Archive for August, 2012

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Biology of Spore Attacks

August 29, 2012

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).

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.

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.

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.

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.

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.

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Biology of 4’33”

August 11, 2012

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?