The “Science” of Silence: How Crobat wings work

Back in generation 1, when we were young and excitable, we began our journey with enthusiasm. What Pokemon would we catch? Where are the Pokemon hiding? It didn’t matter who showed up in the grass, we loved them all! That is, until we took the fateful step into Mount Moon. Inundated by Zubat after Zubat, many of us learned to hate this bat that continuously confused us. But generation 2 was a kinder generation, and somewhat redeemed Zubat upon the introduction of its fully evolved form, Crobat.

Crobat is, obviously, based on a bat. However, it has four wings instead of two. According to the Pokedex “As a result of its pursuit of faster, yet more silent flight, a new set of wings grew on its hind legs” (C). This fast and silent flight is one of the major traits of Crobat, as it is mentioned in many of its Pokedex entries. Bat wings are really just modified hands. If you look at a bat wing stretched out, you can see the long bones that resemble finger bones. The skin over these bones is leathery and so thin it is translucent in the right light. The substantial width of these wings allows the bat to propel itself from the ground (or branch or cave) by pushing air downwards, generating enough force to push itself up. Once in the air, the useful shape and lightness of the wings also allows the bat to glide through the air. The speed we can attribute to its extra pair of long wings, but how does it fly so silently?

Crobat

One of the most notable animals with silent flight is the barn owl. Unlike most birds, you can rarely hear the swish of air that results from a barn owls wings. This is because the fine, primary feathers on the barn owls wings are separated to have a serrated edge, like a comb. This cuts the turbulence caused by their wings” into smaller units, which produce less sound. This is extremely useful to the barn owl, as it is able to sneak up on prey. It is easy to replicate this effect in real life. Wave a hand held paper fan up and down and listen to the noise. Then, slice the fan into segments and separate them slightly, like fingers, and wave it again. The sound caused by the fan will decrease as less turbulence is produced.

Barn owl in flight

However, Crobat doesn’t have feathers, and so must rely on a different mechanism. Insects with wings can only control the joints at the end of their wings, so all they can really do is flap. Birds have more joins, and can therefore use the finger like bones in their wings to increase their manoeuvrability. However, the finger bones in bat wings are far more advanced, and a bat therefore has a huge amount of control over the shape and movement of its wings. Not only do they wave their wings up and down, but they can also subtly change the shape of their wings during flight.

Furthermore, the skin on the wing of a bat is stretchy and can balloon slightly when it pushes down. This allows more air to be utilised under the bat’s wings so it does not have to flap as much as a bird or an insect, even if it isn’t gliding. This makes the bat an incredibly efficient flyer.

Bat wing anatomy

Crobat may utilize this technique also. It possible that it can fly silently through a combination of needing to flap less and opting to glide, and also by subtly changing wing shape to catch up drafts noiselessly because its wing bones are far more advanced than an ordinary bat. It also has four separate wings that can be used individually to catch different areas of wind, in order to glide silently for long periods of time. Furthermore, the four wings may help to break the turbulence into smaller units, in a similar manner to the comb shape of the barn owl.

Obviously, the silent flight of Crobat is likely to be an incredibly complex system, but this may provide a very simple basis.

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The “Science” of the birds and the Combees Part 2: All my sons

In the previous part of this series, we saw that it is pretty easy for a queen bee to decide whether to have male or female offspring. Vespiquen are definitely all female, but Combee has a strange skew in the likelihood of being a male or female. In fact, any Combee egg has an 87.5% chance of being a male. This is particularly strange, because bees have significantly more females in their colonies than males. What’s going on with all these male Combee?

combee

In the bee colony, some seriously strange things go on. Female worker bees grow stingers due to their lifestyle and chromosome number. The bee stinger is really a modified ovipositor, which is the organ responsible for laying eggs. Worker bees don’t bother laying eggs, so their stinger grows sharp and barbed. The Queen has a smoother stinger, and the males have no stinger at all, thanks to not having an ovipositor.

Main organs of a worker bee.
The male Drone, female Worker and Queen. The queen and worker bees both have stingers, but the worker does not have a functioning ovipositor

With Combee, they don’t really need to worry about having stingers or not because they can use moves that animals can’t, such as bug bite and bug buzz, to protect themselves and their colony. Also, male Combee can collect honey and contribute to the running of the hive, which real drones don’t do. Their ability to work is not at all inhibited by their chromosome count.

 

Something still doesn’t add up. When we want a baby Combee, we can put Vespiquen and a male pokemon into the daycare, and we will get a bunch of eggs. However, I don’t think they are actually breeding in the same way as other Pokemon breed. Every so often we will get a female Combee, because the Vespiquen bred with a partner, but most of the time the Vespiquen doesn’t breed, it just produces a haploid egg by itself, which hatches into a male. She may just be in a safe and happy environment when she is in the daycare and so she breeds happily, even though it is just by herself.

 

Is there even a reason she would want to have more males than females in her colony? As we know, the male Combee can actively contribute to the running of the hive. That means they actually have an important role and aren’t limited like Drones. However, because they are haploid and got all their genetic material from their mother, they have 100% of the same DNA as the mother and are very, very loyal to her. Due to a thing called Kin Selection, animals that have really high relatedness to each other are more likely to work together, so these males will work together very happily in order to protect their mother. However, a female Combee is only 50% related to her mother and (because of some crazy genetics) 75% related her sisters, and will therefore be more loyal to her sisters than her mother. Now, females require mating, are less related and loyal to their mother, can only forage and defend as well as a male, and there is always the possibility that they may one day try to usurp their mother or leave the colony if they evolve into a Vespiquen. So from this point of view it is much better for a mother Vespiquen to produce male offspring.

