The “Science” of: Deoxys and Mutation

Deoxys is an interesting Pokemon that was said to have been the “DNA of a space virus underwent a sudden mutation upon exposure to a laser beam” (Ruby). Massive mutations resulting in otherworldly or super natural species is a common trope in literature and media (I am looking at you, X-men) but this is mostly just a fun idea. How does Deoxys relate to DNA and mutation?

Deoxys

The design and name of Deoxys comes from DNA. Deoxyribonucleic acid, actually, if anyone can be bothered saying it. DNA is the coding within our cells that determines how we look and how our body works, so it is extremely important to biology. DNA is a double helix, meaning it has two long strands that twist around each other and bond to form a twisted ladder-like structure.  This is why the arms of Deoxy seem to twist around each other. This strand is made up of the DNA code – nucleotides. Nucleotides are the molecules that, in any given arrangement, form a code that tells our body what to do. There are four nucleotides, Adenine, Thymine, Guanine and Cytosine. To make it simple for us, we often just called them A, T, G and C. These nucleotides form pairs; A bonds to T and G bonds to C. The ATGCs make up the long strand of Deoxys arms, but Deoxys does not seem to have the bonds that join the strands together. Because of this, Deoxys can still unwind the two strands of its arms. In a way, this means that Deoxys arms are more like RNA, which is a single stranded helix.

 

Deoxys attack form

There are many different types of mutations that can occur in DNA, and that’s what we will be covering today. Of the mutations, there are small, insignificant mutations that don’t affect the body in anyway, and other times there are seemingly simple mutations that can actually result in the death of an organism. On the bright side, there are also mutations that happen to be very, very good. But first off, what is a mutation and how does it happen?

Like the alphabet, the arrangement of ATGC means different things. The body has a mechanism for translating this code, called the ribosome, which is a machine that reads the DNA code and builds a protein from it. The nucleotides are read in groups of three, called a codon. Each codon tells the ribosome to make an amino acid. There are 20 different amino acids, and the arrangement dictates what protein is made and how it functions.  After many amino acids are built by a ribosome and joined together, they can go off and become a protein. Proteins are the driving form of life! You may have heard of some important proteins such as Keratin, Haemoglobin, or even Pikachurin!

translation
The ribosome can read our genetic code to build amino acids, which go on to become proteins

This is a long and critical process, and if something goes wrong anywhere along the way, the resulting protein can come out differently. If the trouble arises at the very basic nucleotide level, it is very likely that most proteins produced will be altered. This is where we get to mutation. Whenever our DNA gets replicated (which is constantly) new mutations are introduced. That’s right, you will definitely have some mutations compared to your mum and dad! This is perfectly normal, but something extreme seems to have happened to Deoxys. What potential mutations could that original virus have experienced to eventually result in Deoxys?

Deletions and duplications

As I have said, the nucleotides are read in an arrangement of three. Unfortunately, there aren’t spaces between the codons like there are with words, so the reading mechanisms basically just count in threes from the beginning of the gene. If an extra nucleotide is lost or gained, it makes the entire sequence “shift”, and we call this a frameshift because it is read differently. If we used words to show the same thing, it would be as follows:

Normal – RED TOE LOT SUN

Deletion – RDT OEL OTS UN

Insertion – REP DTE ELE TSU N

These mutations often have the biggest effect, because the final protein is completely different. It is not always a bad thing, but this can lead to loss of function of that gene and protein. On the bright side, occasionally this can be a really good thing and lead to a better protein.

deletion duplication.png
Deletions and duplications lead to a change in DNA

Of course, more than one nucleotide can be altered. Sometimes it is a single codon, and the protein isn’t affected all that much, sometimes it is almost the entire gene. It is also not uncommon for whole genes to be duplication to another region of DNA, so that the genome ends up with more than one copy. Sometimes, this can be a great thing, because more of those important proteins are made! With Deoxys, the original virus may have experienced some deletions or duplications within its genome that caused a severe difference in the types of proteins that were made. Maybe a gene that prevented growth was deleted, so Deoxys grew as big as a human. Alternatively, maybe some genes that promoted intelligence or speed experienced duplications that caused the final protein to perform better, making Deoxys both intelligent and fast. Alternatively, these big mutations may only have affected some traits the down help Deoxys survive, such as the shape of its eyes.

