Archive for the ‘Biology in TV’ Category

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Biology of Group Pokémon

July 23, 2012

My previous Pokémon post got be thinking philosophically about Pokémon. I jested last time about Combee being three different bees stuck together, when in reality one Combee is the set together because the two top bees are not sentient beings, and if you were to split them apart, you would not get three whole bees. Though this idea of Combee having three faces, yet only one brain is incredibly strange, I will dedicate that discussion topic to a future post, as it fascinates me.

But today, I want to  discuss this strange set of Pokémon that are groups of Pokémon, something the writers did many times.

Dugtrio

Dugtrio evolves from Diglett. But strangely, this is a case where all Dugtrio really is, is three Digletts stuck together. I quote, “a team of Diglett triplets….” though later on they mix it up slightly by saying, “Dugtrio are actually triplets, emerging from one body…” either way the fan art really did get interesting for this one.

Magnaton

Another fusion like Dugtrio, Magneton are just three Magnemite that are stuck together. Presumably, they are attached as a result of magnetic forces. Magneton does evolve, into Magnezone. Though this Pokemon looks very different, implying that each Magnemite then differentiates to serve different roles so that the final form can more efficiently get things done.

Metagross

Metagross, though it is hard to see it, is actually 2 Metang stuck together, and Metang is actually 2 Beldum stuck together. So 1 metagross is actually 4 Beldum.

Probopass

As the name suggests, this is a nose Pokemon. Probopass is the evolved form of Nosepass and is just a much larger amd mustachio-ed version of Nosepass. But, Probopass also has attached to it two Nosepass. These nosepass can actually detach and be live creatures. So the question really is, does probopass asexually reproduce by budding, thus once the Nosepass leave, another can be born in that spot, or are these Nosepass born by other means, and then just choose to attach themselves to a nearby Probopass upon evolution, much like Magneton and Dugtrio? To investigate this we could easily do some DNA testing of the Nosepass and Probopass to see if they are genetically identical.

 Weezing

I’m not sure if this one counts. Weezing is said to be two Koffing attached together, but their appearance does change a bit including size and coloration. Weezing is a really unsavory and useless Pokémon, so let’s just not discuss this further.

Exeggcute

Sort of like Combee, Exeggcute is not 6 pokemon stuck together, but rather it is the initial Pokemon, and justconsists of 6 different heads that each express a different emotion. Strangely seeds are not attached in any way, so I wonder what would happen yet they separated…

Klink

Similar to Exeggcute, Klink is two faced objects stuck together, but it seems unlikely they are supposed to both be sentient. I’m not even really sure if the two bodies can be separated even. I don’t think this one really counts, but it sort of belongs in the Combee Exeggcute family.

Thoughts.

The question I have about Dugtrio and Magneton is if they really are three Diglett stuck together or three magnemite stuck together, they should have then exactly three times the power of a single Diglett or a single magnemite. So for example, its hp, attack and special attack should all triple in the evolution if there are three working together. Actually, you would really expect all of the stats to go up with the exception of speed, which should stay the same or decrease. Yet for the most part, though they do gain some obvious strength and advantages, they are not 3 times as strong. That means this union has negative cooperativity, or in other words, by coming together they lose some powered potential power.

