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January 15, 2012
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Title: A dissertation on the hypothetical genetics of the Cake family

There has been dissension among the ranks of bronies as to whether the Cake parents, who are Earth ponies, could produce a pair of fraternal twins with one being a pegasus and the other a unicorn, given only one distant ancestor carried a single representative phenotype of each on either side.  

I have developed a plausible pattern of inheritance to explain this seeming incongruity.

Let's say that pegasi and unicorns were genetically designed, using earth pony as the genetic base, by the alicorns playing god on the mythical continent of Atlantis.  The easiest way to add the genes to the earth ponies would be to design an artificial chromosome carrying all the needed genes.  Then this chromosome's expression could be triggered by a special transcription factor integrated elsewhere in the genome, likely tied via a promoter to other developmental genes.  My bet is the BMP-Bcat-Wnt signalling system, since horns and wings both require skeletal augmentation and early patterning.  

But, you wouldn't normally want a pony to end up with both, so one could also include suppressors on each of the types of artificial chromosomes, such that if any pony ended up with both types of chromosomes and promoter elements, the supressors would shut down the expression and the offspring would be an earth pony carrier of both traits.  Also, if out-breeding with Earth ponies occurred, the different chromosomes and promoters could become separated (aka Au=unicorn artificial chromosome, Pu=unicorn-specific promoter element.  Unicorn genotype-phenotype correlation= AuPu.  Earth pony base:  B=base chromosome Q=null carrier for artificial chromosome.  Earth Pony genotype=BQ.  Assuming they are homozygous for each trait and crossing, you end up with an F1 genotype Au/Q Pu/B.  

Successive generations would further dilute this background.  Assume also the same rules apply for Pegasi Ap/Ap Pp/Pp homozygous genomes: F1 earth pony cross yields Ap/Q Pp/B.  

We can add in the assumption that at some point, any one of the Cake's direct relatives might have reproduced with another Earth pony carrying a promoter or artificial chromosome from the opposing genome. Now, taking into account that each type of artificial chromosome carries the suppressor for the other trait AND that the promoters are specific to each artificial chromosome, we can end up with these diploid genotypes in Mr and Mrs Cake without their developing any pegasi or unicorn traits:  Ap/Q Pu/B  and Au/Q Pp/B.  

Following gametogenesis, these 8 haplotypes can be generated: Parent 1: ApB, ApPu, QPu, QB  Parent 2: AuPp, AuB, QPp, QB.  

As you can see, with such combinations available, there is the chance for the twins (being fraternal rather than identical) to end up with the correct combinations to allow expression of either unicorn or pegasus:  ApB/QPp= heterozygous pegasus, QPu/AuB= heterozygous unicorn.  The raw statistical probability of each genotype is 1/4 x 1/4 = 1/16, which is actually not at all unlikely.  

In my genetics lab, we've done mating with mutant mice for 3 genes with a probability of 1/32, and still end up with some of the combined mutant genotype in roughly every other litter of mouse pups, averaging 8-10 pups/litter.  So, in conclusion, should the genotype function as described in this paper, it is entirely possible for the Cake foals to exhibit the unicorn and pegasus phenotypes despite having earth pony parents.

Soooo, Celestia... is this enough for my PhD in Pony Genetics?  ;3
Given the preponderance of dissent within the community of bronyism elicited by the recent episode of My Little Pony: Friendship is Magic, regarding the seeming implausibility of the phenotypes of the twin foals of Mr. and Mrs. Cake , I felt it my duty to offer a brief, logical hypothesis describing a genetic inheritance scenario which would indeed allow for just such a resultant familial pattern within the realm of statistical probability. My Equestrian scientific adviser concurs. *nods to a life-sized Twilight Sparkle plush* We both hope you will find that my dissertation enlightening.
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:iconthepeacefulprincess:
ThePeacefulPrincess Featured By Owner Jan 7, 2015  Professional Writer
*goes cross-eyed for a moment* EHHH! You just made my poor tired head hurt! XD lol J/K ENTIRELY! I understand the probability of it. ^-^
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:iconlamphobic:
lamphobic Featured By Owner Dec 28, 2012
O.o Can somoene dumb down the complex terms like "representative phenotype", "artificial chromosome ", "chromosome's expression", "special transcription factor", "genome", "promoter", "BMP-Bcat-Wnt signalling system", "suppressors", "diploid genotypes", "haplotypes" and whatnot for those of who haven't taken a class that covers this sort of topic? Please?
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:iconcharlesdeleroy:
Charlesdeleroy Featured By Owner Dec 29, 2012
Oh dear... it would take several pages of explanation to cover all that.

Let me see if I can clarify.

Representative phenotype = the physical form dictated by the expressed genotype

Artificial chromosome = A chromosome built by scientists rather than being a natural one.

