Coping with Phylogenetic Systematics.

     I would estimate that I have read no more than 700 books in total since I learned how to read at age 5. While some have been more difficult than others, one of them has been the most difficult of all. The title is Phylogenetic Systematics, written by Willi Hennig in German. It was first printed in English in 1966.

      I have not yet finished reading this book. I gave it a try back in the summer of 2008 and got half way through. The problem was that every few minutes I'd have to look up some word I had never seen before and quickly internalize it, because it kept reappearing in the text. The unfamiliar words piled up and I found myself thinking about words and not ideas.

     The reading is much easier on my second attempt, as I have had time to contemplate many of the ideas in this book as well as ingest the various abstruse words. One such word is chorology, which comes from the Greek word khoros, which means "place". Chorology is thus the study of the spacial distribution of organisms. The distribution can be euryoekous or stenoekous. Again, we have to go back to the Greek to get a handle on these. Eury means "wide" and  steno means "narrow" and I have found evidence indicating that "oekous" can be equivalent to oikos, which means "house of". Therefore, an organism that is euryoekous is tolerant of a wide range of habitats, while an organism that is stenoekous tolerates very few. The problem with the words in this book is that I often cannot find them in my physical dictionary (American Heritage), published in 1992. It's not that the words are new, rather, they are obscure in the most extreme sense. Not even a google search offers any help with some of them. I have found a book, though, titled Animal Behavior Desk Reference which has many of them defined. I would love to buy the book, but it costs $175 at amazon.com

     While reading this book it is important to keep in mind the differences between three types of genetic relationships. Those are:

1. Ontogenetic relationships, which are those between semaphoronts.

2. Tokogenetic relationships, which are those between individuals.

3. Phylogenetic relationships, which are those between species.

     Don't know what a semaphoront is? Not sure about tokogenetic? Those are the types of early problems I faced while trying to read this book. All of 3 of those relationships together are called hologenetics and the author expressed that the book could be called Hologenetic Systematics. The Greek root holo, which means "entire" was used. It is also common to see this referred to as "Cladistics".

     This book is filled with fascinating definitions. Here's one of them:

     SPECIES: "the study of the evolutionary process in which groups of forms that have hitherto interbred, or at least were capable of interbreeding, become divided into two or more separate groups that for physical reasons cannot interbreed"

     It is also referred to as species cleavage, which you can see here graphically. It is an important concept, something quite obvious that had never occurred to me before.

The Ineffable Soul and Emergence

 
     Here is something I wrote in June of this year:

THE INEFFABLE SOUL

     Mostly everyone else accepts that souls exist, yet I reject the notion. A word that can be used to describe me is iconoclastic, which essentially means I have no interest in the belief systems that have been invented by other people. I make my own. By my reasoning, some other person, now very unknown, came up with the idea of a soul. It turned out to be a cool idea because many people have accepted it, but just because something “rings true” does not mean it’s true.
    My suspicion is that people are confusing the soul with consciousness. What is consciousness? It is an emergent property of densely packed neurons that cannot be found by looking at the neurons, or, inside the brain. It has been said that if the brain were expanded and we were to walk around inside, we would not find consciousness. Is there a better way to explain this? Yes.
    We humans are made of atoms*. It is only when many atoms come together that humans are apparent. Thus, a human can be called an emergent property of atoms. You will not find a human by looking at atoms, any more than you will find consciousness by looking at neurons. Furthermore, we function very differently from atoms. Atoms do not eat, have sex, go to sleep, etc. This indicates that the stuff of which things are made does not have to bear any resemblance to its function. As a further example, we can think, but our brain cells, the neurons, cannot. It’s not until many neurons collect together that something new emerges, such as cognition.
    So, what happens when we die? Since consciousness requires an operating collection of neurons, this indicates that consciousness will stop when the neurons die. In other words, we will not know when we die. Anyone that has an ‘after-death’ experience is remembering something, which indicates they still had a consciousness, even though medical science may say otherwise. If the brain was removed and each neuron was destroyed and the person still remembered something, then that would indicate there might be a soul. But that has never been observed.
   
    *What is an atom? Imagine an empty football stadium with a fly in the center. What have you got? About 99% empty space. That’s an atom. It’s hard enough to imagine the emptiness of which we are constructed, and even more puzzling that we do not pass through one another. But it gets worse. The components of the nucleus, the proton and neutron, are even emptier. We’re here mainly because of forces. The matter of which we are constructed is ineffable, like souls.

