Monthly Archives: July 2011


The general thrust himself into the lab, marching past the intern who had greeted him at the entrance of the building. He had two aids with him, one male one female, both of them looking like they had been manufactured somewhere, despite being perfectly human. They wore nondescript suits and were perpetually muttering things into their devices. The man himself had silver hair cropped in a military style and shoulders that spread out from his head like the wings of some bird of prey. He wore his uniform from his days as a general festooned with medals in the manner of someone you didn’t want to mess with.

Charles Gentry waited for the man and his entourage to approach from inside his clean room suit. He could hear his own breathing, feel the humidity of it as it threatened to fog the clear plastic of the helmet. The plastic was treated, so it would be fine, but there was still the feeling that condensation would form at any moment.

“Good morning, Dr. Gentry,” growled the general, all pleasantness stripped from the pleasantry, “Is there a safety issue I wasn’t informed of?”

“No, sir.” Charles studied the general’s two assistants, who were scanning the room continually but not appearing to see anything. “This isn’t a hazmat suit, it’s for the clean room. I’m in and out of there a lot today, so it’s easier just to keep it on. I just decontaminate the outside of the suit before I go in. You’ll see some of the other researchers doing the same. It’s uncomfortable, but it keeps things moving.”

The general raised his head up slightly in a half nod. The man valued efficiency, especially if it came at the expense of comfort. “Let’s be quick about this then. You say you have a prototype ready?”

It was Charles’ turn to nod. “We keep it in a sort of airlock between the wet lab and the clean room. It’s in a stable form, so you don’t need a clean suit to work with it, but both sides of the lab need access to it for experiments.” He walked, inviting the general to follow him. “ I appreciate you coming down here. Our funding is about to run out and we can’t run the risk of going through the usual channels.”

“I understand your research may prove a security risk. I’m warning you, though, this better be good, Dr. Gentry.”

“Oh it’s good alright,” Charles said as he reached the door to the antechamber. He couldn’t help but smile as he continued, “It might just mean the end to all war.”

The general’s thick eyebrows came together in a frown. “What do you mean? Is it a bomb of some sort?”

Charles realized he let out more than he had intended. He glanced at the general’s assistants. “What’s their security clearance?”

The general studied Charles for a moment, seeming to weigh the risks. He took a percussive breath. “Michaels, Chamberlin, wait here for me. I have a feeling this won’t take long.”

The two assistants rolled their eyes in tandem and stepped back as if security clearances were the bane of their existence and life would just be so much easier if they could just be allowed to follow their boss indefinitely.

“Five minutes at the most,” Charles reassured the general. “And you will be impressed; I can guarantee it.”

The general gave his half nod again and Charles yanked open the door to the antechamber, pulling against the negative pressure caused by the air being sucked out of the chamber and through the filtration system. Charles hoped the general didn’t notice. Then he realized the man probably wouldn’t realize the implications even if he did. It was too late anyway. He was in the antechamber with Charles, alone.

“It’s not a bomb,” Charles pulled open a fume hood and withdrew a vial of a dark, syrupy, aquamarine substance to show the general. He unscrewed the plastic top. “Some would call it a namcub.”

“A what shrub?”

“A self-fulfilling prophecy, an incantation that affects the minds of those who experience it.  It’s basically liquid hypnosis.” Charles could tell he wasn’t getting through, so he tried one more explanation. “With this substance, you can hack somebody’s brain.”

The general immediately seemed to lose all interest. “We already have drugs for that sort of thing. Brainwashing techniques have been around since the nineteen-fifties.”

Charles shook his head, but the movement wasn’t that visible while he was inside his suit. “No sir, not like this. Look at it. Look how clear it is, how it moves just like water.”

“Yes it is clear. It looks just like water. But that’s not the point. We’ve tried these mind drugs in the past. They don’t work.”

Charles lifted the vial. “This isn’t a drug, sir. It’s billions of synthetic organisms and nanomaterials in a nutrient bath. Smell it.”

The general brought the vial to his nose and sniffed. He scrunched his nose at the sharp scent of sulfur and alcohol that burned his nostrils.

“No odor at all, right?”

“Right,” the general agreed as if it were obvious, “The problem is even if it works, it’s still not as effective as a spy with their brain intact. Drug induced sleeper agents have a bad habit of staying asleep.”

