Biology of Spore Attacks

Currently I am playing the classic SNES RPG, Breath of Fire II. While most of the characters in the game are anthropomorphic animals, one character, Aspara Gus, is an anthropomorphic plant (in the version I am playing, his name is Aspara Gus, and goes by Aspara, while in other translations, he is just called Spar).

Courtesy of http://bof.wikia.com/wiki/Spar

Aspara is an interesting character because he must be one of the first truly transgendered characters in a video game. Upon meeting him, they not only refer to him as being emotionless, but they also wonder what gender he is precisely. This sort of makes sense in the fact that he is basically a walking and talking plant. (Plants do sexual reproduce, thus requiring “male” and “female” gametes, but oftentimes plants will produce both, thus having the ability to self fertilize). Interestingly, if you fuse Aspara with one of the elemental shamans, Sesso, he becomes what looks like a small girl with a big hat, making him truly, transgendered.

Courtesy of http://www.capcom-unity.com/marvelvscapcom/go/thread/view/102977/28597689/UMvC3_DLCCharacter_Request_Thread_V3_(READ_THE_RULES)&post_num=3074

In this fusion form though, Aspara has a special ability called “Spore” that can attack all enemies and has what seems like a 1% chance of making them fall asleep. Now here’s my question, how did spores get aligned with falling asleep?

Though many plants, fungi, and bacteria all have the ability to produce spores, fungal spores are usually what comes to mind first. Fungal spores are generally the cause of most mold allergies that plague people who live/work in older, mold infested buildings. Spores cause an interesting problem for these buildings. Spores are the way for fungi to massively reproduce. A fungus can produce millions of spores, release them into the world, where they then find a new warm moist place to inhabit and grow. Because they are being thrown into the wild so haphazardly, these spore cells are specialized to be able to withstand tons of environmental stresses: high temperatures, low moisture, etc. Though these stresses do make it hard for the spores to grow into full on molds, these stresses can’t actually kill the spores (though high heat can, but it has to be really really hot). This makes eradicating the spores virtually impossible.

It is important to note what spores are. Fungi, like plants, can exist as both haploid (one copy of each chromosome) and diploid (two copies of each chromosome (humans are diploid)) organisms, and the spores are the result of diploid organisms (termed sporophytes in plants) undergoing meiosis to form haploid spores. These spores spread all over the place, and grow into haploid organisms (termed gametophytes in plants) that can then produce gametes which can mate to produce new, genetically unique, sporophytes. This whole process is called alternation of generations.

Courtesy of http://www.studydroid.com/printerFriendlyViewPack.php?packId=103941

Pollen, which is what we are generally allergic to with plants, are the male gametophytes. Spores in the anther of male flowering plants become these tiny organisms made up of only a few cells, which then get packaged very tightly and securely, and are often times released into the air and into people’s noses.

Courtesy of http://girlwithoutaplan.wordpress.com/2010/06/18/my-kryptonite/

This is not the only game that uses the moniker “spore” to mean an attack the causes the enemy to fall asleep. In Pokémon, Spore is the signature move of Parasect, a mushroom Pokémon. The strange thing about this attack, is that they had already created a similar grass attack that makes the enemy fall asleep: Sleep Powder. So the only reason why they would have wanted to create the Spore attack would be to fit Parasect’s mushroom like biology better, but in doing so they created an attack that a mushroom could in theory have, but would not cause sleepiness.

Courtesy of http://www.ign.com/wikis/pokemon-blue-version/Parasect

I do want to point out that these are the only games where I have found “Spore” to mean a sleep attack. I can’t find any other game with a spore attack, and most games that have a sleep status effect calls the attack some play on the words Sleep, Hypnosis, etc.

I actually disagree with this whole spore thing because they could have made this work in a much more biological way that would still result in the same desired effect. They could have made sneezing a status effect. What it would do is prevent the person/Pokémon from being able to attack because they were sneezing. Spores can actually cause sneezing, so biologically this would fit, and with how I laid out the sneezing status effect, it would be practically the same as sleep. They even could have made sneezing a different status effect, for example, it prevents the character from attacking as well as does some damage to the user, or even all players. Just a thought.