     I wrote this in March of this year:

EMERGENCE

    Although it is reasonable to assume that I am a walking encyclopedia, that is not the case. The amount of information in my head is really not much, but it appears to be significant because I spend a lot of time reading. Somehow, when I was 5 years old, I learned how to read. I do not remember how, because, I could not read and then I suddenly could read. Reading turned out to be pretty useful because I no longer had to guess what was happening in the pictures, nor did I have to ask someone else to read for me. So, I’ve been busily reading for the past 27 years and have learned an important fact. Few people care about the fact they have reading ability and they try very hard to not use it. This explains why some people think I’m smart. Since they don’t read, all the facts I know seem impressive. But those facts are not secrets - any damn fool can read the same books I read and know the exact same things I know. All of it. If I have a secret, then I’d like to know about it. But why did I not stop reading, like most people?
    Generally, people learn how to read and go to great lengths to ignore their ability by spending time watching TV or playing video games. The advantage of continuing to read is that knowledge accumulates and learning more becomes easier, but this does not mean that one can know everything, nor even come close. I quickly discovered that through reading, I could access information that school did not provide. For example, I read about dinosaurs when I was 5 years old, which was not part of the curriculum. It didn’t take me long to realize that in order to get educated I would need some source other than school. I’ve always been curious about reality and school offers no courses on that topic. Have you ever heard of an Introduction to Reality course?
    What is reality? Most people consider it to be what they consciously experience, such as rising from bed, going to work, watching TV, listening to music, going to restaurants, etc. But a conscious experience has many deficiencies, since we see a small part of the electromagnetic spectrum, hear a narrow range of sounds, and can touch neither a plasma nor objects with most of the heat removed. The amount of information that we can extract from our surroundings without using technology is quite pitiful. For example, our eyes gather a very small part of the electromagnetic spectrum, which we call “visible light”. But we are completely missing out on gamma rays, x-rays, ultra-violet, infra-red, microwaves, and radio waves unless we use technology. So, when we look at objects, we are getting one interpretation of their appearance. Those same objects look different under x-rays or radio waves, for example.
    I view reality as confinement. Analogously, this can understood by imagining sitting in a jail cell. If one is freely ambulating upon the surface of the earth, how can that possibly bear any resemblance to being trapped in a cell? Consider for a moment what is required to escape from a cell and you will see there is little difference. If one wishes to leave, then one may try any of the four forces. While sitting in the cell, you decide to try gravity first. You know that gravity is really strong, because it makes things fall. But the floor of the cell is not falling very far, since the ground is stopping it. So gravity is not that strong. It will not help you. The next force is electromagnetism, which powers your muscles and holds groups of atoms together. After a short while, it becomes apparent that electromagnetism will not help you either. The atomic bonds in concrete and steel are stronger than those in your skin and muscles and thus you tire and get many bruises. After several days of rest you decide to try the third force, the weak nuclear, which is responsible for radiation, or particle decay. Nothing happens for a while and then you start throwing up and become very weak. Weak nuclear decays seem to be more harmful than helpful. Surely, the fourth force will work, you think. After a month of recuperation, you begin to use the strongest force known - the strong nuclear. But nothing happens. You remain in the cell until your very bones turn to particles smaller than dust motes.
    I think of reality in terms of the forces. Gravity is actually the weakest force, by many orders of magnitude. An “order of magnitude” means 10 times. If something is 2 orders of magnitude weaker than something else, then it is 100 times weaker, for example. Gravity is roughly 30 orders of magnitude weaker than the other forces. This only becomes apparent when one conducts a very simple experiment. Just pick up a paperclip. The entire mass of the earth is holding the paperclip down, yet you are able to pick it up. Thus, your arm is able to defy the entire mass of the earth. Electromagnetism is responsible for all of chemical activity, since it moderates the behavior of electrons, through photons. Photons are commonly known as “visible light”, but they move through space like a wave, and have differing amounts of energy, like waves on the surface of the ocean. This is why photons can kill in the form of x-rays; they carry more energy. The last two forces are less common because we can’t directly see what they do; they operate at distances that are smaller than atoms. The weak nuclear force is responsible for radiation, or the decay of particles. The strong nuclear force holds the nuclei of atoms together and can only be broken at very high temperatures, usually exceeding one trillion degrees.
    Back to confinement, it is easy to see that gravity confines us to the Earth, electromagnetism confines our atoms to one place in the form of a body, the weak nuclear confines many particles to a short amount of time (since they decay), and the strong nuclear confines the cores of atoms. Through the notion of confinement, it becomes apparent that life exists in a cell, while life itself is made of cells. It’s not until many things that are similar collect in large numbers that new properties emerge. As an example, many of the cells in our bodies look the same, but they can form objects that look different and have different properties. At even lower levels, all electrons look the same, yet, through interactions with protons and neutrons, are responsible for all of the matter we can see. It’s not until many electrons interact together with many protons and neutrons that something different emerges.
    Emergence is thus a new hot topic in science. This can be extended rather easily to human behavior. While all humans look relatively the same, it’s not until many of them function together that a new property emerges. Just like one atom cannot make a cell, one human cannot make a prison. Atoms took many billions of years to finally form collections with the emergent property of thought. So, one can argue that a human is now the new particle. What will happen after many trillions of humans function together, for many billions of years? What new property will emerge?