“But, if you could get control of specific people in power, if you were smart about it, and remained hidden …”

The general laughed, took the vial and drank the contents in one gulp. “Go ahead, Son. See if you can do it. See if you can convince the president, congress, the American people, that they’ve been a bunch of idiots and they need to listen to you. See if you can change one thing for the better and not have it get corrupted, perverted and spat back into your face. Go ahead, show me how to rule the world. Because I sure as hell haven’t been able to figure it out.”

Charles took a breath as the enormity of what he was trying to do hit him. Then he let it out with slight chuckle. “I hear what you’re saying, sir. It is a difficult problem to solve. That’s why I feel education is so important.” Charles put an arm around the wide shoulders of the older man. “It’s our children who need to learn to rule the world after all. In fact, I think education is the most important issue facing our country. Don’t you agree?”

“Yes,” the general said, “I agree.”

Charles smiled and patted the man on the back before opening the door and letting him out of the antechamber. He told himself he was being responsible, making sure his technology wasn’t used by the wrong people. And maybe the government would concentrate a little more on education.

What could be wrong with that?

Charles tried his best not to answer that question.


Diagram of how an atomic force microscope works

So there’s this amazing protein you want to study, and it might very well change the world, but you have a problem: how do you study the protein when its too small for even a microscope to see?

There have been a number of solutions to this problem over the years, many of which are still being used. You could, for instance, study the protein’s effects by adding controlled amounts of it to a sample, or you could keep an organism from producing the protein  through surgery, drugs, or geneticsand see what what happens when it isn’t there. More directly, the obvious solution is to get a better microscope. What do I mean by a “better” microscope? Well, although there are some drawbacks, there are some microscopes that can give much higher resolution and/or provide added information about what you’re looking at.

One example of this is an atomic force microscope. How this works is that a small needle on a cantilever connected to a computer is dragged across what you want to look at. The computer then measures all the bumps that the needle encounters and gives a visual representation on the screen. As you might suspect this method has a number of drawbacks, (the cantilever is fragile, samples have to be specially prepared, etc) but it is possible to identify single atoms using this method.

Another type of microscope that can help you find a protein is an electron microscope. The idea here is to use electrons instead of photons to look at a sample. There are a number of drawbacks to this idea as well, for one thing, samples usually have to be “fixed” with a chemical such as Osmium tetroxide  and this can sometimes change the way things in a sample look. However, here the drawback can also be a good thing. What “fixed” means in this case, is that the molecules are attached to the things around them, and so aren’t going to move around all over the place like they would normally. If you want to see stuff moving around, you’re out of luck, but often you want to see where something is at a particular time and you don’t really want it to be free to wander.

There is another benefit to using electron microscopes. Parts of a sample will be darker depending on how electron dense they are after they’ve been fixed.  the electrons that the microscope uses to scan the sample will bounce off of that part of the sample, causing there to be a dark region. It isn’t always easy to tell which molecules will be more electron dense than others, but there are ways of making it easier. For one thing, if you have a molecule that you know is electron dense that you also know will form a bond with the protein you are looking for, you can add that to your sample and then you can compare the dark regions in the treated sample to how an untreated sample looks. The dark regions that appear in the treated sample but not in the untreated will most likely be your protein.

How confocal microscopy works

This trick also works with fluorescent and confocal microscopes. These microscopes shoot  beams of light at a constant, controlled frequency on the sample, causing some molecules to fluoresce, emitting light at a slightly different frequency. Confocal microscopes have the added benefit of being able to control where exactly the lasers focus so that it can show not only where something is in terms of up, down, left, and right, but also where it is in terms of depth. Once again, if you know a molecule is fluorescent and that it binds to the protein you’re looking for, you can add it to your sample and then check it out in the fluorescent microscope to find your protein. That’s great, but how do you find a fluorescent molecule to bind to your protein?