Biology of 4’33”

Sorry for the lack of posts lately. I have been away for a yeast conference and have been playing catch up ever since. The conference went well. I got a lot of really good advice and got to meet a ton of very famous scientists in my field, which was very exciting for me.

The meeting was incredibly busy and tiring though, with sessions and talks going from 9am to like 11pm. I did get a chance to skip out for a few hours, explore the city, (Princeton, NJ) and do a little shopping. I found a pretty cool book that just came out called Where the Heart Beats, by Kay Larson. The book is sort of a mix between a biography about the American composer John Cage and a history of Zen Buddhism in the United States. John Cage, though his music is somewhat popular among certain niche groups, is mostly famous for being a music philosopher of sorts. He wrote a lot of incredibly experimental pieces that played with randomness, formally called chance music. For example, he wrote many pieces for a prepared piano, where the piano had been messed with by placing objects inside it, thus creating some very strange noises. The book has received fairly positive reviews, with the main criticism being that the writer spends most of her time discussing Zen and hypothesizing what Cage would have thought, and not enough time on his music or his later life.

Regardless, the book so far has been a very interesting read and has taught me a lot about Zen Buddhism. I did not know before how important Zen was to John Cage. John Cage’s most famous piece, 4’33” is a piece of complete silence. The orchestra, pianist, etc. enters the stage, sits in silence for 4 minutes and 33 seconds, and then bows and exits. Formally, the piece is divided into 3 continuous movements, but the average audience member would not realize.

The purpose of the piece is to reveal the sounds that are always around us. The sounds of people fidgeting, someone coughing, a door opening in the distance all become incredibly apparent when you sit in silence. Cage wrote this piece wanting us to realize that we are constantly surrounded by music, and that everyday noises are a piece by themselves.

But because I was at a biology conference, I started to really think about what this piece means to me, as someone who is not necessarily as in tune to my spiritual, Zen, side. While all the talks I was attending were about genetics and these incredibly high-throughput approaches to answer questions, I realized that this piece forces us to think about the noise in our experiments. In high-throughput approaches to science, we basically want to test everything we possibly can, or in other words throw a ton of money and resources to test every possible gene or protein in every possible way. What we get out of that is a ton of data that we then have to sort through. But what ultimately gets published as a result of all that data mining, are just the most interesting “hits” or things that passed a certain statistical test above the background noise (or all the seemingly unimportant stuff).

4’33” is not just about listening to silence and the random noises that occur around us all the time. It is about realizing that our entire lives are focused on the signal-to-noise ratio; we want the noise to be so low that the signal is obvious, clear, and easy. We listen to music on noise-canceling headphones to ensure we hear just what we want to hear and nothing else. We shop so that we make sure we see everything available to us, so that we know the choice thing we want to buy was the best. As scientists, we want very clear data that absolutely no one could argue with.

I think John Cage wants us to realize that there is something beautiful about the noise. When we listen to music, it is ultimately impossible to completely remove the noise and hear just the orchestra, the singer etc. Interestingly, I think many people do appreciate the importance of the noise. Obviously CD’s and MP3’s will provide the purest sound, yet old school records and record players are still sold today. That static that comes out of the record player is just as much part of the music.

As scientists, we need to accept the noise in our data and realize that it might be meaningful. We so often ignore the noise, only focusing on the hits because they are so clearly going to give us a reliable result. But who knows what we are missing in the noise?

Biology of Gilgamesh

Considered to be one of the oldest stories, the Epic of Gilgamesh originated in Mesopotamia most likely based on a 2500BC King of Uruk, which is now modern day Iraq. I could summarize the story, but in this Star Trek episode, Captain Picard does a mighty fine job.

Gilgamesh, though most likely based on a real king, is supposed to be 2/3 god and 1/3 human. Though we cannot precisely determine why the legend would include such an odd detail, or what the people who passed this story down were trying to say, I was curious as to how someone could be 2/3 of something and 1/3 of something, genetically. I have a few hypotheses that I would like to discuss.

Mathematically, this is impossible.