Bee relatedness

The Pokemon world doesn’t always match up with our world, but using the principles of science we can still look at it and come to conclusions about how it all works together. So next time you think a Pokemon is strange, investigate the reasons it might be that way, because you may come to an interesting conclusion.

 

More stuff to read

Gempe, T. & Beye, M. (2009) Sex determination in honeybees. Nature Education 2(2):1

Foster, K. R., et al. (2006). Kin selection is the key to altruism. Trends in Ecology & Evolution 21(2): 57-60.

The ‘Science’ of the birds and the Combees Part 1: Are you a boy or a girl?

combee
Vespiquen and Combee

Every so often in the Pokemon world, we come across a Pokemon that has a special evolution based on the biological sex of the animal. Some examples of this are Gallade, Salazzle and Vespiquen. The latter example, Vespiquen, will only evolve from a Combee if it is female. Vespiquen, unsurprisingly, is based on the queen bee of a bee hive and is said to look after all the Combee in her colony. The bottom of her body looks like the hexagonal walls of wax that hold eggs and larvae and she also secretes pheromones to control the larvae she raises.

Vespiquen.
Vespiquen

Obviously, Vespiquen are all female because they are based on the female queen bee, but the thing that makes this Pokemon really interesting is how the thing it is based on, female bees, came to be female. It is all based on chromosomes.

In humans, sex determination is due to a certain combination of chromosomes, which group together in pairs. Chromosomes are structures that hold highly compact DNA and genes. Different genes are on each chromosome, so the specific chromosomes can determine various features. Human sex chromosomes we have two variations; the X chromosome and the smaller Y chromosome. The egg produced by females in the ovary only has an unpaired chromosome and it is always an X. When that egg meets a sperm, the other sex chromosome pairs with the X in the egg. The sperm can either carry an X or a Y.  An XX combination will lead to a female, and an XY will lead to a male. We get one chromosome from each of our parents and that determines our biological sex. Having a pair of chromosomes like this is called diploidy (di refers to two, and ploid refers to chromosomes)

human chromosomes
Sex determination in humans is caused by combinations of X and/or Y chromosomes

That is all straight forward in humans and most animals, but bees like to buck the system. First of all, not all Bees are diploid; Some are haploid and only contain a set of single chromosomes, instead of a pair. What really makes this interesting is that it is not the type of chromosome that determines sex but whether the offspring are haploid or diploid, which all depends on the queen.

The bee colony is made up of the mother queen, the female workers, and a few male drones. The queen bee in a colony is responsible for giving birth and will have given birth to most of the colony. In humans, a baby can only be made with both a mother and a father, and queen bee will also produce eggs that have been fertilised by a male, and result in a diploid larva. The queen only needs to mate once, with 10 or so males, and she stores up the sperm from that event so she can use it for her entire life (1-5 years). She gets to decide which eggs get fertilised and when. These diploid larvae will ALWAYS be female.

But this is where it gets weird. The queen doesn’t actually need another male bee to reproduce. If she wants, she can lay a viable egg all by herself. Of course, like the example in humans above, this egg will only have “half” a chromosome pair and will therefore only have a single chromosome. In humans that would be unviable, but in bees, this will lead to a male.

Bee chromosomes
When a queen breeds with a drone, a female is born. When a queen lays an egg by herself, a male is born

So all that weirdness culminates in this; Female bees are produced from fertilised eggs and male bees are produced through unfertilised eggs. Females are diploid, and males are haploid. It is determined by the amount of chromosomes, not the type.

But bee breeding doesn’t stop there. Why, exactly, is it evolutionarily beneficial for a male bee to be haploid? When a male bee breeds with a queen he contributes 100% of his DNA to the offspring and the queen contributes 50% of her DNA. Sisters from this union will therefore share 50% maternal DNA and 100% paternal DNA between them, and leads to a very strange occurrence when all of the females produced from that breeding pair are 75% related, instead of 50% related like offspring from two diploid parents. This method of breeding is a way of keeping the bees genetically related and loyal to each other, as well as attempting to preserve good genes (of course, some are only half sisters with different fathers, but the principle above is sufficient that it doesn’t matter). Having only the single chromosomes prevents males from growing stingers, and they make awful workers, so they don’t bother with that. They are built for breeding, and that is about it.

Bee relatedness.png
Bee relatedness is denoted by a blue arrow. The queen is 100% related to her sons, the daughter is 100% related to her father, 50% to her mother and 75% related to her sister. Female Combee have a red triangle on the bottom head

It is quite possible that female Combee are the only Combee that can evolve because they have a whole lot more chromosomes. The male Combee are just held back by have a set of single chromosomes instead of a pair. In real bees, haploidy prevents stinger growth and workability, but in Combee, it prevents evolution. This method of sex determination may or may not also apply to Beedrill, but Metapod isn’t inhibited from evolving into a Beedrill due to its chromosome count, but it seems like Vespiquen is all about the chromosomes!

First image was made by Haychel and is found at https://haychel.deviantart.com/art/Vespiquen-Speedpaint-397814977

More stuff to read

Gempe, T. & Beye, M. (2009) Sex determination in honeybees. Nature Education 2(2):1

Foster, K. R., et al. (2006). Kin selection is the key to altruism. Trends in Ecology & Evolution 21(2): 57-60.

The “Science” of: Pokemon GM and Transgenesis

Genetically modified organisms (GMO) are organisms (living systems) that have altered through genetic engineering techniques. Some people like to speculate whether Pokemon were the result of a nuclear apocalypse or extensive genetic engineering and mutation.

Mutations are not necessarily bad things, and they are also unlikely to turn you into Wolverine. Mutations occur naturally all the time as our DNA replicates, but can also be induced by outside forces. Sometimes they are bad, sometimes they are good, and sometimes they do absolutely nothing.