Diagram of antibody production

Well, your body has a ready-made system for finding molecules that will bind to proteins that has been tested over millions of years of trial and error. The immune system. If a virus or a bacterium enters your body and starts causing problems, your immune cells will start producing antibodies for the proteins that are present on the surface of the intruder, so that if it shows up again, it will be dealt with before it can cause any damage. Antibodies are large (by protein standards), y-shaped molecules produced by white blood cells. There are binding sites at the ends of the smaller arms of the y that bind to specific parts of a molecule. The binding sites act as a sort of lock, where the key is the part of the molecule the antibody binds to. There are a huge number of different binding sites that are available due to the genetic information encoding the antibodies getting shuffled and mutated all the time. When a cell in the body gets stressed, it sends out a signal that a white blood cell(a macrophage to be specific ) can respond to. This white blood cell then invites another cell (a T-cell) to take a look.  This T-cell will then go out and talk to another cell (a B-cell), which has a catalog of antibodies available for production that the T-cell can peruse by seeing if the peptide, or protein part, that’s in the stuff the macrophage ate, is also in the B-cell. If any antibodies from the B-cell  bind to something in the T-cell saw in the macrophage, then the B-cell knows to produce more of that kind of antibody. After that, wherever an antibody encounters its target, it triggers a response from other white blood cells.

Sometimes a cell might be stressed, but the antibodies will bind to something that isn’t the cause. Molecules, from peanuts, pet hair, pollen or just about anything might happen to be present in greater quantities than the thing that’s really causing the problem. This is how allergies happen.

That’s the bad news. The good news is that because antibodies can be found for almost any kind of molecule around, scientist can used lab animals to produce antibodies to the proteins they want to study. Furthermore, by manipulating the genetics of the animal, they can cause each antibody to be attached to a fluorescent molecule. The antibodies can be stored in a vial in a freezer and transported cold to labs all over the world. All a scientist needs to do then, is bathe whatever he or she is studying in a dilution of the antibodies, and then look at the sample with a fluorescent microscope. Wherever the sample fluoresces, that’s where the protein is.

This process is called immunohistochemistry. Immuno- because it deals with antibodies from an immune response, histo- from the Greek for tissue, and chemistry because it deals with the binding of molecules.

Antibody production diagram is from A Positron Named Priscilla: Scientific Discovery at the Frontier (1994) National Academy of Sciences (NAS) ( ) all other images from wikipedia.

Super8review and excuse

I recently saw Super 8 at the theater. It was great, like a mix between E.T. and Godzilla, I give it a 8.5 out 10.Watching it gave me the same feeling as riding a ride at Disneyland or Universal Studios. I always felt like there was something else going on. There’s practically a war going on through out most of the movie, but the camera focuses on the children who are the main characters. You see a lot of the effects of the war without ever seeing what caused them. In one scene the wall of a room explodes away from the kids unexpectedly. Surprising, and it keeps things interesting. At first the alien didn’t seem very intelligent. It acts like some kind of monster through most of the movie, which I find a little annoying, but the movie makes up for it by the end.

I originally wrote a more extensive review of Super8 as well as some other movies, but it got lost when I hit ctrl-c instead of ctrl-v. My family and I got back late today from garage sale-ing. We ended up going all the way (about an hour) to Brentwood to go to an estate sale, which, it turns out, wasn’t going to happen until tomorrow (my brother’s fault:-)). We went to some other places though, so it wasn’t too bad. I got a bunch of old books, a portable tape player and a CD holder.


It was potato chips. Potato crisps if you’re British I suppose. Doesn’t really matter. They were ubiquitous. They were in every household. The plague rats of the twenty-first century, and nobody suspected.

Now almost everyone is dead. Including me.

Except…Wait… I’m thinking! The plague must not have completely killed me! I blink. My vision is blurry, but it slowly begins to clear. A lady is cornered in an alley by a cadre of my fellow plague victims. Zombies. She wields a shotgun. She shoots a zombie in the chest, but of course all that does is knock it back a few feet. I suppose she didn’t watch any horror movies before the plague. Probably thought they were too gory, or a waste of time.


She’s thin, kind of bony, and she wears dark rimmed glasses. The right lens has a crack in it. One leg of her slacks is in tatters and her blazer is ripped. She was probably a very severe looking woman before the plague. Very conservative. The kind of person you wouldn’t expect to eat potato chips. I guess that’s how she managed to survive.

It’s strange, but I think the post-apocalyptic look suits her. Her hair coming out of her bun in wild wisps, her eyes wide, I doubt if she would look as attractive all tightly put together like she must have been before.