Because Gilgamesh most likely was human, we can safely assume he had two biological parents, like all of us. So the question is, how could the union of two people produce a person who is 2/3 one thing and 1/3 another thing?

Let’s say a god and a human have a child. That child (N) will be 1/2 god and 1/2 human, making him not enough god.

If N1 then had a child with a god, the new child (N2) would be 3/4 god and 1/4 human, making N2 too much god.

If N2 then had a child with a human, he would be way too much human, but if he had a child with a god, he’d be way too much god. So what if N2 had a child with a child like N1 (1/2 god 1/2 human)? He would end up with a child (N3) that is 5/8 god and 3/8 human, which makes him not enough god.

Diagram of the limit as it approaches 2/3.

If we continue this pattern, of child N procreating with child N-1, we will never get a perfect 2/3 god 1/3 human, and that is simply because we are working with pairs. No power of 2 will ever come out to be divisible by 3.

Perhaps there’s a third parent.

When a man and a woman love each other, they can make a baby. While his sperm donates 22 chromosomes and a Y, her egg donates 22 chromosomes, an X, and mitochondrial DNA. So genetically there is inherently some inequality in the amount of genetic information passed down. Disregarding the fact that the X chromosome holds so much more information than the Y, which really holds just the male determining genes (the SRY), the woman is responsible for giving her child good mitochondria, because her eggs hold the mitochondria that the developing baby must have in all of its cells.

Mitochondria are the energy producing organelles in the cell, and they originate from bacteria that formed a symbiotic relationship with ancient cells. Because they used to be bacteria, they also come with their own DNA. Even though over the years a lot of the mitochondrial genome has been transferred into our genome, quite a few important genes are still made in mitochondria, such as mitochondria specific proteins and mitochondrial tRNAs.

Mitochondrial DNA is also implicated in many human diseases as a result of the important genes it has. As a result, many have considered the possibility of a therapy for these diseases; instead of the mother giving her genome and her egg which holds the mitochondria, the egg and mitochondria could come from another woman who doesn’t have a mitochondrial disease. But this sort of procedure is still really in development and requires legal work to be done.

But even if the ancient Mesopatamians did have the in vitro fertilization technology to do this, one god’s mitochondrial DNA is certainly not enough to give her equal credit to the god and human that gave half their genomes.

Polyploidy

Though we are all diploid organisms, or organisms that have two copies of each chromosome with one coming from each parent, there are strange cases of having extra copies of chromosomes. The two most famous being trisomy of chromosome 21, which leads to Down Syndrome, and Kleinfelter’s Syndrome, which is where a man has 3 sex chromosomes: 2 X chromosomes and a Y. Unfortunately, these are the most well known because they are the only ones that are mild enough to lead to live births, any other kind of trisomy leads to death and miscarriage.

But these are just trisomies, where there is just one extra chromosome. Triploidy, or having three sets of each chromosome, definitely does not lead to a live birth, usually ending in miscarriage. These embryos come from either the egg or the sperm not properly dividing and thus still being diploid and not haploid. But the reason these embryos cannot develop is because there is just too much genetic information for the babies to handle. And in many cases, there are genes that we actually only want to have one active copy. Many of genes are called imprinted genes because only the mother or only the father’s gene is usually active.

So this is definitely not a reasonable explanation for Gilgamesh’s 2/3 god and 1/3 human genetics, but it does come the closest. If Gilgamesh’s godly parent donated twice as much DNA as the human parent, and he was still able to develop, then this could work. He would still have two parents, but his triploidy would make him genetically 2/3 god and 1/3 human. And who knows, maybe Gilgamesh’s godly genes have special proteins that can deal with the extra genetic information.

Biology of Group Pokémon

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

Courtesy of http://media.photobucket.com/image/dugtrio%20pokemon%20render/nicelongschlong/051Dugtrio.png?o=1

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.

Courtesy of http://demotivational-posters-the-pokcommunity-forums.funnyimages12.no-ip.org/?q=Demotivational%20Posters%20The%20Pokcommunity%20Forums

Magnaton

Courtesy of http://pokemondb.net/pokedex/magneton

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.