 

Different forms of Mutations that occur during faulty replication

Normally, our DNA experiences mutations during the process of DNA replication, because mistakes happen and our proof reading mechanisms don’t always realise. A common but harmless trait that resulted from mutation is orange in carrots. The mutations occurred naturally, but due to selective breeding, orange became established (1). When selectively breeding, breeders will find the best crops and breed them together.  The “bad” mutations will be bred out of the organism, so a few generations of selective breeding later, we have a superior organisms. However, this can take an exponentially long time, from decades to centuries depending on how dominant the mutation is. However, identifying and inserting or inducing the causes a desirable mutation in that specific gene takes much less time and cuts out a lot of the trial and error of traditional selective breeding. The ideal genetic modification would be indistinguishable from a randomly incurred natural mutation. In a sense, it is used to “speed up” desirable mutations without the many decades of selective breeding in between.

multi14sm
Different colours of carrots 

Often when I tell people that I am a geneticist the common reaction is “Oh, you are making GMOs? So you are fusing shark genes and plant genes?”.  I usually laugh and say yes, because I can’t always be bothered explaining the difference. Genetic Modification is a blanket term, and it doesn’t always require foreign DNA to be introduced to an organism.

When genetically modifying an organism, mutations can be induced by exposing the organism to a mutagen. These mutagens can be a certain radiation or particle bombardment that causes changes during DNA replication (2). These mutations can then be selectively bred and regulated so the end result is an organism with the desirable, but no detrimental, traits. Organism produced through this form of mutation are called Genetically Modified Organisms, or are referred to as Genetically Engineered. When I refer to GM or GMOs from now on, I mean species that do not contain foreign DNA, but have experienced genetic engineering.

Particle bombardment used to introduce DNA

GMO is colloquially used to describe an organism that have foreign DNA, but this is actually too broad of a term to use in science. To avoid confusion, it is better to use the term Transgenic Organism, which is technically a GMO that contains synthetic DNA or foreign DNA . For example, if I took a gene from a fish and put it in a turtle, I may succeed in making a Squirtle, and I would call it transgenic. Sometimes we do add genes from other species in real life, such as attaching the Green Florescent protein originally isolated from jellyfish with another protein. This allows the protein that results from an expressed gene to ‘glow’ in the right light, allowing the proteins location to be observed (3)

For an explaination of how transgenesis works, read about Mewtwo

So, transgenic organisms are genetically modified, but not all GMOs are transgenic. Its the same as how all Abras are psychic, but not all psychic Pokemon are Abras. From now on, when I refer to genetic modification I mean modification that did NOT result from foreign DNA being added, and transgenics will refer to mutations that DID result from the introduction of foreign DNA. So the Type: Null created by the Alolan scientists could either be a GMO or a Transgenic organism. Do we know that either of these techniques actually work?

Plants

Plants have been extensively research in terms of GM and Transgenics. Some crops have been genetically modified without the need for new DNA. A common example are potatoes that were modified to prevent bruising or browning, and to lower the amount of Asparagine, which, when cooked, can be a harmful toxin,  (4). In scienctific research, it is very common to look at plants that have mutations induced by GM to find what gene caused that mutation. Potentially, there are some grass Pokemon that were created through this technique. We already know that Muk was exposed to X-rays, and that is how it came alive, so what about Belsprout, Sunflora or any other grass type pokemon that looks distinctly plantish?

Transgenic plants and crops have also been developed, and this may occur by moving a wheat or bacteria gene into barley, or even introducing a new, synthetic gene. Usually, this is in the context of research, in order to understand the function of a gene. In the future, these new transgenic crops may become commercially available, but because of the controversy surrounding genetic modification and transgenics it can take years for these crops to be approved. Even then, many people choose not to buy genetically modified food for personal or ethical reasons. However, there are some crops that are commercially available. Approximately half of the Papaya crops grown in Hawaii are genetically modified to have virus-resistance genes that were taken from other papayas, or contain genes from the original pathogen, which essentially immunises the papaya (5). These fruits are approved in the USA, and some parts of Asia. Other approved crops are Bt cotton, which forms a pesticide that kills harmful bugs (6). We don’t eat cotton, so it poses no threat to us. Canola oil is also largely developed with transgenic techniques to improve growth and herbicide resistance (7). These techniques could be interesting when we see Pokemon that look very much like more than one plant, or a fusion of a plant and animal. Were tree genes inserted into a tortoise to produce a Turtwig? What about banana genes, bird genes and dinosaurs to produce a Tropius?

Image result for transgenic papaya
Papaya ringspot virus

 

Animals

Genetically modified animals mostly occur in labs, and are used to test how mutations affect more complex organisms. Sometimes, these animals may be mutated so that they over-produce certain proteins that can then be taken for use in medicine Many antibiotics come from modified mouse antibodies. Transgenics is usually the form of mutation that people think about when they say gene splicing, and it is probably the form Mewtwo underwent. This happens when genes are transferred between animals and plants, or animals and animals, and the process tends to work far less in animals than it does in plants. Some may have heard of ‘glow-in-the-dark’ mice that contain green fluorescent proteins (8), or goats the produced spider silk proteins in their milk (9). There is also a certain type of transgenic Salmon that has been developed to produce lots of growth hormones so they can grow larger, but it is not commercially available(10). While it is possible, it is not as easy or stable as genetic modification in plants. But, of course, Pokemon scientists are far more advanced than us, so maybe they were able to take the genes from a fish and insert them into a seagull to make a Wingull, or make they exposed a panda to radiation or particle bombardment to produce a Pancham.