Chromosomal expression = the activation of the genes of that chromosome, producing mRNA, miRNA and proteins from translation of mRNA by the ribosomes in the rough endoplasmic reticulum after the mRNA is transposed through the nuclear membrane (watches you brain explode) Oh dear, I knew that might happen.

Genome = the entire set of genes comprising an organisms DNA.

promoter = a small DNA sequence, frequently located slightly in front of the coding region of a gene sequence, which serves as a binding site for proteins involved in transcription (the production of RNA)

BMP-Bcat-Wnt signalling system = One of many protein signalling cascades which are crucial for various aspects of embryonic development. They serve as master control switches for regulating hundreds or thousands of other genes. BMP-Bcat-Wnt functions in the development of the skeletal system, heart, limb development, formation of the neural plate derivative and neural progenitor line, formation of mesoderm and mesoderm-derived structures such as parts the middle and inner ear.

Suppressors = genes which produce proteins or miRNA (micro RNAs) which can reduce the activity of other genes either by directly binding to a region of the target gene or preventing translation by binding to the mRNA or promoting ubiquitinization (a tagging process marking an mRNA for degradation by RNases)

diploid genome = The normal number of chromosome copies in most animals is 2 sets. Each particular chromosome exists as something of a matching pair in cells. X and Y chromosomes are an example. A female has a diploid XX and a male has a diploid of XY. The pairs of chromosomes segregate, one set to each side, of a dividing cell. Then a new matching set of chromosomes is created from the half set (known as the haploid number) before the cell completes division. Humans have a haploid number of 23 and a diploid number of 46.

Haplotype = The genotype resulting from possessing half the diploid number. Contains 1 of each type of chromosome. Gametes consist of haplotype genomes, as they have haploid chromosome numbers. human sperm = 23, human ovum = 23. Fusion into zygote results in diploid 46. Haplotype is a term most commonly used when speaking about a limited number of genes. For instance, a gametocyte before meiosis might have the genotype Hh for a Hair gene (H being dominant, h being recessive), after meosis, the haplotypes of the resulting gametes would be either H or h.

SCIENCE!!
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:iconlamphobic:
lamphobic Featured By Owner Jan 12, 2013
Specifically why does everything have two sets of genomes and why does these one have one set?

"Unicorn genotype-phenotype correlation= AuPu"

"Earth Pony genotype=BQ"
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:iconcharlesdeleroy:
Charlesdeleroy Featured By Owner Jan 13, 2013
All animal chromosomes come in homologous pairs. BUT they may not have the same variants of genes on each one.

Plus, they need to have both the activator gene and the main pathway initiator gene for the unicorns and pegasus traits.

For the Earth ponies, in the space of those genes, they have variants B and Q, which result in a base Earth pony phenotype.
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:iconlamphobic:
lamphobic Featured By Owner Jan 12, 2013
Thank you for the explanation I (think I) understand this much better now.

Why does everything have two sets of genomes?

EX. "Pegasi Ap/Ap Pp/Pp homozygous genomes", "Ap/Q Pu/B and Au/Q Pp/B", " ApB/QPp= heterozygous pegasus", etc...
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:iconcharlesdeleroy:
Charlesdeleroy Featured By Owner Jan 13, 2013
These are the gene pairs which are the sum of the genes carried by the pairs of chromosomes.

This assumes that the activator and pathway initiator genes are on different chromosomes, which they must be for the mixing of the genes to work and result in non-expressing carriers. If they were on the same chromosomes, only cross-over events would result in variants. You could say that unicorn and pegasus only result from homozygosity and thus the carrier of only one unicorn or pegasus chromosome would be an Earth pony.

But then for the Cake twins to be born, both parents would have to possess a unicorn chromosome and a pegasus chromosome. It's possible, since we aren't given the whole family history, and the odds aren't bad: 1/2 of the offspring would be an equal number of pegasi and unicorns. Now, this would also mean alicorns are due to a translocation which splices all the traits onto a single chromosome. However, since this unusual phenotype also grants large physical size, massive increases in magic, and immortality, it's clear that alicorns are quite a bit more complex than merely splicing a few genes together.