I realize I’m shambling toward her. I try to slow myself, but I still don’t have complete control. Using all my will power I manage to raise my arm. It hurts like hell. My arm shakes. It looks like I’m reaching for her as I stumble forward.

If I can just communicate somehow, maybe I can help her. Maybe I have an immunity of some kind to the disease. I struggle to bend my elbow. To move my fingers. My joints creak with the effort. I do a slow wave. I move my dry tongue around in my mouth trying to work up some saliva. I try to talk, but my first effort comes out only as a moan. I try again, but instead of “Hey don’t kill me, I’m not like the others!” or “I’m not quite dead yet!” it comes out as “Braaiiiinsss!”

“Thanks for the tip,” the lady says, smirking and looking crazed. She re-chambers her shotgun. She apparently is taking what I said as advice on where to aim.

My eyes go wide. My lips crack in a dozen places as I mouth the word “NO,” and I try to move away as she aims the barrel of her weapon at my head and-

Molecular motors

At this very moment, inside every cell of your body, there are thousands, even millions of machines, so small that they can’t even be seen with a conventional microscope, performing tasks in mere fractions of a second without any direct supervision. There are tiny molecular robots working together inside us to accomplish goals that scientists are only beginning to understand, every moment, of every day, through out each of our lifetimes. And it’s not just in our bodies. In the bodies of every living thing these things are active. They are, in fact, required for the basic prerequisites of life, yet individually, they are nothing but dumb molecules, practically inert unless the molecules they interact with are present. These things are called molecular motors.

There are a bunch of examples of these and every time I think about them I’m amazed. I just have enough space to talk about maybe two of them, but really almost all molecular motors rely on three things: energy, tubes, and molecular components.

Chemical structure of ATP

The usual form of energy for molecular motors, the twenty dollar bill in the economics of proteins, is ATP. ATP stands for Adenosine triphosphate, and its called that because it is a molecule made up of adenosine attached to three phosphorus atoms (called phosphates while they’re still bonded to a certain number of oxygen atoms) arranged in a line. If proteins need energy for a reaction, they get the energy by lopping off one of the phosphates of an ATP. ATP then turns into ADP (adenosine diphosphate) and the energy that was stored in the bond between the phosphate and the rest of the molecule goes into whatever is needed by the molecular motor or by the reaction that’s going on. When a molecule snaps off a phosphate, the phosphate is bound to that molecule for a while and the molecule is said to be phosphorylated.

This might be a little boring in itself, but the cool thing is that so many different reactions inside a cell depend on the same ATP molecule. Almost every reaction between proteins involves a phosphorylation or a de-phosphorylation. When you eat food, what you’re really doing is supplying your body with ATP.

Adenosine is actually one example of a class of proteins called nucleotides. They can all carry phosphates, though adenesine and guanine are the ones typically used for energy. The reason nucleotides are called nucleotides though, is that they are all present in DNA, which is found in the nucleus of a cell. There are the four typical nucleotides you might remember from high school biology (Adenosine, Guanine, Thymine, and Cytosine) and then there is another that is only present in RNA, uracil. DNA forms a double helix, or a twisted ladder, with each nucleotide forming a rung in the ladder by binding with a partner nucleotide. As a general rule, adenosine binds with taurine, and cysteine binds with guanine. A goes to T and C goes to G. This is important because, by keeping to this rule, a cell can use single stranded DNA as a sort of photo negative, and use it to make the opposite strand over and over again as many times as it’s needed.

The other “tubes” come in two flavors: microtubules and actin fibers. Microtubules are the scaffolding and road system of an animal cell, keeping thing in place and providing a network of connections to every organelle. Actin fibers are similar to microtubules, except they are more temporary. They are used a lot in things like amoebas to form psuedopods and move around.

Finally there are the actual proteins that make up the molecular motor. Kinesins and myosins are perhaps the neatest looking proteins. They look like thin cartoon characters with really large feet. What they do is they carry or pull things along a tube (a microtubule for kinesins and actin fibers for myosins)by “walking” along it. You can see movies of this like the one below. The feet start out latched to a tube. Then one “foot” will release and latch on again a little ahead of where it was before. Then the other foot will to the same and so on so that the molecule is walking along the tube while carrying some cargo.