     Here are my responses to some responses I received:

Grassie wrote:

From my viewpoint, reality is a biological construct which is here to aid survival and reproductive fitness. We will die if we don't perceive heat, struggles breathing - seeing colors aids our survival. If we stretch it further, seeing a gun will make us afraid. Reality is that guns are dangerous. Reality is, I think, whatever biological and social constructs which (if we were perfectly built,) would aid us taking the right discussions.

         I wrote:

     DNA is the program for biological structures and I feel it's contained within reality and is not a defining factor. Electrons are also in reality, but DNA does not describe their behavior, which means that biology cannot be the final word. However, DNA has the code that builds our brains, which we use to interpret reality. That code is ultimately constructed of fermions, which obey the laws of quantum mechanics. This does not mean that our brains are quantum mechanical, any more than ants are quantum mechanical (the laws of quantum mechanics stop working somewhere between 1 nm to 1000 nm). I'm able to see that you are more interested in a macro-reality, while I am more interested in a micro-reality. I'm more concerned with what I cannot see.

     I disagree that guns are dangerous. While they may be perceived as dangerous, it is ultimately the electromagnetic force that is dangerous. A bullet has enough energy to destroy the atomic bonds in your skin (both entrance and exit). The solution is to either engineer skin that has atomic bonds strong enough to repel bullets or to shoot the other guy first.

Grassie wrote:

From another perspective, as reality is a human construct, it's nothing "real", or "transcendent". It is nothing and everything, like a great paradox. This perspective can also be "mixed" with the one above, to make a kind of spiritual-materialistic duality which creates a feeling of being a solid human being with feet on the ground and a purpose in life (no comment about what that purpose is), and not only a fleeting schiup of nothing-somethingness.

      I wrote:

     The purpose of life is to survive. You intimated that yourself, when you wrote that reality is a biological construct which is here to aid survival. Therefore, we are here to survive. I find that very reasonable, because dying is the alternative.

Grassie wrote:

As we CAN perceive and be affected by all the physical forces you describe, they certainly are a part of reality, but they aren't any more "real" than everything else that we perceive, and the physicist's way of seeing things isn't more "correct" than our everyday way. It's all about how we view it... Think about sound waves. The most correct way to perceive sound is for some reason to visualize it, to see it as waves moving through air. Mass and weight should be measured in numbers. Why shouldn't they be translated to "smell" instead? If we made a system for it, we could've measured the altitude from the sun to the moon in taste instead of visual-auditory numbers.

I guess this doesn't make any sense. :p

     I wrote:


     It does make sense. Perfect sense. It's just that it doesn't make any sense for us to make distance measurements using taste. An alien race might do that very thing, so it could make sense somewhere.

Video Game Music

Note: the acronym "vgm" is short for "video game music".

     Here's a letter I wrote in December of 2007:

    Some of the vgm I have is the result of nostalgia and the pure novelty of having such things. For instance, I was shocked to learn that video game music is actually put on CD and sold in Japan.