GFP mice

So, as you can see, genetic modification and transgenics is possible for us, so it isn’t beyond belief that the Pokémon world can also utilise these techniques. After all, we know some Pokémon have already definitely been created or modified (i.e Muk, Mewtwo etc.). If we have a quick look at Type:Null, it has many features of multiple animals. It looks somewhat doglike, but it has a fish fin tail and hawk-like front legs. While yes, this could just be a case of random mutations, I am more inclined to believe it is a transgenic Pokémon that has the DNA of many different Pokémon, giving it that motley look. Type: Null was created by using the cells of every Pokemon type, which Faba fused together. Potentially this meant that the DNA was taken from these cells and inserted through transgenic techniques into a single Pokemon embryo. Alternatively, these cells or “parts” could have been grafted or stitched together in the manner of Frankenstein’s creature, and then genetically modified or had new transgene introduced. This would make it less of a genetic mutant like Mewtwo, and more of a Chimera, where a single organism has multiple genomes.

So whether Pokemon truly were created through genetic modification or not, it is certainly an interesting and complex idea!

 

End note – A GMO is an organism. A genetically modified pumpkin is unlikely to contain GMOs, unless some mutated radiation worms got inside it. It IS the GMO, it doesn’t CONTAIN the GMO. Semantics, I know.

 

References
  1. Iorizzo M, Ellison S, Senalik D, Zeng P, Satapoomin P, Huang J, et al. (2016) A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nature Genetics, Vol 48, pp 657-66
  2. Altpeter F, Baisakh N, Beachy R, Bock R, Capell T, Christou P, et al. (2005) Particle bombardment and the genetic enhancement of crops: myths and realities. Molecular Breeding, Vol 15, pp 305-27
  3. Chalfie M, Tu Y, Euskirchen G, Ward WW, Prasher DC (1994) Green flourescent protein as a marker for gene-expression. Science, Vol 263, pp 802-5
  4. Champouret N (2017) The Innate potato: from concept to commercialization. Canadian Journal of Plant Pathology, Vol 39, pp 92-
  5. Tripathi S, Suzuki JY, Carr JB, McQuate GT, Ferreira SA, Manshardt RM, et al. (2011) Nutritional composition of Rainbow papaya, the first commercialized transgenic fruit crop. Journal of Food Composition and Analysis, Vol 24, pp 140-7
  6. Romeis J, Meissle M, Bigler F (2006) Transgenic crops expressing Bacillus thuringiensis toxins and biological control. Nature Biotechnology, Vol 24, pp 63-71
  7. Arnoldo M, Baszczynski CL, Bellemare G, Brown G, Carlson J, Gillespie B, et al. (1992) Evaluation of transgenic Canola plants under field conditions. Genome, Vol 35, pp 58-63
  8. Hadjantonakis AK, Nagy A (2001) The color of mice: in the light of GFP-variant reporters. Histochemistry and Cell Biology, Vol 115, pp 49-58
  9. Jones J, Rothfuss H, Steinkraus H, Lewis R (2010) Transgenic goats producing spider silk protein in their milk; behavior, protein purification and obstacles. Transgenic Research, Vol 19, pp 135-
  10. Devlin RH, Biagi CA, Yesaki TY (2004) Growth, viability and genetic characteristics of GH transgenic coho salmon strains. Aquaculture, Vol 236, pp 607-32
Images (all accessed June 2017)
http://www.carrotmuseum.co.uk/carrotgenome.html
https://www.intechopen.com/books/transgenic-plants-advances-and-limitations/methods-to-transfer-foreign-genes-to-plants
https://geneticliteracyproject.org/2014/11/09/mcdonalds-mulling-embrace-of-simplots-bruise-reducing-innate-gmo-potato/
https://geneticliteracyproject.org/2014/12/08/can-gmo-technology-sustainably-rescue-threatened-florida-oranges-tomatoes-and-papayas/
http://www.2ndchance.info/miceaspetstransgenicjpg.htm

The “Science” of Making Mewtwo

Of the many adventures we encountered over our journeying, one of the most mysterious was stumbling across Mewtwo. In the Pokémon Mansion on Cinnibar Island we are able to find the abandoned journal of a scientist, who documented his horrific gene-splicing experiments in order to create a highly skilled Pokémon of Herculean strength. The tragedy of this story is that the experiments performed on the offspring of Mew lead to the cold-hearted and malicious Mewtwo, who then destroyed the mansion in order to escape the abuse.

Image result for mewtwoMewtwo

Technically, gene splicing is completely possible, although the case of Mewtwo would be too advanced (and unethical) for present day scientists. In theory it is quite simple to splice a gene into another species even though it is much harder in practice.  But first, let’s talk about what gene splicing is.

The type of gene splicing that Mewtwo experienced refers to cutting the DNA of an original genome and adding in new DNA. This new DNA can be a gene, or part of a gene, from the same species, a different species or even completely artificially created. In science, gene splicing is a common method of learning how genes function (although we don’t call it gene splicing – we call it transgenics or gene knock in). Sometimes, if an organism is lacking a particular trait, we can insert a gene into the organism to see if it regains that function. Other times we may move a gene from one species into another, in order to make the new transgenic species grow better or produce a hormone (such as insulin) that we can use in medicine. Most of the time this happens between species that are similar, or is used solely for research purposes (such as florescent genes in animals or plants to understand gene expression), and you have to get an awful lot of licences and training to be allowed to do it. Even then, breaching the laws or genetic engineering or the terms of your licence can end in hefty fines and extended jail time. Obviously, we don’t know the law in Kanto, but if Team Rocket was funding the experiment it’s safe to say that the scientist who experimented on Mewtwo was probably doing it illegally.