DNA polymerase is another molecular motor, though it’s often classified as an enzyme. It latches on to a single strand of DNA, takes phosphates of nearby nucleotides and then uses the energy from the phosphates to attach the nucleotide to its partner on the DNA. If the nucleotide is the wrong match, it gets thrown out. DNA polymerase is basically like a factory worker on an assembly line.

But it’s just a protein.

We’re talking atoms bound together, people. And yet they’re doing these sophisticated things. Perhaps its time we recognized our protein overlords.

Incidentally, if you are interested in this, you might want check out this blog as well:

Garage Sale-ing

My family and I have developed a new past time: Garage sale-ing. Of course other folks have no doubt been doing this for awhile, but its new for us. We look through the local paper to find out where they’re having yard sales and then drive to them and look for things to buy. It’s a lot of fun and sometimes we find some good deals.

I mostly look for books and movies. My mom found some antique silver pieces, and my brother made some good deals on ebay. Recently, I got a videocamera that doesn’t appear to work and a lamp, pictured here to the left. I’m hoping to fix the video camera, or figure out how it works.

As for the lamp, I just thought it looked neat. It didn’t have the lampshade when I got it. I paid a dollar for it.  Pretty cool.

Anyway, it’s fun stuff.

Human Error

Marcus stood on the catwalk looking over the trucks and airplanes as they were being loaded with vaccine. “Ladies and Gentlemen!” He called, his voice echoing from the walls of the hanger. “We are about half an hour from go time, those of you who have finished loading your transport may want to take this time to pray. Whatever you believe in, whether it’s God , the Devil, or your lucky rabbit’s foot, get them on the horn. We need all the help we can get. Good bye, and good luck.”

Marcus wiped the sweat beading on his forehead, turned around and walked toward the stairs, wanting to say more, but knowing there wasn’t more to say. Nothing more to do. It was all up to the drivers, the pilots, the guards.

“A rousing speech, Marcus.” Hamilton’s crisp, English voice sang from behind him. “May ask what you believe?”

Marcus paused at the top of the steps then continued down. “I believe in the human race, Hamilton. I have to spend all my energy just doing that. What’s going on with the air conditioning?”

Hamilton was quiet for second or so before answering. “The repair man says it will be at least another hour before he can fix it. We’ll just have to endure it, I’m afraid.”

Marcus whirled around facing the retired British officer. “I’m not asking for my comfort, damn it! If those crates of vaccine get too warm, they’ll be worthless.” When he saw the older man’s lined and weathered face, though, he calmed himself. “I don’t mean to snap at you. You’ve been a great help to us.“

Hamilton raised a hand to say he didn’t mind. “I’ll ask the man to put a rush on it as soon as we get back inside. Maybe an extra body on the problem would help speed things along.”

Marcus nodded and turned back around to continue down the stairs. Hamilton had provided the hanger for them.  Of course the Air Force probably wouldn’t have problems with the air conditioning. Of course any of the military divisions would have probably operated with much greater efficiency. But aside from the National Guard, all the military branches were preparing for an extraterrestrial onslaught that might never happen.

Marcus walked down the length of the hanger, to the door that led to the office area. He had to wait for several people to exit before he could enter. The hanger wasn’t meant for this much traffic.  One of the people leaving, a young man with a mop of blond hair, noticed Marcus, though, and stopped him. “Sir! They’ve translated some of the Glitch message!”

The news had started calling the aliens Glitches, because that was what they seemed to be at first. The Glitches had started their siege by co-opting all satellite communications with what sounded like a mix of feedback and whale calls. Then, without any warning, people started coming down with what seemed at first like a new strain of flu, only the victims started feeling pins and needles sensations, then complete numbness. They became paralyzed, locked in their bodies, unable to move as their nervous systems were systematically destroyed.

“What are they saying?” Marcus asked.

The kid shook his head, flinging a bead of sweat from his eyebrow to the floor. “They can’t tell for sure. They can only make out three words. Exist, allow, and cannot.”

Marcus nodded slowly. “Thanks, son. Get out there and help load, we’re running out of time in this heat.”

“Yes sir!”

“What do you make of that?” Hamilton asked once they were both inside.

Marcus shook his head. “I’m impressed we were able to get that much. An alien language… Heck we didn’t know it was a language until a few weeks ago. But I don’t know how those words help us.”

