Exposition ahoy!
Fluttershy banked sharply, careful not to wake the sleeping alligator.
She spotted Rarity and Pinkie below. She gently landed.
"Pinkie I need to have a word with you about proper pet care. It's not polite to change your pet's size then send them to go play, somepony could have been hurt."
"Oh, you found him! Gummy you're a naughty boy! Sorry Fluttershy, one stray thought about wishing he would grow up just a little and suddenly I had a giant alligator on my hooves. He kept biting at my wings, they are really sensitive!"
"Oh, I see... well you should still be more careful with him."
Fluttershy spoke in aside to Rarity. "Did you two finish the party preparation?"
Rarity shook her head a bit, vague images of ponies with multiple heads and talking plant life were dulled by recollection tinted with a heavy haze. What had that pony with the two heads and five legs called it? The... Pan... something. Until Pinkie had done... whatever she had done she had felt much like her brain had been smashed out by a slice of lemon wrapped round a large gold brick. "In a manner of speaking, Pinkie found a party already in progress and adopted it since nopony else seemed to want it."
Fluttershy seemed pleased. "That was nice of her. Should we go in?"
Rarity shook her head again, but the sense just didn't seem to want to return to her day. "I wouldn't recommend it dear, it's a bit... startling."
Pinkie seemed focused on something in the sky. "Earflop, eye twitch, twitchy tail. Girls, we have exposition coming!"
-------------------------------------------------
"-and then I got to the library, but Twilight had already left, took a big piece of the floor an' a couple bookshelves with her."
"Six and a half to be precise." Twilight looked embarrassed.
"I don't think he cares about the durn books Twi'. So I spotted a letter on the ground-"
Applejack looked hesistant.
"Twi' sorry but I was trying to figure out where you'd gone off to. I read Celestia's message about sending a carriage."
"I understand, I bet you were worried."
"Durn right I was, but then I remember wishing I could give you a piece of my mind about this whole mess. Things kept happening around me an' I had a big set a wings I didn't want. No offense or nothing Twi' but the last time that happened it was your fault. Plus I figured if it weren't maybe you could figure out what the hay was going on anyway. So I got kinda irritated then everything went all orange on me."
The professor nodded. "I see, so you teleported completely by accident to Canterlot."
"Guess so Prof, dunno how exactly, but I was there then I was in front of Twi'."
"Prior to that you'd only moved an apple and a door?"
"Well not on purpose, I just got kinda mad at em and they moved for me."
"Fascinating, We'd never even considered an earth pony undergoing this change, I always thought it would be solely unicorns because of their natural affinity to magic. Thissdens insisted it would be possible for a pegasus to do so as well. Our research was halted by a falling out over the direction it would take."
"What's wrong with earth ponies?" Applejack looked a bit angry.
"Nothing! Don't mistake me, it's not so much that an earth pony was incapable of it. The three races all have powerful magic at their disposal. It comes partially to will, partially to talent. A unicorn has no innate magic, so all of the magic they are born with can be directed into spells."
"Pegasi magic is... different. It's partially innate, that's what keeps them from falling from clouds. A large portion, however, is will based. A skilled pegasus can do more than simply move a cloud, they can manipulate clouds to make storms, and lightning. Some can manipulate the air itself. The act of flight itself is will based, the wings on a pegasus are far too small to ever hope to lift them. Speed is somewhat controlled by wing size, but largely by the pegasus in question moving the air around them. Most of them are unaware of what they are doing, Thissdens was an expert. That was why I sought him out for Celestia's study."
"Earth pony magic is entirely innate. Merely walking in a field you can encourage growth. Your magic encourages life and health to all things that surround you. That is why you heal so quickly, and why earth ponies tend to make the best nurses while unicorns tend to make the best doctors. The magic flows through your body, making you far stronger than the other two races. It also makes it possible for you to do things like buck trees without breaking your own legs, the magic inside you bolsters your endurance."
"So why didn't ya think an earth pony could be one of the ones that changed?"
"Thissdens and I theorized if a unicorn or pegasus were powerful enough the magic inside would trigger a change that caused them to become an alicorn. We based this on the fact they were the only two races to use magic intentionally. An earth pony's innate magic would grow no more powerful over time, it being sort of like a muscle that was never really used. Unicorn and Pegasi can become more powerful over time by practicing their respective magics intentionally."
"Prof... yer an idiot." Applejack smirked.
"Applejack! Be nice, this is a very respected member of the magical studies circle-"
"He's also a durned fool. If what you're saying is true then earth pony magic durn sure does get stronger. Every Applebuck season I can buck more trees easier than the last, and my trees grow better for me now too."
Cann nodded, abashed. "It's true, we overlooked an important area of study. I also regret my falling out with Thissdens over his theory of the pegasi transformation."
Celestia came into view. Rainbow Dash flew beside her.
"-can't believe some of the stuff you pulled princess! You were just amazing! You're a truly fantastic flier!"
"I ought to be, after two thousand years my little pony." Celestia chuckled.