Courtesy of http://bulbapedia.bulbagarden.net/wiki/Magnezone_(Pok%C3%A9mon)

Metagross

Courtesy of http://gallery.gtsplus.net/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.

Courtesy of http://bulbapedia.bulbagarden.net/wiki/Beldum_(Pok%C3%A9mon)

Probopass

Courtesy of http://media.photobucket.com/image/probopass/samdiceque/Probopass.png?o=4

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

Courtesy of http://pldh.net/dex/sprites/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

Courtesy of http://pokemondb.net/pokedex/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

Courtesy of http://pokestation.net/dex/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.

Reflections on Ramadan

Today is the first day of Ramadan. Ramadan is a month on the Muslim calendar where Muslims fast for during the day for an entire month. Basically how it works, one wakes up while it still dark, and eats a quick morning meal before the first prayer at dawn. Then throughout the daylight hours, Muslims abstain from eating and drinking, including water, and perform three more prayers. Then at sunset, Muslims perform one more prayer, then they break their fast with a meal called Iftar. Iftars are usually wild celebrations that can many times go very very late into the night.

I want to implore though that the fast is not the point of Ramadan. Even though it sounds like it is an awful challenge of the mind and body, the goal of Ramadan is to reflect on yourself and your spiritual self, and to give back to the poor and needy. Community service and giving is a cornerstone of Ramadan.

For the last two years I have somewhat successfully participated in Ramadan. My first Ramadan in 2010 began August 11 and ended September 11, three days before my graduate school qualifying exam. Needless to say, the stress of the exam did not mix well with the fasting so I quit with 10 days left in the month. My second Ramadan began July 31 and ended August 30. This time I was actually able to complete the month, and it was incredibly rewarding.

The reason why the date for Ramadan changes every year is because the Muslim calendar is based on the lunar calendar, which only has about 355 days/year. A a result, Ramadan moves up 10 days every year. Which makes the next decade seem somewhat daunting as Ramadan will be slowly moving to earlier and earlier in the summer where the days are longer and longer. Other religions and cultures that use the lunar calendar also face this problem, but deal with it differently. For example, in Judaism, the timing of their holidays are also determined by the lunar calendar. But in order to prevent Hanukkah from moving up 10 days every year, every three years they add an extra 30 day month to the calendar, to correct for the difference. Brilliant!

The actual start and end of Ramadan is actually somewhat controversial. Some believe we should determine the start and end of the month the traditional way by looking at the moon. So if you go from new moon to new moon, the start of the month is when you can see a sliver of the moon. But if it is overcast at Mecca, and the moon cannot be seen, then the end cannot be determined. So the predicted very last day of Ramadan might be delayed if one cannot prove that the month has ended. In other words, the fast continues one more day just in case. The other school of thought is that we have technology and a global society, we can figure out with science when the exact dates will be so we should just use that.

But I do want to discuss some biology. Notably how difficult it is to fast. Now fasting is not unique only to Muslims and the Islamic faith. Judaism has days of fast that are spread throughout the year. They are pretty much the same, where you fast during the day and eat and celebrate at night, but they are single dJainism also has many different kinds of fast, most notably a fast where one does not eat or drink water for 3 consecutive days (which can also ramp up to 8 or 9 days, which sounds unbelievable). Interestingly, they also have a fast called Santhara, where one, who has determined that they have succeeded all they want in life, begins a fast until they die.

Though I could describe the biology and health of someone fasting, I think most people have either fasted, or skipped a couple meals in the day to understand the difficulty of fasting. What I want to discuss is how difficult the marathon is. Not eating every single day for a month plays a huge toll on the psyche. Last year, during Ramadan, I ranked each day with how difficult it was to get through the fast. I ranked the days from 1-10 where 1 is easy and 10 is difficult. Here are my results.

Basically, for me, there was an adjustment period. The first couple days were very difficult. But then you just get used to it. Getting up in the morning for breakfast became essential to getting through the day without exhaustion, and eating at night was not that big of a deal. There were a couple days in the middle that were just difficult, but mostly just because I was kind of fed up with it. But once you get into a routine, everything is easy. Those last few days though, were incredibly difficult. The anticipation of end mixed with being so tired of the routine made those days so hard.