This is me sort of using a term strangely. Negative cooperativity in biology usually refers to when an enzyme binds a substrate, which then makes that enzyme somewhat less able to bind another substrate. So the first thing makes it harder for the second thing. Positive cooperativity also exists, and that just means if an enzyme binds a substrate, the enzyme becomes more able to bind another substrate. If I were to continue this analogy, it would be like if one Diglett had a base attack power of 55, the Dugtrio, with powers combined and helping each other, having a power of 200 instead of 55*3=165. But instead they are incredibly negative in cooperativity, so their attack power together is only 80.
But the whole idea of a single Pokémon being many sentient beings grouped together is so strange. I mean, a single Vespiquen is thousands of organisms! In real life, we would never refer to a beehive as a single being. And even if we had a conjoined twin situation, we would still refer to them as two different beings. Yet in Pokémon, we can have different sentient beings in a little group, and we refer to it as one.
Although, the idea of what an organism is might actually be hard to determine biologically. First of all, humans are a huge collection of cells. In evolution, multicellularity evolved a few times. Groups of cells living together decided to start dedicating certain groups of cells to specific jobs, in spite of having the same exact genes. One of the major cell types usually determined are the germ cells for preservation of a complete intact genome, and naturally the somatic cells, which are all the other non-germ cells. For example, the first animals were sponges, which are really incredibly complex and massive colonies of cells that have a few different cell types for feeding, signal transduction, and of course, reproduction.
Secondly, in most animals, we contain tons of cells that aren’t ours per se. We have so much bacteria inside us that are crucial for our digestion, and something and something. Microbiology has made huge advancements into understanding how our gut bacteria contribute to our physiology, and there is still an unbelievable amount of work to be done. But to refer to a human and not include his or her bacteria would be just wrong. They are such an essential part of us that we can’t ignore.
Lastly, even organisms we consider to be single celled organisms show multicellular characteristics. A few labs study how bacteria can form incredibly complex colonies as well as how bacteria can talk to each other.

Colonies of cells. Even “single celled organisms” can show incredibly multicellular characteristics. Courtesy of http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2174258/

So who am I to say a group of sentient beings referred to as one Pokemon is strange. We are all groups of organisms all working together to survive. And to a certain extent, isn’t that what society is? Not one of us can easily do all of the things needed for survival, like grow food, prepare it, protect ourselves, shelter ourselves, etc. Ancient animals realized a long time ago that by living in societies and giving certain people certain tasks, we could accomplish much more. Thus we have a positive cooperativity, or we all gain something by working together. So maybe that’s whats the true error with these group Pokemon. By forming the group, they should actually become much stronger than the sum of the parts.
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Biology of Bug-Type Pokémon II (Combee)

July 16, 2012

In my last Pokémon related post, I discussed some of the cool things the Pokémon creators did with the bug-types. Though there were flaws, they really did do a good job of including some real ecology and biology, and it made for a great educational tool for me to discuss butterfly and moth life cycles.

Now I want to discuss one of my favorite organisms on the planet, and Pokémon’s attempt to do it justice.

Combee->Vespiqueen

A strange Pokémon nonetheless, it starts out as three bee-like organisms inside their honeycomb, flying around as a unit. The interesting thing about this Pokémon is that it has an incredibly skewed gender ratio: 87.5 percent of Combees are male while 12.5% are female. But the reason why most people catch a ton of these Pokémon are to get that elusive female Combee, because only female Combees can evolve into the incredibly powerful Vespiquen (which I think was supposed to be Vespiqueen, but they ran out of letters?)

Vespiquen is a strange Pokémon in that it is not only supposed to signify the queen bee of the hive, but the Pokémon is the hive itself. This sort of makes sense when you think about Combee being the three bees and the combs they live in; so it is natural to assume when they evolve they would also evolve those three little combs into a hive. The truly strange thing about Vespiquen is that she is not only the queen and the hive, but Combees actually live inside her. So to have a Vespiquen is to have thousands of Combee as well.

For fun.

As an aside, I’ve been thinking about how this evolution could work. If you dissociate the Combee into three little bees, then each bee has a probability of being a female Combee with the potential of becoming a Vespiquen. So in reality, your 12.5% chance of catching a female Combee is aided by the fact that you get to technically catch three little bees at a time. So the real female Combee percentage in the population is more like 4.16%. But if only one of the three little bees in the Combee are required to evolve into a Vespiquen, then it is natural to ask what happens to the other two bees? It is safe to assume I guess that they just join the hive inside their friend Vespiquen.

This is all incorrect of course because one Combee is the three little bees all together. Only the bottom bee has an abdomen and the top two bees have 1 wing each coming out of the comb. The bottom bee is supposed to be the thinker, and is the only bee that has a designation signifying if it is female (a red jewel.) But it was fun to do a little math.

Understanding words.

So the name Combee is clear: they just stuck together the words comb and bee to get the Pokemon’s name. By using bee, they naturally want you to assume this is supposed to be some kind of honeybee Pokemon, so most likely based on the Apis mellifera species. Additionally, the Combee’s ability in the game is called Honey Gather, which makes it possible for the Pokemon to sometimes collect honey at the end of a battle, a seriously strange ability. And using the word comb makes sense because this Pokemon includes the hexagonal homes bees live in.

