Author Archives: zorknot

Switchblade Pisces: Pt. 10

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The room I’m in isn’t too bad. It’s a little on the small side. It’s even smaller than my efficiency apartment where this all started. There’s a double-sized bed, and the room can fit maybe three more beds of the same size and that’s it. On the other hand the refrigerator is well stocked with tv dinners, the microwave works well, and best of all, the flat screen opposite the bed takes up almost the whole wall. It’s got all the satellite channels, and all the latest operating systems, including the ones for video game consoles. Sony, Microsoft, and Nintendo, all in one Frankenstein set up. Testing the system out earlier, I started up all three versions of the same game using the same disc slot, giggling madly when they all ran flawlessly. I felt like a mad scientist. And that’s when I remembered where I was.

So I’ve been lying in bed, staring at the ceiling for the past hour or so. I should try to escape. But I’m not really a prisoner. The FBI is possibly going to try to kill me, but probably not. If I just go the police or something… I want to help out Janis, though, even though she killed those people. That was kind of my fault though, wasn’t it? And maybe they aren’t dead.

I’m stupid for agreeing to stay here. Baxter is a madman, I don’t care how good his intentions are. Teaching Janis self defense, okay. Surgically attaching knives to her wrists? Crazy. Even if it is kind of badass.

Letting out a growl of frustration, I get up and look at the games available on the entertainment system. It looks like Baxter’s got Biomechanica 4. It just came out last month. I really liked the other three games in the series. They had a lot of action, and a nice linear plot. None of that role playing crap where you had to figure out what the right thing to say is and depending on what you do the game could change.  All three console versions of Biomechanica 4 are in the display case underneath the television. The Playstation version is supposed to have better resolution, but the Xbox version is supposedly more stable. The Wii version would normally be my last choice, except I’ve heard that there are some extra features they put in that version since it was the last one they rolled out.

I rub the bridge of my nose with my fingers. I rummage in my pockets. I normally carry a six-sided die and a coin with me for just this kind of predicament. I left in a rush though. I’ve got my wallet, but no change. I don’t even have my keys, much less anything else. I could maybe try to flip one of my credit cards, but they’re too light. I want to be able to see whatever I use spin a few times before landing. That way I can sure it’s truly random. Maybe I could fold one of my dollar bills into a foot ball shape and mark one of the sides?

I shake my head. Too lopsided. I’m in a huge building. There has to be a coin or a die somewhere. I’m still dressed, I just need to put my shoes on. I usually put my right shoe on first, because I’m right-handed, but the left one is closer this time, so after some deliberation, I put that one on first and then the right.

Before I open the door to leave, I close my eyes and take a few deep breaths. I’m acting crazy. Why can’t I make a decision? Is Baxter right? Is it a lack of willpower? I swallow. I feel like I have willpower. I can go days without having one of these attacks of indecision. It’s probably just stress. Whenever I get stressed, it’s like the part of me that knows what to do just takes a vacation. I always kind of thought everyone was like that. Maybe they are a little bit. Maybe whatever it is most people go through, I just go through more. Or less. Or something.

Maybe I’m just tired. If I sleep for a while, maybe I can figure all this out when I wake up. I don’t know how I’m going to be able to go to sleep though. Maybe if I just lie down, though, I’ll calm down enough. It seems like a reasonable plan.

I hesitate at the door while I consider it. My hand turns the knob.

Why am I even leaving? For a coin so I can flip it to make a decision? That’s stupid!

I push the door open.

I should just stay in the room and think about things a little more.

But the door is closed and I’m outside of the room in the hallway.

It’s two in the morning, and the front part of the clinic, where I am is mostly empty. The room I came from is at the top of a T intersection in the hallway. I can go forward, left, or right. All three ways seem to disappear into shadow.

I feel utterly lost.

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Gels

http://bit.ly/uMnIip

You might think that gels are just things you put in your shoes or in your hair. You might just think of Jello when you hear the word. But gels can do a surprising number of things and can be used in a lot of interesting ways.

First off, what exactly is a gel? The part you know is that a gel is basically a material that’s somewhere between a liquid and a solid. It holds its shape like a solid, but jiggles and deforms as if it were a liquid. What you probably don’t know is that this strange state is caused by a battle between several different forces, some of which try to pull a gel apart, while others keep it together.

Most gels are made up of long stranded proteins or sugars that have a strong negative charge in environment of neutral pH, a situation similar to what  molecules of DNA experience. However, unlike DNA, gel molecules can cross link to one another if they are heated and then cooled. Because of these crosslinks, as much as it would normally take a lot of force to bring the negatively charged molecules together, the crosslinks hold them so they can’t disperse. It’s like a small crowd of people that decide to hold one another’s hands. If they then try to get as far apart from one another as possible, they will form a fairly stable circle. The spaces between the molecules in a gel are usually filled with water or some other liquid medium, giving them their liquid-like properties.