Hence, why I stuck with my idea that the entire race was engineered with these activators and repressors; alicorns then being the result of translocational mutation merging the artificial magical pathways, which would be tapping into the magical field of Equestria via some manner of very intricate biochemical structure acting at the quantum level to channel magic (perhaps catching it akin to the way chlorophyll traps light energy), resulting in an exponential increase in abilities.
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:iconsmunsch:
smunsch Featured By Owner Jul 12, 2012  Hobbyist General Artist
I would actually like to see a dissertation on the genotypic and phenotypic variances among ponies, and see if we can't establish some sort of family tree. DJ Pon-3 (aka Vinyl Scratch) currently has unknown parents, but I don't doubt she's related to somepony else that's visible as an extra. Her coloring resembles Twinkleshine's quite a bit; there may be a relationship there.
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:iconcharlesdeleroy:
Charlesdeleroy Featured By Owner Jul 15, 2012
Given the Cake's genetics, I'd say anything is possible family relation-wise unless it's ruled out by canon.
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:iconkelcius:
Kelcius Featured By Owner Jan 22, 2012
Common Pegasus Ancester

GGGGGgrandma-------------GGGGGGaunt
↓ ↓
GGGGgrandma First cousin Thrice removed for CCGaunt
↓ ↓
GGGgrandma Second cousing twice removed for CCGaunt
↓ (pegasus)
GGgrandma

Ggrandma

Grandma---------------CC Gaunt

Mom

Cup Cake
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:iconcharlesdeleroy:
Charlesdeleroy Featured By Owner Jan 22, 2012
Or aliens.

The Greys did it all! *hides in basement with foil hat*
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:iconsm51:
SM51 Featured By Owner Jan 19, 2012
Didn't you post a shortened version of this on EQD as Alondro?
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:iconcharlesdeleroy:
Charlesdeleroy Featured By Owner Jan 19, 2012
Yep, once I got thinking about it, I just had to write out the entire hypothesis. :3
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:iconskaijo:
Skaijo Featured By Owner Jan 16, 2012
OoOOoooooohhhh... spoken like a true biologist. I think this is the first bottom-up explanation I've seen on the internet, that is, the first explanation that assumes every pony has the genetic make up necessary to be an alicorn, but has specific genomes suppressed by transcription factors.

I've gone about it as a biochemist where, post zygote, external factors such as diet, temperature, pH, altitude, AND FUCKING MAGIC, determine what type pony the new organism will mature into. There are some species of newt that have their sexual nature determined by this factor and I think that analogy fits will enough without being too complicated. This makes sense in a "lifestyle dictates what you'll get" sort of way. So pony who is repeatedly exposed to magic will have a higher chance to give birth to a unicorn regardless of their race. The Cakes aren't sedentary and often go to other cities to perform catering events, this only slightly increased their chances of having unicorns/peguses themselves.
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:iconcharlesdeleroy:
Charlesdeleroy Featured By Owner Jan 16, 2012
I like my idea cuz it involves Atlantis and alicorns meddling with nature! :D

It kinda melds with an idea I had for a fanfic, which was split between two similar plots: one, that Atlantis was with humans playing god and made alicorns and then was destroyed by trying to create a true god and ended up with Discord, who fled to Equestria until the alicorns showed up, blah blah blah. I'm kinda swaying away from this version for now and trying to stay in-world entirely.

The second took the parallel universe idea where the Equestrian version of Atlantis was destroyed by Discord after the alicorns created him in their quest for absolute power over their universe. The rock beneath the Everfree forest is a piece of their Atlantis blasted half-way around the world (ballistic suborbital trajectory) imbued with the entropic power let loose in the catastrophe. This idea includes other places around their world which are also chaotic like the Everfree. All the Pony types were due to the alicorns experiments' on Earth ponies, teasing out the genetic mechanisms of the magic they possess. Twilight would be one unicorn carrying a recombinant artificial chromosome, which has a mutant pegasus suppressor that can be forced completely off, giving her temporary alicorn-level power. Celestia, Luna, and Cadence (maybe, depends on what she's up to when it gets to her episodes) were among only a handful of alicorns to survive, which they only did because they left Atlantis over their objections to the experiments (which were often cruel to the Earth ponies, whom the haughty alicorn race mainly deemed inferior animals). After this, Celestia and the rest, out of their shame, dedicated the rest of their existence to making Equestria a paradise for the ponies, as penance for the wickedness and self-centered pride of their people and to try and ensure it would never be repeated. It kinda also gets into Blueblood's lineage a bit.

This is why I don't usually write fanfiction. I get so deep into the logical foundation of what I'm writing that it becomes a science textbook rather than a story! XP
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:iconskaijo:
Skaijo Featured By Owner Jan 16, 2012
You and I are the truest of nerds at heart. Let us never, ever, change.
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:iconcharlesdeleroy:
Charlesdeleroy Featured By Owner Jan 16, 2012
Yosh! :D

I really like my idea, because it adds another layer to Celestia's genuine hatred of Discord. It's not simply his cruelty, it's the knowledge that his existence is the fault of her own people. There's the shame of this evil part of her unwanted Atlantean inheritance, and the fear that this greatest of alicorn mistakes could destroy the happy land she and the last few alicorns have created. Also it lends to the Nightmare Moon story too, as Celestia would have seen her younger sister becoming exactly like the power-mad alicorns whose lusts had led to the near-extermination of their kind.