But why does that happen? You don't see vgm on store shelves in America, so why Japan? This is purely my opinion, but I believe part of the answer lies in the way that the original Nintendo system was marketed. In Japan, the system was called 'The Family Computer' and was marketed to entire families, to be used by children and adults alike. In America, the system was called 'The Nintendo Entertainment System' and was marketed to kids, to be used as a toy.

Another part of the answer (probably The Answer) is that a video game company in Japan in the mid 80s, called 'Enix', was looking for a person trained in classical music to make music for their video games. They found Koichi Sugiyama, who was trained in classical music, and he composed music for 'Dragon Quest'. The music was good enough to be released on CD and it was put on the market in 1986. It sold well and an orchestral concert was held, with music from Dragon Quest, in 1987. Since then, there have been well over a hundred video game music concerts in Japan.

The reason why I listen to vgm is because I prefer music that has a strong melody and does not have vocals. Sound quality is not that much of an issue, since my imagination can fill in the gaps. For instance, when I listen to original 8 bit music, I can 'hear' what it sounds like if played with real instruments. My guess is that some people are unable to transform music in their minds to what they want it to sound like.

Most of the vgm I listen to is not taken directly from games, but 'arranged'. If vgm is arranged, that basically means the sound quality is much improved, often with real instruments. Sometimes, popular singers in Japan add lyrics. As one might logically suspect, the Japanese might play video game music on the radio. I asked someone in Japan about that, and they don't. It's not considered popular music at all. It's made because there is some money to be made. Generally, the company that owns the video game would hire an orchestra or a band to arrange the music. This is not done very much anymore, since the newest generation of video game systems produces sound that is indistinguishable from real instruments.

I mentioned that nostalgia is a factor, but its influence is minimal, since much of my favorite vgm is from games I have never played. And it would be quite difficult to play some of those games, as reading ability in Japanese is required.

What style of music is video game music?

As far as I can tell, there does not exist a style of music that has not been used in a video game. So, video game music is not a style of music, but rather, video games are a medium for playing different
styles.

How many video game soundtracks exist?

Definitely more than 50,000. The amount that has been transferred to CD and sold in the marketplace now stands at more than 6,500 different albums. 

EDIT (7-17-2011): There are now more than 20,000 different video game music albums.

PARTICLE PHYSICS - Summary and Essay

     When I'm not watching Korean movies, reading speculative fiction, or listening to music from video games, I'm probably reading or thinking about real science, most notably, particle physics. I made a summary of them earlier this year:

ELEMENTARY PARTICLES

These particles are not comprised of any smaller particles and are generally referred to as point particles, since they are akin to the notion of a point from high school geometry.
There are two main types of elementary particles - fermions and bosons.

FERMIONS
Fermions are the matter particles - we are made of them, along with everything else. Except dark matter. There are at least 24 different fermions, divided up into two main categories.
I have listed the masses of the particles using the accepted unit - the electron volt. For example, MeV is short for million electron volts and GeV is short for billion electron volts.
It's easier to express the masses of particles in units of electron volts because, if we used kilograms, then the numbers would become tiring (even with scientific notation). Just one GeV expressed in kilograms is about .000000000000000000000000001783

    QUARKS (The top quark is the heaviest known particle.)

• Up (2 MeV)
  
• Charm (1.25 GeV)
  
• Top (171 GeV)
  
• Down (5 MeV)
  
• Strange (95 MeV)
  
• Bottom (4.2 GeV)
  

    LEPTONS (The neutrino masses are only a few electron volts each.)

• Electron (0.511 MeV)
  
• Muon (106 MeV)
  
• Tau (1.78 GeV)
  
• Electron Neutrino
• Muon Neutrino
• Tau Neutrino

As you can see, I only listed 12 fermions, yet I have claimed there are at least 24. This is because they each have an antiparticle, which raises the count to 24. For example, the antiparticle of the electron is called the positron.
Antiparticle names are not always so clever, however. Physicists generally just place anti- before the particle name, such as antimuon. The main difference between matter and antimatter is the charge. Electrons have a negative charge, while positrons have a positive charge.

BOSONS
Bosons are the particles that mediate forces. We are not constructed of bosons, yet we are greatly affected by them. There are four currently accepted forces - strong nuclear force, weak nuclear force, electromagnetism, and gravity.

    PHOTON
    Photons are the most well known bosons, since light is made of them. This particle mediates the electromagnetic force. It has no mass and has no known range, other than the size of the universe.