Because gels have these spaces, they can be used as nicely uniform filters as in polyacrylamide and agar gels used in electrophoresis. You can also make aerogels or xerogels by quickly evaporating the liquid inside a gel without allowing the gel structure to change. The resulting materials are light weight (because they are mostly air) and have incredibly large surface areas.

http://bit.ly/vyKHu3 : A picture of the structure of a dried hydrogel (or xerogel)

To illustrate this last quality, imagine a solid centimeter-wide cube. The surface area of the cube would be the area of one face of the cube times 6, or 6 square centimeters. Now imagine the cube is broken up into eight cubes each a half a centimeter wide. The surface area of this arrangement is going the six times the area of all the faces on all the cubes, or 6 times 8 times ¼ square centimeters, or 12 square centimeters. That’s twice as much surface area as before, even though the combined volume of the cubes hasn’t changed. If you imagine this happening several more times, you can begin to see what a staggering amount of surface area an aerogel can have.

Why is surface area important? If something has a large surface area, dust and other materials have more opportunities to land on it. This is why if you look at air filters they’re made up of dense meshes of stringy material. Air filters are, in some ways, a primitive form of aerogel.

Another neat thing that we can do with gels is use them as sensors. Because the space in between the molecules of gels can be filled with many different solutions, and the molecules themselves can be engineered to have different properties, gels can be made to drastically change their properties with temperature, in the presence of different chemicals, or when the pH changes. Gels that do this are sometimes called smart gels. Gels can also be made from protein fragments to provide a scaffold for specialized cells, allowing them to be used for a variety of applications in medicine.

Probably the most amazing gels however are living cells and tissue. If you think about it, almost every tissue in your body is made up of a network of molecules connected together and filled with liquid. You are essentially a conglomeration of gels.

Switchblade Pisces: pt 9

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After going through the office door, there’s a short antechamber, and then another door. There are more hallways after this, only these are a more modest size with rooms that remind me of a retirement home. When I look back at the door, there’s a sign reading “employees only” in serious-looking blocked script.

After the wide expanse of the other hallway, these corridors seem positively claustrophobic. They turn and exit in several different ways. Along one branch I see what looks like sunlight.

“This is the front of the clinic. The only part most people see. Everyone thought I had gone mad when I put so much money into this place. Baxter’s Vegetable Garden, they called it.” Eklund stops at a room. He opens a door. Inside there are bright decorations, stuffed animals, a girl sleeping in a bed connected to machines. “They told her parents she was brain dead.” Eklund shakes his head. “It’s only part of her brain. Just twenty five percent. People have survived with less. But it’s her personality that’s missing, her dreams. Her will. There’s no way to give that back to her, the doctors say. They say it’s better to give up.” Eklund closes the door and faces me. “I will not give up.”

I’m impressed, but the force of Eklund’s convictions scares me a little too. I actually step back away from Eklund into Jazz’s chest. Swallowing, I say, “I still don’t see where I come into the picture. I don’t think I have much willpower. Why are you interested in me?”

Eklund looks down, a small smile coming to his face. “That’s precisely it, Ethan. You have the lowest amount of willpower of any otherwise healthy person we have documented. You are intelligent, you’ve gotten admirable marks in all the classes you’ve taken in college and in high school. The jobs you’ve had have all been brief, but you’ve gotten good reviews when I’ve interviewed your employers. Still, you’ve been in that efficiency apartment next to the university for over a decade now. You’ve changed your major eighteen times. It’s astounding that you’ve been able to keep going the way you have.”

“I’m just trying to figure out what I want to do,” I say, “That’s not that strange.”

Eklund raises a bushy white eyebrow.

I swallow nervously. “Well, I mean, it’s a bit weird I guess. Ten years is kind of crazy. But I’m just interested in a lot of different things.”

“You see?” Eklund raises a finger. “You can’t even stick to your guns on your own opinion of yourself.”

I want to protest, but I can’t think of a workable argument.

Eklund glances at Janis and Jazz behind me and looks down. “I can only imagine how you must feel. To never be sure of anything. I’ve had my doubts before. It is true I need security to protect myself and this clinic, and it is true that I can’t risk this place being discovered by the wrong people. Using Janis and Jazz as I have, giving them their modifications… It was a creative solution to a problem. It protects them, and they have not suffered for it. Still, sometimes I feel like I’ve taken advantage of them.”

“We would not exist without your assistance. Any advantage you take from us is therefore morally acceptable.” Jazz states, his prosthetic cortex whirring a little. Janis’s whirs some as well.

“Thank you, Jazz, but I’m afraid I can’t take your words to heart, especially when you act like a cult member about to drink the kool-aid.” Eklund sighs, looking a little older. “The kool-aid comment was an allusion to the Jonestown cult. I am speaking about a conflict between philosophy and emotion. Do not attempt to understand.”

“Thank you, Baxter. I will not.” As I look back at him, Jazz seems to relax a little.

