h1

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.

Advertisements
h1

Back to Blogging

July 6, 2012

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!

h1

Biology of Prometheus

July 5, 2012

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!

h1

Ramadan 2010

August 14, 2010

Hello everyone. It has been a while.

So just in brief summary:

– First year graduate school, done
– Joined a lab
– Started thesis work
– Getting data
– Preparing for graduate board orals

This last one is the kicker. In mid-September, I will be taking an oral exam with 5 of my professors. Basically I need to write a 10 page proposal on my research interests, research design, and research goals in the form of a mini grant, present my work to the 5 professors plus my boss, and then answer random questions on anything in biology they feel like asking. It really sounds more overwhelming than it really is. But I’ve been reading up on my field, learning the major players in it, and the current opinions, so by a month from now, hopefully I will be ready.

But in more interesting news, this year I’m celebrating a traditional Muslim Ramadan! In case you don’t know, Ramadan is a month of fasting in the Islamic faith. During daylight hours (between the onset of dawn and the beginning of dusk) one does not eat or drink anything with the goal of becoming closer to Allah, focusing your priorities to Allah and your fellow man, and just in general becoming a better person.

Now one of the interesting things about Ramadan is that every year it moves up about 10 days. This is because it follows the Lunar calendar instead of a typical 365.25 days per year Gregorian calendar. So what this means is that every year, Ramadan moves up by 10 days. So if Ramadan this year is between the hottest days of August 11-September 10, next year it will occur during an even hotter and longer, August 1-August 30, and so on and so forth. I remember in high school when Ramadan was in late fall, and the days were quite short and cool, and how easy it would have been to start doing Ramadan then and not now.

But I’ve been pushing through and really discovering a lot about how my body works. I have some pretty good Ramadan stories already but I’ll share those at a later time. I promise to keep writing in this not because I feel obligated, but because I feel like it will be a good exercise for me. Anyway, enjoy eating while the sun is out, and don’t rub it in people’s faces that you can. Time to finish my experiment, go home, and wait to eat.

h1

Where am I?

September 27, 2009

Yesterday, as part of our “orientation”/ department sponsored social events, a small group of us went hiking at a nearby state park. Although poorly attended by my fellow classmates (which is hypocritical for me to say because I almost didn’t go…) the trip was definitely highly anticipated and definitely worth it.

I love to hike. I never really got to do it a whole lot in undergrad as a result of being extremely busy with school and living so close to a major metropolitan area (it’s hard to convince your friends to drive an hour and a half away to go hiking when the big city is a 30 minute el ride away).

But getting away to nature is definitely a favorite past time. There’s something about being in it, being surrounded by life, surrounded by freshness, surrounded by old trees, that really puts things together. Life makes sense in the chaos of the forest.

As I sit in the cold confines of my laboratory bench and chair, reading about the godlessness of the universe when I should be reading about the homology, or sameness, between yeast and humans, I wonder what the heck I’m doing. Is this gel that I just accidentally set on fire because I misread the voltmeter going to get me closer to understanding? Is this book about the inanities of religion getting me farther from god? Or do I just need to go for a walk, and let my mind wander the light peaking through the trees, the scent and musk of the flowers and animals, the babble of the brook and the crackle of the creek?

h1

Networks

September 14, 2009

Sorry for the lack of updates. It’s a busy time.

But I’m going to post this pretty awesome article theorizing how social networks play a role in our health and happiness. The idea of networks is something I’ve always wanted to study more (the sociologist in me). How one person can affect their friends and strangers, how the type-A personality can start a revolution, how ideas and open-mindedness can lead to progressive change, etc.

The statistical work they do is a little on the sketchy side, and the source of data, though large, needs to be a little more comprehensive. But all in all, a good, long read.


Here’s the article

h1

Lateral Meme Transfer

September 6, 2009

So the first paper I had to read in my Cell Bio course was a paper by Carl Woese at the University of Illinois from 1998 called “The universal ancestor.” LUCA, or Last Universal Common Ancestor by many scientist, is our sort of Adam and Eve: some simple cell from which environmental factors and genetic mutations led to the vast array of organisms we see and observe today, including ourselves. His theory, in short, is that LUCA could not have been one species as we know it today, having all of the essential little biological processes we see in our cells or even simpler organisms like bacteria. Instead he proposes that LUCA was instead a community of “progenotes” or extremely simple cells that lack large RNA sequences with each cell providing a different crucial aspect to life. As the community of cells survived, they had to give and share with each other, proving that the cells were not self sufficient as we would see later.

In the paper he says that the method of evolution for LUCA was different than the method we see today. Today we evolve through genetic inheritance. Family trees. Mom and Dad are different from each other, they have a kid, and if that kid got good aspect of mom and good aspect of dad, he will survive to adulthood and produce a bunch of children who hopefully will also have those same good aspects. Aspects in this case being genes that lead to a stronger ability to survive. But in the chaotic … cluster fuck … of the progenotes, everything evolved differently. Calling it lateral gene transfer, he proposes that the cells of LUCA easily shared genetic information. If things worked well the genetic information could move around and be taken by other cells and if things failed, the information would be quickly lost as those cells died. So evolution moved extremely fast with direct genetic movement from cell to cell instead of what we have today that requires slow generational movement.