Hamilton frowned. “I don’t like it. ‘Allow’ and ‘exist’ should not be in a sentence together. Puts our position in a rather different perspective.” An uncomfortable moment passed as the weight of what Hamilton said settled in both men’s hearts. Hamilton coughed lightly. “I’ll talk to the maintenance man.” He rushed away at a speed that was shocking for a man his age.

Marcus walked to the first desk he came to. A young woman was just hanging up the phone, her face pale despite the temperature of the room. “Are the police giving us an escort or not?” Marcus asked.

She shook her head. “They can’t, sir.”

“What do you mean ‘they can’t?’”

She swallowed. “Sir, it’s never been this hot. The wheels of all the police cruisers…they’ve burst.”

“What?” Marcus didn’t bother waiting for an answer. He bounded to the nearest window and opened the blind. The light blinded him at first, the intense heat hitting him like an oven. When his eyes adjusted, he saw the air rippling over the tarmac, the grass yellowing and smoldering.

Marcus closed the blinds quickly. He turned around, his heart and stomach feeling like they had switched places. “Everyone,” He started, but it was too quiet. Everyone was continuing their work, unaware of how the situation had changed. Cannot allow exist, cannot allow exist….

“EVERYONE!” Marcus yelled, and this time he was heard. “Radio all drivers, loaders, and pilots. No one leaves this hanger!”

Marcus ran in the direction Hamilton had gone, dodging people and furniture until he reached the air conditioning control room. Hamilton just finished making his case when Marcus approach the man he was talking to, a small, rough looking man with a moustache and beady eyes. “Can you get us to a sewer?” Marcus asked.

The man nodded. “Great,” Marcus said, “lead as many people down there as you can and get to the city as soon as possible. The aliens have turned the heat on us.”

“Are you sure about this plan?” Hamilton asked, “Won’t the people panic?”

“Have faith, Hamilton,” Marcus said, his eyes wide as he grabbed the Hamilton’s shoulder, “Have faith.”

Flagella and Philosophy

Most bacteria, including E. Coli bacteria, which cause food poisoning, move around by using flagella. Under the microscope, flagella look like kinked up hairs sticking out of the cell and undulating rapidly. If you remember high school biology you might already know, or think you know all about flagella. They’re those hairl-like  things that cells whip back and forth to move forward right?

Not exactly. There are basically two kinds of flagella, the ones that bacteria have, and the ones that eukaryotic cells have. The eukaryotic ones do in fact whip back and forth. The bacterial ones, however, actually propel the cells they’re attached to by corkscrewing through the fluid. As I went over in a previous post, the situation bacteria are presented with isn’t the same as a submarine in a ocean. It’s more like a submarine in a large silo filled with vibrating pebbles. Drag is a huge deal. Bacteria need a powerful technique to move around and a corkscrew type action works rather well.

When you use a corkscrew on a wine bottle you basically turn it around in a circle as it progresses into the cork. So here’s a question: how does a bacterium do that? The flagellum has to be attached to the cell with a buttload of strength to pull the cell along, but at the same time it has to be able spin around like a drill bit. If you look at all the different components of the flagellum (pictured below) you can see that the structure is pretty complicated. WTF? Aren’t bacteria supposed to be primitive organisms?

Well, yes and no. You see, the thing that’s easy to forget about evolution is that every thing that’s around has been evolving for just as long as everything else. It’s just that while our cells were busy trying to figure out how to differentiate and work together to get to places where there was better food and water and such, bacteria were hunkering down and learning to live in the environments they found themselves in. They’re just as good at being bacteria as our cells are at being part of a larger organism. Still, the flagellum is so mind-bogglingly complicated and yet robust in its implementation, that it has from time to time been used to prove or disprove the non-existence of God.

The argument runs something like this: “We and the organisms of Earth have to have been created by a God,” say creationists, “because the bacterial flagella is so complicated that it could not possibly have been formed by chance, any more than a hurricane could blow through a ship yard and create an aircraft carrier.”