Once Ramadan ends, the Muslim community celebrates for 3 days in a holiday called Eid ul-Fitr. This is sort of the Islamic Christmas where people celebrate, spend a lot of time with family, and just enjoy life. And after the marathon that is Ramadan, I’m sure for many Muslims, it is a truly great couple of days.

Biology of Bug-Type Pokémon II (Combee)

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

Courtesy of http://pokemon.neoseeker.com/wiki/Combee

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?)

Courtesy of http://pokemon.neoseeker.com/wiki/Vespiquen

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.

Courtesy of http://alamancebeekeepers.org/2012-beekeeping-class/class-handouts/honey_bee_chart/

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.

Biology of Cyclops (X-Men)

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.

Biology of Bug-Type Pokémon

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

Courtesy of http://www.sora.net.au/caterpie.html

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.)

Courtesy of http://www.butterfliesandart.com/

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.

Courtesy of http://6legs2many.wordpress.com/

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

Courtesy of http://www.sora.net.au/weedle.html

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!

Courtesy of http://juliezickefoose.blogspot.com/2008/03/caterpillars-north-and-south.html

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

Courtesy of http://www.pokemonelite2000.com/16779/review-of-poison-types-of-generation-1-part-2

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.

Back to Blogging

As you can probably see from my most recent post, I have returned to blogging. As always, the goal of this blog is to get me writing as well as teach some biology in interesting ways along the journey.

I have come up with some new and fresh ways to keep the content exciting and different. I will regularly try to do posts where I hypothesize about biology and science in different cultural media, for example my last post looking at how the technology in the movie Prometheus would work. This is an exciting thing for me because it will stretch my knowledge as well as make me really think deeply about strange things most may just overlook. Also, it might give me the opportunity to teach a small biology lesson.

I will also try to regularly post about topics in science I happen to be interested in at the moment, and wish to share with the world. I will definitely put citations in these kinds of posts, but will also try to have citations in any post where I use other people’s direct ideas.

I will try to do at least a post a week, and if that works out well, perhaps 2 posts a week. My method for making me write is a method used by many incredibly successful people. I have a calendar, and every day I write for at least 1 hour, I mark off that day. This way I can see how well I am doing on a daily basis!

That’s all folks! And if you have ideas of topics to cover, feel free to shoot me a line!

Biology of Prometheus

The movie Prometheus, which came out June 8, 2012 and is supposed to be a prequel to the Alien series, is about a team of biologists, anthropologists, archaeologists, and spacemen that travel to a planet they suspect holds the origin of our lives, which they heartwarmingly refer to as answers. Their hypothesis is that human culture has been fascinated with a certain star system over millennia, and in that star system is a race of beings they call, “the engineers,” who created us. Their goal is to meet their makers, and figure out why we exist, (or why they made us).

Spoiler alert!

They discover these humanoid engineers, but they are all dead from some experiment gone wrong. The experiment turns out to be some weapon of mass biological warfare intended to destroy human civilization, that ultimately produces the Alien we all know from the original movies.

Spoiler over!

Ultimately, these engineers seem to be some kind of biological engineering experts, and the technology they created, though fictional, are the topic of today’s post. Specifically, I want to discuss how it might work, some issues, and some thoughts I had about it.

What we know.

In the first scene in the movie, they basically show their entire technology/process that led to our creation.

(Note: This clip is not the complete opening)

We see a humanoid man(?) eat some kind of black sushi roe, his blood vessels go crazy, he keels over, then falls into the water. As his body and cells disintegrate, we see his DNA turn black and degrade. Then cells appear with new DNA, and the cells divide in a manner very similar to early developmental cleavage.

We are to assume that these dividing cells lead to human development, but it remains unclear if these cells then evolved, or if those things became little Adam and Eve embryos.

Additionally, later in the movie we see three more similar processes happen. The first involves a man ingesting just one of these black eggs, the second involves a man getting attacked by a large eel (which we should note is the result of the virus infecting little worms), and the final is one of the “engineers” being attacked by a large squid.

In the first of these, they torch the man prior to his development into some kind of creature, while in the second, we see the body dead, but then he later becomes some kind of super zombie. And finally the third results in the death of the engineer, but the birth of the characteristic alien from the original movies.