Vespiquen on the other hand comes from the Latin vespi, meaning wasp, and queen. So this would imply that this is not a bee evolutionary line but rather a wasp evolutionary line. This could not be the the case for many reasons, but mostly because in Japanese this Pokemon is called beequeen. In other words, they were clearly going for the queen bee but that got lost in translation (though in English Vespiquen does sound much cooler.)

Compared to Honeybees.

The writers attempt to bring some real honeybee biology to the game of Pokémon was a solid try, but unfortunately lacked nuances that I understand they could not include. But the resulting Combee is actually much more incorrect than if they had ignored biology all together and just stuck to something simple, like Beedrill, which Combee is supposed to be a distant relative of…

Honeybees are actually not gender skewed towards males. In a typical hive there is one queen bee, several thousand worker bees, and a dozen or so drones.

The Queens and Workers.

Queen bees are fertile females that are raised on a specific diet of a special honey made by workers called royal jelly. Inside royal jelly is a special protein called Royalactin that induces special epigenetics changes (or changes in gene expression not the genes themselves). Hives usually only have one queen, and the queen’s job is to lay all the eggs for the hive. She lives the longest of all the bees (3-4 years) and is physically the largest in size, a result of the different diet.

The worker bees are sterile females. They are actually genetically no different than the queen other than the fact that they were not fed royal jelly as a larvae, which led them to a life of sterility. (Actually, as larvae, they are fed royal jelly, but only for a short time early on, and then get switched to a regular honey diet.) The workers are the ones that do all the work in the hive: they forage for nectar, they make honey and royal jelly, they protect the hive, they build the hive, and they care for the young.

When a queen dies in the hive, the hive is instantly put into a mode of panic. As eggs, the future queen and future workers are the same, so surviving workers will instantly sequester the most recently larvae to emerge so that it can be specially taken care of. All larvae are fed royal jelly, but this special larvae will basically be put into a bath of royal jelly for the rest of her development.

Drones.

The final type of bee is the drone. Drones are the result of unfertilized eggs laid by the queen, a really crazy idea considering most animals lay many many eggs that don’t get fertilized. Could you imagine if every egg from a woman’s menstrual cycle led to a baby? That would be crazy! But this means that drones are haploid: they only have one copy of each of their chromosomes. This is because eggs are start out haploid waiting for a sperm to fertilize it and make it diploid. Thus, queens and workers are diploid, or have two copies of each chromosome.

It is important to note that most metazoan organisms, including humans, are diploid, which is advantageous because if one copy of a gene on one chromosome is bad, they can get a good copy from the other chromosome. This is the basis for all the genetic inheritance stuff we learn in school because we get one set of chromosomes from our mother and the other from our father, so if dad has a recessive disorder, we will definitely get that bad gene from him, but as long as mom doesn’t have the disorder, thus having a dominant gene, we have a chance of being fine. This is also what gives us the high genetic variability that keeps us evolutionarily poised for any obstacle.

Drones are the pseudomales of the species. They mate with the queen, and they produce sperm. But because the drones are haploid, every single haploid sperm they produce are exactly the same genetically, unlike humans where our sperm are all different because we are diploid so the sperm we make only have half of our genetic information, so variation is rampant.

The duty of the drone is to mate with the queen. Typically, a hive will have a few dozen drones, and the queen will mate with 10 or so of them. She only needs to mate with them once because she, like many insects, has a special organ called a spermatheca that stores sperm in her body.

Once the drone mates with queen, he dies. Actually, the force required for him to ejaculate is so strong, it kills him. Many drones don’t even get to mate with the queen, and they are generally left to die in the winter, because they are not allowed to stay in the hive, and they lack the ability to forage on their own. So they either get to mate and die violently, or starve.