    W and Z BOSONS
    The W and Z bosons are not well known, nor is the force they mediate, the weak nuclear force. This force is responsible for the decay of neutrons and other forms of radioactivity.
    W and Z bosons have a very limited range, only .000000000000000001 meters. This force is much weaker than electromagnetism and the strong force, but vastly stronger than gravity.
    The mass of the W boson is 80.4 GeV and the mass of the Z boson is 91 GeV.

    GLUONS
    There are 8 different types of gluons, they have no mass, and they mediate the strong nuclear force. Gluons are cleverly named, since they act like glue and hold quarks together. Quarks make protons and neutrons, which in turn make atoms, which in turn make us.
    Since quarks are held tight by gluons, we should be thankful for their adamant adherence to proper behavior. Gluons do not feel the electromagnetic force, nor the weak force. They certainly do not feel gravity as well.

    GRAVITON
    The graviton is unconfirmed. None have yet been observed, but their existence has been theorized in order to explain what mediates the gravitational force. Gravity is a force and no particle has been discovered to explain it. This may be due to the weakness of gravity.
    As an example, it is easy to defy gravity. Just pick up a paper clip. The entire mass of the Earth is holding the paper clip down, yet you are able to pick it up. In numbers, gravity is approximately 1,738,590,000,000,000,000,000,000,000,000,000 times weaker than the weak force.
    Since gravity is so weak, any particle that mediates it would need to be quite massive. Massive particles are difficult to find, which explains why we haven't found the graviton (if it exists).

    HIGGS BOSON
    This is another unconfirmed particle, but many believe the LHC will find it. It is thought to permeate space like a fluid and impede W and Z bosons, which limits their range. We might know much more by 2011. As for now, it's too early to say what the Higgs really is.

COMPOSITE PARTICLES

Composite particles are constructed of more than one elementary particle. They are all called hadrons, which are themselves divided up into two types.

HADRONS
Hadrons are collections of quarks, in sets of 3 or 2.
   
    BARYONS
    These are collections of fermions, specifically, 3 quarks. The proton and the neutron are the most well known baryons.

    MESONS
    There are not any well known mesons in the general public. These are quark-antiquark pairs. This may have no meaning to you, but the most well known of the mesons are the pion and kaon. Mesons are responsible for binding protons and neutrons through the strong force.
    Mesons are typically referred to as composite bosons, even though they are not made of bosons. This is because a meson acts like a boson - it mediates a force.

     Bear in mind that my summary above does not even begin to cover how many different particles actually exist. I don't know. No one actually knows that answer. I easily left out more than 100 particles and there's no telling how many more are yet to be discovered. But all particles can be divided up between those that are elementary or composite, or matter or force carriers (I would hope so).

     Here is the essay I wrote earlier this year (click to read) while bored at work one evening:

     You'll notice I put a part in brackets [They have zero mass, but not zero energy, which seems like a contradiction]. I did that due to my own uncertainty (at the time). I now know that photons can indeed have zero energy, so there is no contradiction. To check this yourself, refer to page 53 of this book:

     I strongly recommend that book if you want to check your own knowledge, or simply get a summary of everything known about particle physics up until 2007.

신하균

     신하균, or Shin Ha-Gyun, is a talented Korean actor. I first saw him in 공동경비구역 JSA (Joint Security Area) back in early 2005, when I first started watching Korean movies. Last night I watched his 2008 thriller 더 게임 (The Game), which was equal parts funny and bizarre.
     In case you're not sure who I'm talking about, Shin Ha-Gyun played the green haired deaf-mute in Sympathy for Mr. Vengeance (If you haven't seen that, then what have you been doing? Get with it!)
     I've seen the following movies starring 신하균 :

반 칙왕 / The Foul King (2000)

공동경비구역 JSA / Joint Security Area (2000)

킬러들의 수다 / Guns & Talks (2001)

북수는 나의 것 / Sympathy for Mr. Vengeance (2002)

지구를 지켜라! / Save the Green Planet! (2003)

친절한 금자 씨 / Sympathy for Lady Vengeance (2005)

웰컴 투 동막골 / Welcome to Dongmakgol (2005)

예의없는 것들 / No Mercy for the Rude (2006)

 

더 게임 / The Game (2008)