An interesting aspect of his paper is his discussion on translation. Translation is how genetic information, like RNA and DNA, become proteins, proteins being the workers of the cell. He says the poor early ribosomes, ribosomes being the RNA machinery that does translation, were extremely inefficient. This means that mutation rates were high, and only small proteins could be made from equally small genomes. And with eventual efficient ribosomes being made that had much better accuracy, traditional vertical, family tree inheritance could occur. Because with better ribosomes meant less mutation and larger proteins which could not be genetically transferred laterally. This all just reminded me of HIV. HIV relies on a poorly functioning reverse transcriptase to be able to adapt to anything. But this is a side note and I’ll get back on topic…

While this theory of his is based on supposition, although his reasoning is extremely well thought out and very believable, the idea of lateral inheritance is an important one. I’ve been thinking about religion a lot lately. Being around the nonbelievers (aka, the biologists) have really got me thinking. Biologists tend to, more than any other science, reject religion. This is the result of evolution being a major aspect of our career. “Nothing in biology makes sense except in the light of evolution” a famous quote by Theodosius Dobzhansky. We stake our experiments on evolution. I’m currently working on a project in yeast that looks at a system in yeast that is conserved in humans. Without evolution, I’m wasting my time: who cares about yeast. But with evolution, I’m looking at a system so important to life, even a single celled organism has it.

But is rejecting religion a bad thing?

I’m going to make the case, with lateral gene transfer, that it might be. This is coming from a biologist, remember. A godless biologist at that.

Religion is a very important aspect of our development into society. Religion brings our people together and gives us a culture. For I don’t know how long, religion has worked in doing that. Look at marriage. A religious institution, it has for the longest time, brought two people together to care and nurture their children. What is more evolutionarily stronger than this institution? We have a long tradition of courtship that leads to two dissimilar people (opposites attract) getting together and sharing their differing genes. Then we bind them together to ensure that these children survive the difficulties of childhood and become successful, child bearing adults. Marriage is a meme that proved to succeed in raising tons of strong children, so it stuck.

(Skip this is you know about memetics) A meme is a cultural gene. The theory of memetics is relatively new (1970’s Selfish Gene by Richard Dawkins). It states that we pass down genes to our children. But with human thought, we have developed a new self replicating “gene” that strictly relates to culture. He called these meme’s, or the cultural genes that like genes, go through evolution and natural selection. Some memes survive, marriage, and some die, Pogs. And some memes evolve, in this case religion.

So religion is, in my opinion, the most successful meme(s). It has held so many societies together, keeping children alive, and getting us to work together and live longer. It keeps us moral, defining what is good, like helping out your neighbors, and bad, killing your neighbors. It has led to cultural bloom: JS Bach is considered one of the best composers, and his Mass in B minor is considered one of the best works ever written, and it’s church music!

But only recently have we seen a different ideology spread. With mass communication and an acceptance of free thought, we are seeing it possible to be moral, care for children, form a working society without religion. Atheism is spreading, and not resulting in tons of anarchists burning houses down and lynching Christians. So is this the end of religion? Maybe.

But I doubt it. Because as ironic as it is, religion, specifically Christian religion, has child bearing in it’s roots. The Duggars have 19 kids with more on the way. Not because pregnancy is some kinky infatuation, but because God told them children are gifts from up above, so more gifts are better than less. But that’s evolution! The person with the most successful progeny wins! And ironically, the godless people working in media are providing them with money to show godless America a crazy Christian household. Guess what, the godless are giving this Christian family money to be even more successful, both evolutionarily and societally.

But are the atheists producing 19 children? Are we listening to the word of Darwin and crapping out as many children as we can to spread our thinking in the world. And I have a feeling we’re not. Even Richard Dawkins, who many biologists have come to view as the atheistic leader of evolutionary thought, has only one child. That guy should be producing tons of children to someday spread his thought to the world. He preaches a militant atheism. How does he plan to do it without vertical, family tree inheritance of ideas?

He does it by lateral meme transfer. If atheists aren’t having enough kids to pass this ideology down, they need to spread it laterally. Show the rising youth, confused by war and famine in spite of one dollar spicy chicken sandwiches at BK, a scientific view of life. Show them that hoping for a peaceful, paradise heaven is affecting their happiness in the life they are experiencing today. Show them that they too can have a family, a marriage, and a happy, successful life, without god.

Atheism depends on lateral conversion. So many families are ingrained into their religious ways, and with atheist families so small in number, the only way to make is to convert them.

Will it succeed? I don’t know. My advice? Atheists need to instead of talking about a rejection of God and the importance of evolution, give people a sense that they too can question life, questions fate and destiny, and still create a viable, happy family. And that vertical meme inheritance, allowing your numerous children to also freely believe what they want, and listening to the facts, needs to also be prioritized. It’s worked for religious families for thousands of years. We need to utilize every memetic tool at our disposal. Or else we will see atheism and free thought disappear, just like that your super awesome shiny gold pog that just landed facedown.