Unfortunately though, because drones are born haploid, they encounter even more hardships. If they do inherit some bad gene, they either don’t live, or they aren’t able to mate. The advantage here though is that the hive can suddenly very rapidly select against genes they may not want. Actually honeybee genetics are incredibly complicated, and I get confused by it. I can’t figure out how much of an advantage they really have…

Compared to Combee

In real life then, the hive is actually 99.99% female, with 99.99% of them being sterile females. And the 0.01% that is kind of male isn’t actually even male! But in Pokémon, 87.5% of Combees are male and 12.5% are female, with only the female being able to evolve into a queen. This was their attempt to show that only a very small number of bees can turn into a queen. By making the gender ratios so different, they do accomplish this, but they get the biology wrong. But it would have been hard for the creators of the game to really explain the epigenetics and dietary needs that would be required to make the genetically female Combee larvae differentiate into either a sterile female worker or a fertile queen. What the writers did instead was treat the workers like the males, and thus make the potential queen the rare female, and thus ignore the drones all together (which is what happens in real life sadly for the drones).

But if they wanted to make it truly like biology, they actually could have made it work, especially with how complicated the world of Pokémon is. Instead of using gender ratios, which are incorrect biologically because most bees are female, they could have instead made Combee evolve as a result some other evolutionary mechanic the games use for many of the other Pokémon. For example they could have had it evolve when traded while holding the item “Royal Jelly” that you have to collect from other Combee. Or they could have Combee evolve only after it has high friendship with the trainer, like you do with Togepi, Budew, and countless others. But if they really wanted the biology to match the Pokémon, then 100% of the Combee would be female, and to get a Vespiquen you would need to do something special.

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Biology of Cyclops (X-Men)

July 12, 2012

I thought it would be fun if in this blog, I tried to figure out, hypothetically, how different superhero superpowers could work, biologically. Obviously, I can’t do a lot of superpowers because they are just so fantastical that there really would be no basis for a biological explanation (such as Storm’s ability to control weather, though if you think there is a way, please tell me!). But a few superpowers may be kind of fun to think about how that could actually happen, and though the topic of today’s post is a huge stretch, considering how it could work might teach us a little about biology.

Cyclops, whose real name is Scott Summers, is a leader and one of the founding members of Marvel’s X-Men. Though I have read a lot of comic books, I certainly don’t have a complete and extensive knowledge, so some of the descriptions of his powers are based on what I have read, seen on many movies and animated cartoons, and read on wikipedia.

The Superpower.

Called the “optic blast,” Cyclops has, what many may consider a disability, the power of shooting beams of high energy light from his eyes constantly. Though these beams are illustrated as red beams, this is most likely an artistic rendering of a much more powerful electromagnetic radiation than just red light. (Can you imagine how lame it would be if his power was just his eyes glow really really brightly red?) His optic blast is said to not give off any heat, as well as not have any kind of recoil effect (meaning shooting the beams doesn’t push his head backward, which makes sense because otherwise he’d constantly feel his head pushed back). His power as well as his own life depends on sunlight, with him getting weak and even losing the optic blast after prolonged time in darkness. The comics describe him having the ability to metabolize sunlight and even little amounts of energy that surround him.

He is also immune to his own power, meaning though his beams can hurt other people he doesn’t feel any pain, thus allowing him to be able to close his eyes with no eyelid damage. Additionally, his brothers Havok, or Alex Summers, and Vulcan, or Gabriel Summers, have similar powers where they can use light and ambient energy and change it in different ways, though Vulcan probably has the strongest amount of control. Interestingly, while Cyclops and Havok are immune to each other’s beams, neither are immune to Vulcan’s, and Vulcan is not immune to Havok’s, which is very strange.

Note: I thought I would try to cover a biological basis of ALL of Cyclops’ powers, but I only ended up really getting at one. Stay tuned in the future when I try to tackle more!

Metabolizing the Sun’s Energy.

This is definitely not a foreign concept. You may have heard of the organisms on our planet that can convert light energy into chemical energy. They are called plants, and they use photosynthesis to do this everyday. Photosynthesis occurs in a special part of their cells called the chloroplasts, and these chloroplasts are little membrane sacs that are filled with chlorophyll, which does the action of using light energy to split water into protons (H+), oxygen (O2), and electrons. These electrons are high in energy, so the chlorophyll convert that energy into usable chemical forms of energy, like ATP and NADPH.