Image result for transgenic examples Transgenic glowing fish

Introducing a transgene requires a few steps. First, you need to know the sequence of the gene you want to add. For many organisms, the genome has already been sequenced and it is easy to find the gene sequence on an open source database. It is also useful to know the function of the gene. Many databases can tell you this, but often the purpose of the transgenics is to learn the function. Secondly, you need to have some idea about where the gene is expressed. That means where or when the gene is “turned on”. Some genes will be expressed all the time, and others will only be expressed during a particular developmental stage or in only one tissue. It takes a little consideration, because it will depend on which vector you use in the next steps.

One you have chosen the gene and found the sequence, you need to isolate that DNA. This is actually really simple! We have special machines that are able to make lots of replicates of a chosen section of DNA (called Polymerase Chain Reactions). You need to choose two small sequence (about 20 nucleotides) that exactly match the sequence, one that matches it forward, and one that matches it in reverse. These sequences will recognize the area of DNA you want to target, and help to replicate only the section. After a few hours, you will have lots of DNA of your gene! You can then clean that DNA and prepare for the next step.

After you have your DNA, you have to prepare it so that it will be expressed in your organism. There are lots of mechanisms that are outside of your gene that need to work in order for your gene to be expressed. You need to put the gene in a special vector that will help it be expressed and that will deliver it into your organism. Again, this is relatively simple in theory, but it’s the step that likes to go wrong (for me at least). The double helix of DNA contains two strands that are bonded strongly together. This is because nucleotides make base pairs, where two molecules have a very strong affinity towards each other. This is useful in putting our gene into the bacteria for delivery. We use some special enzymes to make a (usually) uneven cut in the DNA of the vector that will help our gene express, so that it has a little over hang of a couple of nucleotides. Because of our careful planning, this overhangs will match the sequence we have engineered for our gene. When we put the cut vector and our gene fragment in the same tube, we can add another enzyme that will join the two together, because the nucleotides want to bond together.

Image result for digestion ligation

To add a gene into an organism, you need to use a bacterial pathogen that can break into the DNA and add the gene. The most common thing with use is a pathogen called Agrobacterium tumefaciens, which is able to infect the cells with its own DNA in a similar manner to a virus. We use this to deliver our gene into the organism. It can be as easy as dipping the flowers of a plant into the solution, but the more complex the organism, the harder it is. Your gene will then be delivered into seeds or eggs of that organism, and you can select some of the offspring that have your gene. Your gene will be delivered, but the rest of the genome will remain unaffected. Now you can grow those offspring up, and you have your own genetically modified organism!

Image result for agrobacterium mediated transformation

It’s important to deliver the gene into the organism when it is only a single cell. This is because it is much, much easier to change the genome of one cell than multiple cells. If it is at the single cell stage (such as when it is seed or a zygote) all the cells that make the organism will have originated from this transgenic cell and will contain your transgene. Mew gave birth to Mewtwo, so Mewtwo would have needed to be changed well before it was born. Potentially, Mewtwo was made with a fusion of embryos, which would make it a genetic chimera.

Image result for genetic chimeraA genetic chimera peacock!

This is the inconsistency with Mewtwo. From the flashing scenes in Pokemon: The First Movie, it sounds like he did a lot of the genetic mutation AFTER Mewtwo was born. This would be exceedingly difficult, because fully grown, somatic cells (like skin or liver cells) are tough to change. Even if you were able to, you would have to change every single one of the billions of cells in the area you wanted to target. Maybe the scientist only want to change, say, one finger, in which case he could potentially (but with great difficulty) mutate Mewtwo after birth. That would mean Mewtwo was a Mosaic – an organism with cells of different phenotypes. Furthermore, it seems like Mewtwo has an awful lot of different genes changed in it. It’s very, very hard to add multiple genes at once, so usually we will add one gene, and then add the next gene in the offspring and the next gene in the offspring after that. That would mean there would have been lots of different Mews giving birth to mutant offspring until we finally had Mewtwo, but it seems there was only one.

 

Alternatively, the scientist completely, synthetically built the entirety of Mewtwos genome, and used that to clone into mews egg. The problem with this is that it would have cost billions of dollars, so that would be a significant red flag that he was up to no good!

Image result for mewtwo experiments

Of course, the Science in Kanto is far more advanced than our own science, so this scientist may have simply perfected a way of delivering multiple genes after birth. However he did it, I think we can agree that it isn’t something we recommend Pokémon scientists should do, because we have to care for Pokémon, not abuse them!

The “Science” of Multiplying Pokemon

Generation V brought a lot of new Pokemon with it, some of which were based on non-animal designs. While Pokemon such as Vanillux, Chandelure and Trubbish were based on inanimate objects, the designers did something fun and based one line of Pokemon on a biological process.

Solosis, Duosion and Reuniclus were based on the cellular process of Mitosis or the formation of a baby, causing me to have an immediate affection for these little green blobs.

So what is the process of mitosis?

As many of you will have learned in school, mitosis refers to cellular division. In order for the body to grow or repair itself, new cells must be made that contain the same genetic information as the rest of the body. One of the most important components of the cell is the nucleus, which is the “brain” of the cell and holds the genomes. The genome contains all the genetic information that each cell needs in order to process properly, so it is important that new cells have a copy of this genome.

The cell starts off as a stem cell with a full genome, which is comprised of pairs chromosomes (called diploid cells). These chromosomes are replicated inside the cell, so that the cell contains two complete sets of the genome. Cellular mechanisms then pull these genomes away from each other, so they are on opposite sides of the cell. From there, each is contained within a nuclear envelope. A process called cytokinesis then splits the single cell in two, making two identical copies (if nothing goes wrong). These stem cells may choose to undergo some more mitosis, or differential into somatic cells. Somatic cells are the cells that make up almost all of our body and tissue, such as liver cells or skin cells. This is the process of Mitosis, where a genome creates a copy of itself. It is different from Meiosis, where a genome duplicates and then halves itself.