How it might work.

Clearly, inside these eggs is the ability to transform a host organism into a monster via a couple different mechanisms. What this basically sounds like is a virus. Except viruses big enough to see with the naked eye have not really been discovered, though we don’t know if one of those black egg things are one unit of virus or maybe a big bag of them. Additionally, this virus is potentially one of the most sophisticated viruses, so perhaps it needs to be big. Regardless here’s my schematic for how I think the process works:

1. A creature must be infected.

a. via – ingestion, sexual contact, attack
b. Can be transmitted straight from the eggs/virus, or from host to host.
c. Sexual contact can transmit the virus to mother, but not actually infect her, instead opting to become an embryo in her womb.

2. The egg/virus DNA then takes over the host DNA.

a. This is the viral life cycle, a virus injects its DNA into a cell, forces the cell to use that DNA to make more virus, then destroys the cell to release more virus.
b. Though it may seem like the virus should be self-sufficient, in this case and in the case of real viruses, a host is required to provide nutrients.

3. A novel creature forms.

a. One option is for the entire body to completely disintegrate, and creatures to form from what remains. (Humans would be an example of this)
b. Another is for the formation of a monster/zombie.
c. Lastly a monster forms within the body of the host.

So the technology seems to require viral DNA and a host for the viral DNA to take over, or absorb nutrients to create a new creature.

Some issues.

The main issue I want to discuss is really how DNA is perceived. The writers did a good job of really creating a complete story around this technology, and the way they illustrated DNA is really quite exquisite, but how they described their process was a little suspicious sounding.

The writer says things like “DNA getting infected” a couple times, and they ultimately choose to illustrate it as the engineer’s beige DNA turning black to mean it has become infected. Unfortunately, this just shows what a foreign concept DNA is to many people. DNA isn’t some kind of liquid one poisons, or a cloth you can spill wine on. It is a macromolecule (meaning a molecule that is made up of molecular units called monomers) that has information coded into it based on the sequence of molecules. If something were to “infect” it, it would have to either physically break the molecule apart and add things to it (which is how viruses many times work), or it would have to actually change the molecules into other things to scramble the message (which is how mutagens such as UV rays and carcinogens work). If either of these mechanisms were the case, they both require something of the virus to interact with the DNA, either viral DNA coming in and adding itself, or some kind of protein or other chemical messing up the bonds in the DNA. (I doubt UV rays or another kind of energy could be contained in the eggs and cause such specific kinds of mutations.)

But perhaps my analysis is incorrect then, and the technology is not viral, but instead biochemical; so instead of viral DNA inserting itself into the host genome, the eggs instead mutate the host genome in a specific way to create the beast. This would require the black eggs to have encoded in its genome, genes that make incredibly sophisticated proteins that can specifically bind certain sequences of the host’s genome, and mutate it in a specific way to create the monsters. This could actually work quite well as a mechanism. And if this were the mechanism the writers were going for, then the way they illustrated the infection, from an abstract point of view, is not necessarily the worst, though you should remember that this kind of mutation would require some kind of protein or chemical interacting with the DNA.

But another strange issue with how they illustrated the process is showing the DNA disintegrate, and then come back together spontaneously and form cells around it. I can not honestly think of a way for this to really work without taking an incredibly long amount of time. Especially for cells to form de novo, or more simply put, from raw materials. Additionally, if the DNA actually does disintegrate, then all information should be lost, regardless if the eggs use viral DNA, or scramble the information by mutagenesis.

Some thoughts.

Though our understanding of proteins and their structure get better with every passing day, we are not yet at the sophistication to be able to create proteins that can specifically mutate specific sequences in a specific way to create something different. And we know a whole lot about viruses, their mechanisms, and their history, but we are far from being able to create a virus with the information capacity to make huge organismal changes like this.

But could you imaging the applications of these kinds of technology? We could create proteins that could specifically target a site in the genome and change it to something different. This would revolutionize medicine. People with genetic disorders could be cured as an embryo and literally never even have the possibility of passing the disorder to their children. It would wild!