Photosynthesis is a crucially important biochemical process for life on earth as we know it. Animals, a group in which humans are included, cannot convert light energy into usable energy, instead requiring energy from their diet. That energy naturally comes from plants. But I must note that plants, like trees and flowers, don’t contribute to the majority of photosynthesis on the planet. The algae and the cyanobacteria in the oceans contribute most of our planet’s photosynthesis. So you should really thank these single celled organisms for all the oxygen you breathe in. Cyanobacteria don’t have chloroplasts, but instead just have the chlorophyll and thus the capability to do photosynthesis. Additionally, scientists have discovered that plants’ chloroplasts are the result of ancient cyanobacteria going inside and living harmoniously with ancient cells (endosymbiosis), and they slowly evolved to be dependent on each other. (The evidence for this lies in the fact that chloroplasts have their own DNA, which is very similar to cyanobacteria DNA).

How Humans Could Get this Power.

So the ability to turn light energy into chemical energy is not necessarily a superpower as it is seen in the natural world. But for a human to be able to do it is remarkable. There are a couple ways I can think of in which Cyclops could have been able to biologically get this ability.

1. He could have spontaneously had a few random gene mutations that turned a few genes he had into genes that are photosythesis-like genes.

2. He could have had some strange endosymbiotic event while he was an embryo that led to a photosynthetic organism becoming part of his physiology.

The first of my ideas are completely implausible. It would be to say photosynthesis was created in a day. Though photosynthesis does require the use of a few proteins we have in the animal world, namely the electron transport chain which we have in our mitochondria (as do plants in their mitochondria), the shear number of other proteins that would be required to spontaneously appear in his biology would be impossible.

Additionally, the fact that his brothers also have the ability to metabolize sunlight makes the likelihood of this spontaneous generation of photosynthesis implausible. Though in the comics his parents don’t have any superpowers, making that impossible.

But the more likely explanation is the second way. Instead of having all the right mutations to be able metabolize light, perhaps at an early embryonic stage, his cells absorbed some bacteria that could do photosynthesis, and thus gave him the ability. If this were the case, then that means the real mutation was in his mother. One option is that his mother had some kind of maternal effect gene that causes her embryos to absorb cyanobacteria and enable a mutualistic relationship. This is an attractive idea because that would mean she would have had a mutation that would not result in a phenotype for her, aka she can give her children powers, but she has none. Another option is if she had the ability/bacteria, then she would have passed down the bacteria in her eggs. But this is unlikely because she would have known she had this ability. Note that in either case, the father doesn’t matter, because the embryos don’t develop inside of him so he can’t give them anything special during development, and he only donates sperm which does not pass down things like mitochondria or other organelles, just DNA. This theory is supported by the fact that none of Cyclops’ children (Cable and Rachel Summers) can absorb and use sunlight, instead all inheriting abilities more similar to their mother Jean Grey.

Metabolizing Ambient Energy.

Finally, the more intriguing thing about this power is that they can absorb and use ambient energy, or as I interpret it, any kind of extra heat energy given off from any number of sources that just flows out into the environment. Thermodynamically, this sort of energy is usually thought of as energy that cannot be recovered. Though I don’t believe any organism is known to be able to capture this kind of energy, if something could, that would be a huge development. So here is where the biology sort of escapes me, and this ability to absorb energy really does become a superpower.

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Biology of Bug-Type Pokémon

July 9, 2012

When it comes to Pokémon, three kinds of people exist: people who don’t know anything about them, 151ers, and people who have played more than just the first generation of games, red, blue, or yellow. (“151ers” refers to people who have only played the the first generation games and thus only know about the first 151 Pokémon.) If you are in the first category, you really are missing out on some great games, but if you are in either of the other categories, you know how truly pathetic bug-type Pokémon can be (though there are few worthwhile ones).

Metapod vs. Metapod

Currently there are 63 bug-type Pokémon, of which 15 are pure bug-types while the others are dual types (most commonly dual with poison or flying). While discussing the biology of ALL of the bug Pokémon may be out of the scope of this post, I do want to go over a few select cool ones that really show how well the writers thought about real world biology in creating these Pokémon, as well as a few obvious mistakes. Bug-types, though they are not my favorite to use, are some of the most interesting evolutionarily in all of the Pokémon games, making them some of my favorite to catch and collect. In this post, I will be focusing on a few choice bugs from the first generation of games. Stay tuned for future posts, where I will discuss other awesome bug-type Pokémon.