Substitution

This is when one nucleotide is substituted with another nucleotide. This often has no effect on the final protein, but sometimes it has a little effect. This is because some amino acids can be coded by different codons (For example, the codons GGT, GGC GGG and GGA all code for Glycine), so a switch between GGT to GGG makes no difference to the eventual protein. Sometimes the substitution will lead to a different amino acid, but because of the location or properties of that amino acid, the function of the protein is only minimally affected. However, sometimes it can make a big difference, and lead to a new, refined or detrimental function.

Normal – RED TOE LOT SUN

Substitution – RED TOM LOT SUN

Substitution.png
Small substitutions only have a small effect on the DNA

For smaller mutations that affected Deoxys, these kind of mutations would likely only be effective after many generations of Deoxys. If every baby born experienced a few mutations, over time these mutations would accumulate and have an effect. Maybe these are the types of mutations that helped an already useful protein become slightly better at what it does. These are likely to make subtle differences that don’t affect how Deoxys survives, like making Deoxys a little more orange over time.

Inversion

Inversion is a mutation that occurs when two or more nucleotides are swapped around. This could be small, such as two nucleotides that are next to each other, and sometimes it can be big, such as lots of nucleotides in a row. The first type can have a similar effect to a substitution. Sometimes, but not always, it has no effect on the body. The second example is when a whole section of the chromosome detaches and rejoins in reverse. If the entire gene does this, it does not always matter too much, but if a section of the gene inverts, the final product can be very different.

Normal – RED TOE LOT SUN

Inverstion 1 – RED TEO LOT SUN

Inversion 2 – RED NUS TOL EOT

Inverted DNA.png
Small inversions can have almost no effect, and large inversions can have huge effects

Like with deletions and duplications, a large inversion could lead to an entirely different protein. If the inversion was large enough, Deoxys would have experienced a big difference in the genes of the original virus. Maybe these mutations are what caused it to become a multi-cellular organism, or helped that original virus to successfully and completely take over the body of another creature.

These are the main mutations, but a simplified version. In reality there are many ways these mutations can manifest, from the minute to the fatal. Very often, the mutations can be passed to offspring, and if they are good mutations, end up helping the organism. It seems like Deoxys was the product of some very good mutations!

Origin of Deoxys

Deoxys resulted from a virus. The main function of a virus is to replicate as fast as possible and infect as many cells as possible. A virus “hides” in a cell and introduces its DNA with it, causing its DNA to be incorporated into its host’s genome if it succeeds.  Any mutations in the original virus quickly become prevalent in the population. Sometimes this can be a major problem, because the mutation might cause resistance to a certain medicine, and the virus quickly becomes immune. In the case of Deoxys, the virus was mutated with radiation. When something is mutated with radiation, it is likely that A LOT of mutations occur in many different genes, and so it likely experienced all the different mutations we have talked about. Most likely, there were many viral cells, but most of them had mutations that caused them to die. However, one virus experienced mutations that helped it survive. This new mutant virus replicated super-fast, potentially invading the cells of some other organism that was a precursor to Deoxys, and, over time, a new species was born. I don’t think that there was a rogue virus that got mutated and became Deoxys all by itself, but more likely a virus was mutated and then ingested by another space Pokemon. The virus, because of its mutations, proved absolutely no match for the poor host, so the DNA  of the host that was responsible for reproducing was infected. When that host had a baby, it was a Deoxys (or a Deoxys ancestor).

Deoxys.png
The possible origin of Deoxys

We use radiation mutation and viral infection in science to knock out the function of a gene to study it. It is highly controlled, though, so you don’t need to worry about loose Deoxys or Mewtwo running around!

 

Picture references
Deoxys  Attack form by AbelVera. Sourced from DeviantArt

 

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