“But,” say non-creationists, “each protein that makes up the structure of a flagellum looks similar to proteins used in other, less complicated bacterial structures. Furthermore the flagellum of E. coli is only one variant of many, indicating that one Doesn’t it make sense that flagella might have come from mutations that put the proteins together in ways that were somewhat beneficial? If even one bacterium survived a trying situation better than its neighbors, it would quickly begin to dominate. And evolution of bacteria has been directly observed in nature and in the lab. At the very least that seems more plausible than everything getting poofed into existence through some unknown process by a magical man in the sky.”

You can probably tell which side I favor.

Something that you start to notice if you study biology is how complicated and diverse proteins are. Proteins aren’t just little specks that bump into each other in random ways. Each protein has a different shape and different areas that have different properties that interact with other proteins in different ways depending on environmental factors. It’s an imperfect analogy, but you could almost say proteins have personalities. Almost like people, proteins will work together, compete with each other, and even find things in their environment and use them to accomplish a “goal.” A protein may be stuck in a bad position, for example, and it may come into contact with another protein that likes to pry things apart, and then they will help each other out.

So it’s not exactly the same situation as a hurricane picking up a bunch of aircraft carrier parts and arranging them into a complete aircraft carrier. Its more like a bunch of people who don’t know how to make an aircraft carrier getting a steady supply of parts and enough time and resources to try things out. Eventually, given enough time, people in that situation will eventually make something like an aircraft carrier. Though they’d probably start out making houses, cars, and a number of other things out of the parts before hand. In fact you could look at the current real-life production of an aircraft carrier as an example of evolution. Evolution is simply the effect of variation subjected to some environmental pressure. There were many different types of ship before the aircraft carrier came about. For one thing, there had to be aircrafts in order for there to be any use for one. Humans wanted a place to put planes on the ocean and the aircraft carrier fulfilled that purpose

In a similar way, proteins just want to be in equilibrium, and so they will often use things like enzymes to make equilibrium easier to achieve.

If you are doubtful of any of this, you need only see a video of how a flagellum is formed in a bacteria. The formation of a flagellum is a marvelous and awe-inspiring dance and it happens hundreds of times a second in a single organism ALL THE TIME. You don’t need religion for miracles. You just have to look around.

Turd Polishing

Earlier I posted a review of a production of The Great American Trailer Park Musical  in which I basically praised the cast and crew, but made a few remarks about how I didn’t care for the source material. This review was part of a deal I had with a friend of mine where he would post my reviews of local events to his website, so he can get content and I can get practice and/or recognition for my site. However, my review was apparently a bit upsetting to someone involved with choosing the productions . I’ve since gotten rid of most of my criticisms in my review. The way I figure it, I’m supposed to help promote these events so I should leave my issues with them out of it. However combating this idea is the idea that even if I’m promoting something, I should be as frank as possible so that the promotion rings true. Also there’s another layer to this, as I don’t necessarily have to promote all the events if I don’t want to, and in fact maybe I shouldn’t.

I don’t do this professionally. I’ve done a lot of reviews of movies and some books on my livejournal page, but those weren’t done with any real attempt at quality. I’ve done one other review for my friend’s site, and that’s it. I don’t work for a newspaper or a magazine. I might like to some day, but I’m doing this in my spare time, and I don’t really have a lot of that. So I’m not as prepared as some to deal with these moral quandaries. Am I peeing in the punch bowl by giving criticisms in my reviews? Or if I don’t give criticism am I being a soulless shill?

My guess is the answer is yes on both counts. So I try to go middle of the road, but in this case going middle of the road means you get hit by both lanes of traffic.

Anyway, I’m being overly dramatic. Unfortunately or fortunately, we live in a world with other people who we sometimes disagree with. I disagree with the person who chose the musical. I think the players did an admirable job polishing it and making it look pretty, but that ultimately GATPM is a turd. That isn’t to say I’m right and the people who like it are wrong. Just that my opinion, amateur though it may be, is that GATPM is a disturbing example of wish fulfillment and has no moral compass.

The reasons I think this are perhaps unique to myself and a small set of people. First off, I don’t find infidelity to be very funny. It’s one of the reasons why I don’t mind that I don’t get Showtime stations in my cable package (watch an episode of Californication if you don’t know what I’m talking about). I’m not married, but my parents still are, and I have friends who are, and so I see marriage as an overall positive thing. Furthermore, while I don’t believe people who cheat on their spouse are going to Hell or anything of the sort, I do think that a marriage is a contract between two people, and if someone breaks that contract, then they are despicable and cannot be trusted. In GATPM, Norbert cheats on his wife the moment he gets a chance, but it’s the wife’s fault he cheats, because she can’t leave the trailer due to her agoraphobia. It’s sickening to me, and that kind of distracts from the humor.