Mitosis is very important in how babies grow and happens AFTER the parent cells have experiences meiosis to produce sperm and eggs. First of all, a sperm and an egg fuse, making a cell called a zygote. This single cell will undergo a lot of rounds of mitosis and cell differentiation, eventually allowing the embryo to grow into a fully formed baby. The embryo is suspended in an amniotic fluid, which keeps the baby from bumping around too much. This is what is released when a pregnant mother’s “water breaks”.

Image result for embryo

Now, back to Pokemon!

Solosis is possibly the representation of a single cell, prior to mitotic division. Its head looks like a nucleus, and it is encased inside a green liquid that may represent to cytoplasm (the liquid and organelles inside a cell). Duosion is also encased in a cytoplasmic-like substance. It has two little bumps on its bottom half, a separate bobble above its head, and a series of lines down its face. It also has two independent brains. These seem to suggest it is at the stage where the genome has been duplicated, but has not been separated. Reuniclus has long arms that contain lots of little balls, and a line down the middle of its head, presumably between its two brains. This seems as though it is the stage of mitosis where the chromosomes are being pulled to opposite ends of the cell, and the cell is beginning to be divided.

Alternatively, these Pokémon could represent the different stages of embryonic growth of babies. Solosis may be the zygote, the tiny little cell that is the result of an egg and sperm fusing. Duosion seems to have little arms, much like a foetus in the early stages of development. Reuniclues may represent the more developed foetus, more like the ones we see in ultrasounds. But babies don’t usually have two brains, you say?

Occasionally, the zygote will get a little confused when it is replicating itself, and instead of replicating cells that remained joined to it to form the embryo, it completely replicates itself into another zygote, resulting in two genetically identical embryos. Usually, these grow up into identical twins. However, sometimes if single embryo is old enough (around 13 days old) it will try to fully replicate itself and run into complications. On rare occasions, this complication will be that the embryos do not completely separate, and it results in conjoined twins. These twins can have two separate, individually functioning brains.

Now comes the really big question; what IS Reuniclus? There is a big difference between an embryo and a cell undergoing mitosis, as one is a multicellular organism and the other happens within a single cells. Is Reuniclus a single celled organism or a multicellular organism? Is it a conjoined embryo with super brains, or the largest cell in the world?

Some unicellular organisms have cell organelles just like the cells in our body (Eukaryotic cells). They usually have a functioning nucleus and a few other organelles, but a few select species can have more than one nucleus (or other organelles) that float around in the cytoplasm of the cell. Some of the cells can grow quite large, and a few even look eerily like Solosis.  Many unicellular organisms can survive extreme conditions (volcanoes, ocean vents, etc.), much like Reuniclus, “Because their bodies are enveloped in a special liquid, they are fine in any environment, no matter how severe” (B2W2). Furthermore, Reuniclus and Duosion have little parts of them that are separate but float around in their aqueous outer layer. Multicellular organisms don’t have separate bits that still function, but unicellular organisms have organelle that float around separately. Unicellular organisms can also live in large communities and communicate with each other, and “When Reuniclus shake hands, a network forms between their brains, increasing their psychic power”. Embryos don’t communicate, unless they are in the same uterus.

Image result for unicellular organism

However, Duosion and Reuliclus both have two, fully formed and functioning brains. Unicellular organisms don’t have brains or nervous systems, and have very basic functionality (essentially they know to feed and reproduce). So it seems that the middle part, at least, is a multicellular organism.

The Pokedex speaks of the fluid surrounding its body as a separate fluid, so it’s possible that it isn’t part of the central organism. Maybe, Reuniclus is a multicellular organism that lives in a symbiotic relationship with a unicellular organism through psychic control, whereby Reuniclus receives protection. The little arm blobs may be cell organelle of the outer unicellular organism, but are still controlled by Reuniclus’s psychic powers.

Alternatively, the liquid that encases Reuniclus is cytoplasm that does not belong to another organism, and the arm blobs are just floating body parts. Cytosol, the gel-like component of the cytoplasm, maintains structure of the cell as well allowing diffusion of different beneficial molecules. Some people have even proposed that cytosol can adopt a solid or glass like state when necessary. Considering Reuniclus can “crush boulders psychically” (W) with its arms, they may actually be cytoplasm. Amniotic fluid only protects the baby from minor environmental changes, but is mostly to stop the baby from bouncing around too much, so Reuniclus is unlikely to use it. I think this may be the mostly likely theory about what Reuniclus is. Of course, it may just be that Reuniclus, a multicellular organism, has coated itself in some unknown, non-organic substance that never stagnates or evaporates and its arm blobs are just bits of its disconnected body.

Whatever Reuniclus is made of, it is a fantastic homage to science!

Image result for reuniclus

Disclaimer – I do not own any of the images in this blog, nor do I own the names of the Pokemon

The “Science” of the Pokemon Protein: Pikachurin

Scientists can be a very boring bunch when it comes to naming things. Mostly, proteins are named after their function, and end up with rather mundane names, such as Glucose Transporter 1 (GLUT1), or Cluster of Differentiation 8 (CD8). However, very occasionally, somebody creative comes along and gives a newly discovered protein a really cool name. One of these proteins is called PIKACHURIN.

As you have probably already guessed, this protein is named after the Pokémon mascot, Pikachu. It was discovered by a scientist called Shigeru Sato and his colleagues*, and was named because it “has lightning fast moves and shocking electric effects”**. But what does it do? Let’s start from the beginning.