Caterpie-Metapod-Butterfree

A truly beautiful evolutionary line that is probably one of my favorites. You have the ever adorable Caterpie, one of the cutest cartoon caterpillars of its time, which then evolves into Metapod. Metapod is the chrysalis stage (more on this in a moment) of the developing Caterpie/caterpillar, and as you can see from the video above, is a generally useless Pokemon, but is a means to an end. Because when it evolves, it becomes the beautiful Butterfree, which the animated show really did make a glorious moment of.

Metapod Evolves

Note how different this evolution was animated. Most evolutions in the show have the Pokémon turn white and glow, then change.

Its beauty though does come from how well it outlines the basic, holometabolous insect life cycle. This cycle involves a complete metamorphosis of the animal in its lifetime, and includes four stages: embryo, larvae (Caterpie), pupa (Metapod), and finally emerges (the technical term is eclose) to imago (Butterfree). They even go to pretty good detail making the pupa Metapod actually look like a monarch butterfly chrysalis. (They may or may not have actually been going for this, but monarch butterflies are usually the butterflies people think of first.)

The only issue is that Caterpie is not what a monarch butterfly larvae looks like, with Caterpie more closely resembling maybe the caterpillar of the polymorphous moth or the luna moth.

Note that the butterfly pupa is called chrysalis, which is distinct from the moth’s cocoon. In butterflies, the caterpillar starts its pupa stage by attaching itself to a tree via a small silk pad, and then sheds its skin revealing the pupa. Around the pupa is a hard chitin (pronounced KITE-in) based shell. Chitin is a macromolecule related to cellulose in plants, but is used to give fungi support, as well as used in crustacean shells. This whole thing, pupa and shell, is called the chrysalis. Moths on the other hand spin silk to wrap around themselves before the pupa stage, making a cocoon shell for protection. So only moths have cocoons.

While the Butterfree evolution series is incredibly well done, and made for a great teaching tool for the butterfly life cycle, the first generation of games had an analogous evolution series that made absolutely no sense whatsoever.

Weedle-Kakuna-Beedrill

What a mess. First of all, Beedrill is clearly supposed to be a bee Pokémon, but while bees do have a typical holometabolous life cycle, the larvae and pupa spend their entire time in the beehive combs, fed and cared for by the adult worker bees. I’ve learned that this is apparently a recent evolutionary change as ancient animals in the family had caterpillar like larvae that moved around and ate leaves. But now they really are more like maggots, similar to flies.

Weedle is described to eat leaves and shoot a sticky silk like substance. Clearly they were going more for a moth-like life cycle, where the larvae are independent, spin silk to form a cocoon, and then emerge. Kakuna even looks fairly reminiscent of the brown moth cocoon!

I just don’t get why they would make the Caterpie/Butterfree evolution follow so closely with reality, but then make Weedle not evolve into a moth! And we all know how much cooler moths really are over butterflies.

You could argue that a final evolution moth is just not as scary or awesome as a final evolution bee (which I would actually agree with because bees are freaking awesome.) Or maybe just the idea of a moth Pokémon is super lame. Well the former can’t be true because Beedrill only has a base stat of 385 (where most gamers only use Pokemon with a score of at least 450), meaning it sucks. And the latter can’t be true because…

Venonat-Venomoth

An even bigger mess. Here we have our moth. Strangely, I would argue in the first generation, this is probably one of the better bug type Pokemon; it has a base stat of 450 and is one of very few bug types to be a regular member of a gym leader/elite four member’s team (Koga). Yet this powerful moth, which would fit much better as the last evolution of Weedle and would dominate its rival bug type, Butterfree, evolves instead from Venonat, which is clearly supposed to be a gnat.

So instead of having any kind of biology, we choose to have a gnat turn into a moth. A gnat, which is an adult insect. A gnat, which is so distantly related to moths and has no similar appearance, size, behavior, or environment, turns into a moth. Incredible.

Stay tuned, as my next bug-type Pokémon post will focus on bug types beyond the first generation, including Combee-Vespiquen, Shedinja, and maybe others.