That isn’t the worst part though. Jeannie, Norbert’s wife, has agoraphobia because the last time she left the trailer, her baby was kidnapped. Her. BABY. Was. KIDNAPPED. So she’s afraid to leave her trailer for twenty years. There is no indication however that any attempt was made to try to find the baby. No police were consulted as far as the audience knows. If it weren’t for the fact that the kidnapping is performed on stage, the audience might miss that it even happened in the first place. Nobody seems to care that a baby has been taken from his home by unknown persons. Maybe I wouldn’t be as upset about this if it weren’t for the trial of Casey Anthony that was recently concluded. Kaylee wasn’t kidnapped, of course, but something about watching a baby get stolen while the audience is supposed to laugh reminds me of stuffing a baby in the trunk of a car to go partying. Again, this distracts from the humor.

Finally throughout GATPM, different characters sniff markers to get high off their fumes. I don’t find this particular funny either. Maybe if I didn’t know that a great number of people in trailer parks are addicted to meth or some other drug I would think this was perfectly fine. But I can’t help thinking sniffing markers is a placeholder for all types of drug use, and to see it be promoted to such degree…well again, it distracts from the humor. It’s difficult to say why I have a problem with this and yet still enjoy movies like the Hangover, which blatantly promote drug use.  The humor of the Hangover arises from the characters dealing with the downside of drinking and taking drugs to excess. Another movie I enjoy that promotes drug use is Fear and Loathing in Las Vegas and again, its how the character deals with the effects of the drug, and not the taking of the drug itself which is funny.

Perhaps that’s the central issue with GATPM. Sad things happen in the plot, and they’re laughed at, and yet we only rarely see characters dealing with them, which I think is completely backwards. I’ve seen movies about sad subjects from divorce to suicide which were hilarious, but they were funny because of how the characters dealt with the problems, not because of the problems themselves.

GATPM was written by David Nehls and Betsy Kelso. I don’t know what involvement Betsy had in the writing, but I suspect some amount of wish fulfillment on David’s part. Norbert has an affair with a stripper and at some point both his stripper girlfriend and his wife are singing about how much they love him. All is forgiven by the end of the play. There are no repercussions. Granted, this is a comedy, but repercussions can be funny. In fact, I’d say that almost half of comedy is repercussions.

So I think GATPM is a turd. The people who performed it did a good job with it, but that doesn’t change my opinion of the musical.

Yay for digging deeper holes.


Goraff the Destroyer

The airport bustled with all manner of biped  from short and hairy to long, thin, and slimy. There were no quadrupeds or many legged creatures, thank Telrok, but a thin miasma of stench nonetheless assailed Goraff’s nasal ducts. Damn earthlings with their toleration of subspecies. Sometimes Goraff wished his government had eradicated them from the outset instead of setting up trade.

Goraff looked up at the gate number. Z-56.  Eighty three more gates to go. What was the use of faster than light travel if one had to walk for eighteen miles to get to it? And all the security! If Earth and the aligned worlds had just obliterated the moon based Quookle colony when they had the chance, they wouldn’t have to worry about the spine covered beasts sneaking in with someone’s luggage now.

Goraff read the time from his left tentacle. It was the hour of Kartam. 2:40 pm Earth time. He was still early, but only by 20 Earth minutes. He stepped on the treadmill boost and gripped the guide rail tightly with his tentacle. He whizzed past the bipeds buying useless trinkets and postcards from the duty free shops and he was all the happier, even with the fetid air that blasted his sensitive face skin. He would be purple by the time he reached his gate, he was sure.

He stepped off at the end of the tread mill onto the decelerator which slowed him to walking pace. He looked up at the gate number. Z-130. Almost there.

An announcement issued from a ceiling intercom in English: “Galactic Flight 34268 to Pamff has been delayed due to foam liberated from the craft on reentry. Please contact the nearest Galactic terminal to reschedule your flight.”

Goraff cursed in his mother tongue. At this rate he’d never make it to his womb-mate’s wedding in time.

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