Proteins are what we call macromolecules; they are big molecules that act as the machinery in our body. Proteins are made from amino acids. There are twenty amino acids, and depending what order they are in, the protein will be different. Some proteins will only be 100 amino acids, but others are much longer and can be hundreds of amino acids long. Our genes are responsible for causing the proteins to be made, by telling the “protein making machinery” what order to put amino acids in. When somebody tells us to eat more protein, they actually mean that we need the extra amino acids from the protein. The protein gets broken down into amino acids and made into new proteins.

Proteins are responsible for almost everything is our body. They help our cells grow, they help us metabolise our food and they even make more proteins! There are so many varieties of proteins, that we haven’t functionally characterised a huge proportion of them. We do, however, know that they are extremely important.

Pikachurin is a protein that is found in eyes. Eyes have photoreceptors, and these will move in a certain way depending on the light they receive. Photoreceptors send a signal to a synapse. The synapses are important structures that allow information to move around the brain. Synapses send signals to the brain about photoreceptor movement, and this translates the information into pictures. However, synapses can’t work alone and need the help of many different proteins. One of these proteins is Pikachurin.

Pikachurin is 1017 amino acids long*** and is found in most animals that can see. It was discovered by using a technique that allows for tissue to be scanned to see what genes and proteins are in use through testing concentrations. Another clever technique is to use fluorescent markers that bind or are bound specifically to that protein, and this was used to show that Pikachurin was found around eye synapses. The funny thing about Pikachurin is that we don’t know what its function is, we just know that it is needed in order for proper synapse function (and for some other proteins to function). Without it, the electrical impulses that send information to the brain are disrupted, and incorrect movement of synapses and proteins can lead to muscular dystrophy of the eye. It is, therefore, an important protein.

In this picture, the genes are expressed everywhere, but you can link the fluorescent protein up to a single gene/protein to see where the gene is turned on. Often, then will be in a very specific tissue, as is the case with Pikachurin.

It is normal and common to know what a protein interacts with, but not what its specific function is. The way scientists learn about gene and protein function is to look at subjects that lack the protein. Whatever is effected is probably influenced by that protein. My job is to learn about plant genes in pollen. If I want to know what a specific protein does, I will knockout the gene that makes this protein (this is quite easy to do). If the plant that no longer has this proteins grows tiny pollen grains, I will then know the protein is important in pollen growth when it is functional. This doesn’t tell me how the gene or protein helps the pollen grow, it just lets me know that the gene or protein is important in pollen growth. Pikachurin was studied in the same manner, but using mice instead of plants. It is very difficult to know how they work because we can’t just sit and watch them; they are too small.

Hopefully, as we learn more about science and improve our technology, we will be able to understand what the specific function of Pikachurin is, and how it interacts with synapses. Until then, we just have to be happy that Pokémon was so influential to the scientific community!

*Sato S, Omori Y, Katoh K, Kondo M, Kanagawa M, Miyata K, Funabiki K, Koyasu T, Kajimura N, Miyoshi T, Sawai H, Kobayashi K, Tani A, Toda T, Usukura J, Tano Y, Fujikado T, Furukawa T (August 2008). “Pikachurin, a dystroglycan ligand, is essential for photoreceptor ribbon synapse formation”. Nat. Neurosci.11 (8): 923–31.

**Levenstein, S (2008). “Lightning-Fast Vision Protein Named After Pikachu”. Inventor Spot. 

*** That is a huge protein! Usually, proteins are around 300 amino acids. The ones I work with are only 131 amino acids! I bet they didn’t know how big it was when they named it, otherwise they may have named it Zapdos instead.

The “Science” of Partners: Part 5 – Even More Symbiotic Relationships

Other Pokemon in symbiotic relationships

Mantine and Remoraid

Shellder and Slowpoke

Pancham or Butterfree and Heracross

Paras or Joltik

Honourable mentions

Although I only planned to make four parts in this series, I have found that there are many symbiotic relationships in Pokemon, so I will give a few honourable mentions.

Mutualism

Plusle and Minun – These two often seen as partners, as their positive and negative charges complement each other.

Plusle (right) and Minum (left)

Bulbasaur and its bulb – Bulbasaur gains nutrients from its bulbs ability to photosynthesis, and the bulb gains the ability to move around and collect more sunlight.

Shelmet and Karrablast – When traded at the same time, the two swap “shells” and are able to evolve.

Tropius and its bananas – Tropius gets a nice, convenient snack. The bananas are able to grow happily on Tropius and drop their seeds across a wide geographic area due to Tropius’s movement. Another method of spreading seeds is through Poo (yes, many trees have been planted from seeds in poo), so these banana seeds might be specially adapted to resist Tropius’s digestive juices in order to get pooed out.

Tropius

Pokerus – The Pokerus survives and spreads thanks to its host, and the host gets the ability to power EV train.

Tangela – Tangela, and its evolution Tangrowth, are able to use the vines that grow in it to scare of enemies. The vines have a nice place to grow, and may avoid predators due to Tangelas movement.

Illumise and Volbeat, Nidoking and Nidoqueen – According to the Pokedex, these Pokemon are different species. If this is the case, they are in a mutual relationship because they rely on each other to breed,*

Commensalism

Roserade, Torterra and Bellossom etc. and their plants – Based exclusively on the data provided, these plants do not seem to pose a threat to their Pokemon hosts, nor do they provide a benefit. However, they could potentially be an example of all three different symbiotic relationships mentioned, but we just don’t have enough information.

Lotad and small land Pokemon – Lotad will sometimes ferry smaller Pokemon that can’t swim across lakes or rivers. It does not seem to receive a benefit, but does it out of the goodness of its heart. Lotad likes to float around anyway, so it isn’t detrimental to help out. When a commensal relationship entails one partner using the other for transport only, it is called Phoresy.

