perhaps the animal-like grass Pokémon lived in regions poorly suited to serving as nutrition, so they incorporated algae and perhaps other, more parasitic plant tissue to gain energy from photosynthesis. Or, it could just be possible that parasitic plants seeded certain herbivorous animals and mixed their genomes with the genomes of the host creature. In any case, animal-plant symbiosis (for whatever reason) seems to be the most likely method of creating one's own Bulbasaur.
The plant-like Pokémon, on the other hand, takes a little more stretching. Michael Davidson provides a look at plant cells and notes that they lack the formations necessary for locomotion. However, it does not take a great leap of imagination to see a plant in a hostile environment, especially those descended from Mew (who will be discussed in part two of this essay), retaining the common ancestor's animalistic organelles, while keeping a more flexible version of the cell wall to accommodate greater movement. It may be necessary at times to use Mew's almost stem-cell capacity as the origin of Pokémon as a catch-all for improbable Pokémon abilities or physiologies. Certainly the plant-like grass Pokémon would fall into this category.
Perhaps the toughest to describe so far are the ground and rock Pokémon, such as Geodude, Onix, Larvitar, Diglett and Groudon. Fortunately, most of these Pokémon seem to be merely animals associated with the ground, such as Diglett, mole-like Pokémon that eventually group together in threes to form Dugtrio. Almost anything with a tough hide (Rhyhorn, Gligar, Swinub and Phanphy) is given a ground designation, as it can withstand a great deal of physical damage, and it can channel a great deal of kinetic energy through the ground or rocks nearby. Grass and water-type attacks, however, seem to cause harm because they weaken the hide to the point of losing its defensive capacity entirely, threatening exposure to vital areas. The golems (mystical creatures made of rock) such as Geodude and Onix are a little harder to come up with a good explanation. There are two possibilities we can think of: 1) The creatures paste bits of rock and earth on them like some crustaceans do in the ocean, giving them a rocky appearance for camouflage and physical resiliency, and 2) the Pokémon absorb tremendous amounts of minerals in their diet, which does not create a fatal toxicity but instead imbues upon the Pokémon a rock-like nature. There is evidence to suggest both in the PokéDex entries of Graveler and Golem.
Dragons, the wonderful mythical creations they are, are terrible in the sense that it takes hours just to find some decent scientific information about them. Pokémon has many dragons, based on various cultural traditions, from the river-god look to the winged-reptile look to the "whatever Altaria is" look. This section will not focus so much on their physiology (but someone went to a lot of trouble) as their abilities.
What makes the fire breath from a dragon like Gyarados different from the Flamethrower attack of a Cyndaquil or Charizard? In the games and the anime, it is presented as an entirely different concept, doing great damage to other dragons when something like Flamethrower, a fire elemental attack, does nothing special. I suspect the dragons are creating blasts of plasma. This state of matter is different from fire, and may explain why Dragonbreath tends to paralyze my character's Pokémon (it's electromagnetic), and may negatively affect other dragons to a greater extent than it does other Pokémon (remember, Rayquaza is a dragon that lives high in the stratosphere, where a great deal of ionization occurs-- perhaps this is relevant).
Finally, this site mentions some good ideas on how different dragons can come up with different elemental "breaths." In summary, the author of the site muses that a dragon's diet determines the type of "breath" emitted (such as methane for fire, nitrogen (put fertilizer in water-- see how cold it gets) for ice, and standard stomach acid for acidic attacks).