Archive for the ‘Musings’ Category


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.


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?


Biology of Group Pokémon

July 23, 2012

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

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


Dugtrio 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.


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


Metagross, 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.


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.


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.


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…


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.


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

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

July 19, 2012

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 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!