Lotad carrying a mudkip

Ledian – Ledian sleeps in a leaf at night, which provides it protection. The leaf does not seem to be effected. This is the same for numerous Pokemon that live in trees, such as bug or flying types. The technical term for this is Inquilinism, where one partner receives a permanent house and the other is unaffected.

Corsola and small sea life/humans – Large Corsola colonies provide hiding places for small sea life to find protection in, and sometimes humans can even build floating villages on their backs (Pacifidlog). The Corsola don’t seem to mind either interaction, but they also do not gain a benefit.

Corsola

Parasitism

Vileplume and its flower – The flower on Vileplume’s head is so huge it affects Vileplume’s mobility, as it is too heavy to hold up. It is unclear whether the flower provides a benefit. In saying this**,

VIleplume

 Conclusions

Clearly, there are many examples of symbiotic relationships in the Pokémon world. These are just a few of the many potential relationships, but there are probably many, many more!

*I am not convinced that they are different species. In the past, species were categorized by morphology (How they look) instead of genetics, but not all species that have similar DNA look the same. Occasionally throughout history this has meant two species that were in the same genetic family weren’t recognized as such. I am convinced that these examples of Pokemon would be shown to have the same DNA, and that is why they can have babies of both male and female types. If this is the case, they would not be in a symbiotic relationship because the male and female counterparts would be the same species.

**Gloom seems to benefit from the scent its flower releases, so they could also be in a mutual relationship.

Disclaimer: I do not own any of the images in this post, nor do I own any of the Pokemon mentioned

The “Science” of Partners: Part 4 – Parasitic Symbiosis

Part 4: Symbiotic relationships are defined as a relationship between two species where at least one party benefits from the other. Parasitism is when one partner benefits from the relationship, but the other partner suffers. Today I want to talk about the prime example of Pokémon Parasitism; Parasect. I would also like to mention Joltik as a potential parasite. For more information on other Symbiotic Relationships in the Pokémon world, have a read about some Mutual or Commensal relationships.

Paras and Parasect

Paras

Originally, Paras was a cicada-like bug Pokemon that went about its business as merry as can be. Somewhere along the line, a Paras or a Parasect came in contact with a specific type of mushroom spore, which attached itself to the bug Pokemon. Any eggs produced from the original Paras or Parasect were exposed to these spores, and all resulting offspring were also infected.

The fungus that is attached to Paras sucks nutrients from Paras’s body, but also has some mind-controlling abilities and is able to tell Paras where to go to get more nutrients. The mushroom fully engulfs Parasect and also has complete control over its mind. What makes this a parasitic relationship is that the mushroom slowly sucks the life out of Paras and Parasect, taking over its body until death. Paras and Parasect receive no benefit from the mushroom, but it is not a Commensal relationship because the mushroom is heavily detrimental to the Paras. It is, in essence, a case of ’Till death do we part, where only the Paras will die.

Parasect

So what is this mushroom? In Japanese, it is called Tohchukaso, but this is really just a blanket term for many types of parasitic fungi. The Latin name for this genus is Cordyceps, and consists of about 400 different species of parasites. They mostly infect insects or other small animals with exoskeletons by replacing the host tissue with their own. This will eventually lead to the death of the insect, but the fungus doesn’t mind because it has plenty of time to produce spores that will infect other insects. The most interesting (or disturbing) thing about these fungi is that, like in the case of Parasect, they are able to alter the biochemistry of the insects brain so much that they can cause it to nestle itself in a prime position (e.g. On a nice fruit tree) where it will wait for its own death. The fungus can then share its spores with fruit that other insects eat, and they will also become infected. It is a seriously morbid relationship, so ultimately we should feel rather sorry for Paras and Parasect.

An infected ant

There is no escaping this fungus, so Paras and Parasect are doomed to a life of mind-control and nutrient loss. Even its name denotes what a sad relationship this is. It is, indeed, an example of Pokemon parasitism.

Joltik

Joltik

Joltik is a tiny, 4 inch long electric bug that cannot generate its own electricity. As a result, it attaches itself to larger electric Pokémon (maybe things like Zebstrika) in order to absorb some of their electricity. Now, before I start, I have not read anywhere that explicitly states that Joltik is a parasite, so this is just speculation.

There are a few reasons I think Joltik is a parasite. Firstly, it is based on the real life tick, which is known for attaching to animals (and occasionally humans) and sucking out their blood. The bites can be itchy or painful, and pose absolutely no benefit to the host at all. I have personally had to pull ticks off a dog, once, and there is nothing pleasant about them.

Tick

The Pokedex says Joltik “Sticks onto large-bodied Pokémon and absorbs static electricity” (B2). While this doesn’t say the host Pokemon is detrimentally effected, I would assume it is because the Pokemon is based on a tick. Also, because electric Pokemon generate and need their own energy, Joltik is taking it and the host would need to generate more (Unless Joltik only takes a negligible amount). Furthermore, in the episode “Crisis at Chargestone Cave!”, Joltik is shown to be “stealing” electricity from other electric Pokemon because all of the electrically charged stones have been removed from the cave. In this case it is more that the word steal implies the host Pokemon does not what its own electricity to be absorbed by Joltik, suggesting Jotik may be a parasite in this situation.

Of course, with such little evidence, it is also possible that Joltik is actually just in a Commensal relationship with other electric Pokemon, whereby Joltik benefits and the other electric Pokemon remain unaffected. However, it is very difficult to tell in this situation.

 

Disclaimer: I do not own any of the images in this post, nor do I own any of the Pokemon mentioned

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