Oh lord, but the story would have to be crafted so carefully. How would I reveal all this information without constantly info-dumping or relying on mysterious information vaults and large pieces of monologue from the Princesses? Not to mention, what should be the reason for this sudden exposure of long-hidden history? An accidental discovery by a science pony? Archaeology? Discord breaks free again? Twilight gets too curious for her own good (again)?

Bleh, it's daunting to try structuring such a complicated tale.
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:iconskaijo:
Skaijo Featured By Owner Jan 16, 2012
I'm going to make another animation that will either have Discord or Princess Cadence terrorizing the CMCs. I'm just mentally gathering enough funny lines in my head to compile into a list.
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:iconcharlesdeleroy:
Charlesdeleroy Featured By Owner Jan 19, 2012
I'm really curious about Cadence. Will she REALLY be an alicorn? Or some sort of evil spy? Or have rebellious plans? Is she a cruel dictator who wishes to seize absolute power (at least that'd help Celestia shed the tyrant image)? Does she intend to turn Luna back into Nightmare Moon? Is Discord involved somehow? Is she DISCORD'S SECRET LOVER (ok, maybe not that one)?!?!?! SO MANY POSSIBILITIES!!!

Anyway, looks like it'll be a three-parter, maybe even a season-end cliffhanger with an UNEXPECTED TWIST which will leave us all DESPERATE and WAILING for season 3!

That'd be the mark of the creators really catching on to how to hook geeks along FOREVERRRR! ;3
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:iconskaijo:
Skaijo Featured By Owner Jan 20, 2012
YOU'RE TOO EXCITABLE.
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:iconcharlesdeleroy:
Charlesdeleroy Featured By Owner Jan 20, 2012
*watches the 3-parter at long last!* They... are just kinda... sipping tea. And then... they're having some hay fries. Oh! Something's happening! It looks like Cadence is about to bust into evil with that twisted face and... oh... she just had gas.

*episodes end* So the whole thing was just about the impracticality of Cadence wanting all the ponies to wear socks.

BRILLIANT!!! It was clearly a metaphor for her EVIL DARK POWERS AND LUST TO SUCK ALL THE PONIES BLOOD OUT!!! *bounces around insanely*

Sleep deprivation will do that. ;3
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(1 Reply)
:iconcharlesdeleroy:
Charlesdeleroy Featured By Owner Jan 17, 2012
How about this tidbit of cutting mockery! Discord to Scootaloo: Ah-durr... you is a chicken... and you have chicken poo. And bird lice. Cuz you're a chicken, which is a bird.

...

Eh, I got nuthin. :B
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:iconskaijo:
Skaijo Featured By Owner Jan 17, 2012
I honestly don't get the whole chicken vibe, is it because Scoot doesn't fly?
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:iconcharlesdeleroy:
Charlesdeleroy Featured By Owner Jan 18, 2012
It's from the "Stare Master" episode. Applebloom makes fun of Scootaloo calling the lost chicken says, "This is how you call a chicken: SCOOOTALOOOO! SCOOT-SCOOT-A-LOOOOOO!"

And thus, the meme began.
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(1 Reply)
:iconpixelkitties:
PixelKitties Featured By Owner Jan 16, 2012  Professional Digital Artist
This is wonderful! And I'm certain it's a load off poor Mr. Cake's mind!
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:iconcharlesdeleroy:
Charlesdeleroy Featured By Owner Jan 16, 2012
*looks at Mr. Cake, who has fallen on the ground, twitching, with X eyes after trying to read his thesis* I think I broke him. :C
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:iconarchonitianicsmasher:
Archonitianicsmasher Featured By Owner Jan 15, 2012  Hobbyist General Artist
I'm not gonna answer this one, you'll reach epiphany someday...
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:iconelliotxclaris:
ElliotxClaris Featured By Owner Jan 15, 2012
Logic, the key to the mind. I'm so glad I'm taking a biology course this semester in community college.
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:iconcharlesdeleroy:
Charlesdeleroy Featured By Owner Jan 15, 2012
Oh you should see all the weird things genetics can do. Now there's the discovery of thousands of tiny genes coding small snippets of RNA, called micro-RNAs, which can bind to complementary regions of messenger RNAs of protein-coding genes and fine-tune the level of proteins produced during translation. It's just the sort of delicate sort of control mechanism I had long suspected must exist (though I had no idea what it was at the time), given that certain cells can up- or down-regulate the levels of proteins they produce very rapidly in response to changing signals. I knew it couldn't be at the DNA transcription level, as once mRNA is made, the ribosomes translate it and there is only a limited means by which that process can be altered without something like micro-RNAs (which can be produced quickly since they are small and can directly influence the translation of the mRNA without any additional intracellular signalling required) providing a means to tighten the metaphorical spigot. :3

You probably won't get into genetics this deeply. It's masters-level material, and only became widely accepted a few years ago.
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