Cann stared at Rainbow, his face fell. He groaned.
Celestia and Rainbow entered the carriage.
"Celestia... was I a good student?" Cann asked in all seriousness.
"Of course Cann, why do you ask?"
"Was I a good pony overall? Did I ever wrong you in any way I wasn't aware of?"
"You have always been a wonderful pony Professor!"
"Perhaps my ancestors irritated you?"
"Cann I love all my subjects why do you keep asking these questions?"
"I just cannot understand what I might have done to deserve this. This is clearly one of my test subjects, and I can see she began life as a pegasus."
"Why yes, Rainbow Dash is the element of loyalty."
Dash looked angry. "You got a problem with pegasi pal?"
Cann waved a hoof. "Not in the least, but now I have a problem. I need somepony's help and I just sent them a snarky letter gloating over a stupid bet I made with them in anger two decades ago."
"Howey what did you do?" Celestia looked concerned.
Cann blushed at the use of her nickname. "The worst part is he bet me five hundred bits I'd come back for his help one day!"
-------------------------------------------------
Author's Note: Hey look at that, 14 chapters in and I almost have my other professor in the story proper.
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Ha! Nice to see the professor get schooled by AJ.
wow
those were funny bets
I laughed so hard at the "Howey what did you do?" line. I literally fell out of my chair laughing.
Ponies sure do love to gamble.
A wager with friends allow one friend to give the other money, without his having the obligation to give it back. It can be a very powerful social devise. Occasional I use this tactic to insentivise others to succeed. "Losing" a bet is often the whole intention. Winning the bet is everyone's good fortune.
I do love to "gamble".
I bet you can't make 14 more amaysing chapters Steel.
263869 Only Scientists. They need to gamble and prove each other wrong. If they don't, what is the point of trying to learn new science?
for knowledge? Ha! 
It's so we can rub it into other scientist's face! 
264012 I make no claims about all scientists, but my professors are a couple bored academics at the tail end of their careers who enjoy a good bet to prove a point, its tangible evidence of "I was right and you were wrong, now pony up."
That was a funny chapter. I laughed. Thank you. I eagerly await more.
264012
I my case I want more knowledge so I can become more than human.
with all the mess of pinkie pie party you almost lost me, too much chaos (missed references?) there for me, even the Who reference was a near miss, not everypony can catch all that stuff happening so fast
the main story is fairly intresting 
but with this last chapter you got right back on track! looking forward to meet the pegasi expert
What is this place, filled with so many refrences? but really, that made me so happy
I toss them about like easter eggs, some I'll point out, others may be more subtle. I love to invoke certain memories.
SPOILER ALERT!!!
(Note that I am muzzy-headed from a cold... the quality of this and my previous chapter's comments may be lower. Same for anything I write for the next few days.)
one stray thought about wishing he would grow up just a little and suddenly I had a giant alligator on my hooves.
-Ah, so not as insane as it sounded. Thought she had done it intentionally. She still shoulda turned him back.
What had that pony with the two heads and five legs called it? The... Pan... something.
-Nice refinement...
Pinkie found a party already in progress and adopted it since nopony else seemed to want it.
-Awwww.... like a stray kitten....
Earflop, eye twitch, twitchy tail. Girls, we have exposition coming!
-Is that a combo she has had before in the course of the story, did she have it before alicornification in your continuity, or do her twitches now come with an instruction manual?
Your magic encourages life and health to all things that surround you. That is why you heal so quickly, and why earth ponies tend to make the best nurses while unicorns tend to make the best doctors.
-Interesting idea... I assumed that a unicorn did an area-of-effect fast-healing spell in the hospital, and that more is NOT better when it comes to healing magic. Thus explaining why Rainbow Dash could be back in the air about 10 days after a break all the way through a bone... actually, just the idea that "ponies heal magically fast regardless of kind" makes almost as much sense as either of these two theories.
it being sort of like a muscle that was never really used.
-A more apt analogy might be the heart of a non-pegasus pony born with no legs. Not much chance of aerobic exercise without major limbs.
If what you're saying is true then earth pony magic durn sure does get stronger. Every Applebuck season I can buck more trees easier than the last, and my trees grow better for me now too."
-Good clarification and that IS pretty face-hoof of an assumption not to check.
"The worst part is he bet me five hundred bits I'd come back for his help one day!"
-How was the unicorn ever supposed to collect on that bet if he won? Have his heirs collect it after his death? Maybe it was an entirely one sided bet with Thissden not wagering anything? Perhaps counterbalanced by the 50 bit one-sided bet that Thissden lost?
"whatever she had done she had felt much like her brain had been smashed out by a slice of lemon wrapped round a large gold brick". hahahaha i love the hitchikers guide to the galaxy refrence
annddd This children is why you don't make bets when angry great work on the chapter.
Exactly
Pan Galactic Gargle Blaster
263146
Its possible since earth pony is not as noticeable the fact they were growing stronger was overlooked.