“That goes for you too, Janis.” Eklund warns. “This subject might make you overheat.”

Janis nods.

“She overheated a bit on the way over here,” I said. “She was upset about the agents she killed.”

There is a soft sound of something sliding against skin, and Janis’s cortex begins to whir.

“Janis,” Eklund said, “Please retract your blades. You are angry at me, but you probably don’t want to kill me.”

I whip my head around to see Janis snick-ing her blades back into her wrists.

“Janis, you should visit Dr. Kisugi to make sure you haven’t hurt yourself.”

“Yes, Baxter, I will do that.”

I watch her turn and walk down the hall, through the employee’s only door.

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Why Death Valley is Better than The Walking Dead

For those of you who don’t know, there are (at least) two shows on television right now that deal with zombies. One is on AMC, called The Walking Dead, and like many shows on AMC it has a lot of interesting elements but tends to be a little…artistic. The other show is Death Valley, which shows on MTV and is fast paced, humorous and done in a reality tv style similar to Reno 911 where a task force of police are in charge of taking care of paranormal nuisances that are plaguing the city. On the surface, Walking Dead seems to be the show to watch if you have the choice, but here are a few reasons why I think watching Death Valley is the better way to spend your time.

1. The Walking Dead is boring. Yes there are some intense scenes of zombie violence, but these are brief moments in a series of long, drawn out scenes where people talk about how they’re feeling and admire the scenery. You can call this “atmosphere” if you want. I call it filler. The stuff in the book you flip past to get to the good stuff. While you can scoff at Death Valley’s sophomoric humor and sensationalized violence, when it comes right down to it, things actually happen  in Death Valley. The plot moves forward, whereas in Walking Dead the characters  can spend a whole hour long episode trying to fish a zombie out of a well

2.Death Valley has vampires and werewolves as well as zombies. Much as l like a good zombie movie, the intense feeling of trying to escape a shambling, inexorable wave of undead former friends and loved ones is something that is difficult to sustain over time. After a while, I begin to wonder why the zombies haven’t expended all their energy yet. How are they moving? Why haven’t the people tried a more systematic approach to eradication?  These questions start to come up during quiet moments of building tension, and Walking Dead doesn’t really do much to answer them. Death Valley, however, neatly skirts these problems in three ways. First, it’s not all about the zombies, so there’s some variety to distract from niggling details. Second, the premise centers around a task force in charge of systematically eradicating the zombies. The zombies aren’t an apocalyptic force, they are just problems that need to be dealt with so that the general populace can be protected, which to me seems more realistic. Third, even though in the title sequence of the show, Death Valley says that no one knows why the zombies came to the city, the show actually explains a lot of the questions about how the zombies operate. Because of the reality TV-esque nature of the show, the characters will often argue over whether a zombie does one thing or another, and by the end of the scene you find out.

The cast of Death Valley

3.Death Valley has better, more rounded, believable characters, whom I actually care about. Every character has humorous moments, moments where they are the hero, and a definite worldview that you can see play out against the other characters. Even the most MTV-ish character, the guy always says perverted things as part of his schtik (he’s holding his pistol gangsta style in the photo), looks out for his partner (the older-looking bald guy) and actually works as a foil for him. Death Valley doesn’t have to endanger children to get its thrills. Its characters are good enough that when they’re in danger, you worry about them without any added reason. Walking Dead’s characters, on the other hand, are all tortured souls living one day to the next. At least half of them have threatened suicide at one time or another and all of them have done something morally reprehensible. The women all have to cry at least once an episode, and the men all want to sleep with their best friend’s girlfriend. Nobody seems to have a plan to stop the zombies. They’re all just stumbling over each other and dying at random intervals. This isn’t to say there aren’t some interesting arcs. It’s just that I’m not as vested in characters if they don’t have any motivation, aren’t any good at what they do, and have only a vague sense of morality.

4.Death Valley has an arc. One thing you can say about Walking Dead is that it’s not episodic. Things don’t go back to normal at the end of every episode. Story lines thread through several episodes and end naturally. At first glance, Death Valley doesn’t seem to do this. Everything seems cheerful and breezy, there’s heart gripping terror, things get resolved and that’s the end. But slowly, as the episodes continue, a conspiracy is starting to reveal itself. Although some of the culprits are known, there is a tantalizing amount of mystery to it. It creates a new challenge for the characters they have to figure out. Meanwhile, the arc in Walking dead, while not episodic, hasn’t moved forward much. The people are still trying to survive in the face of a zombie apocalypse. No new information, no real change in the problem. Basically every episode involves retrieving some resource from a zombie infested area. No one has thought of, say, luring a large number of zombies into a trash compactor. Or off of a cliff. Or using a series of traps to keep them in place. Or figuring out what keeps them moving. Or anything really.

5.Death Valley has a higher death toll. I watched a little of the Talking Dead, a interview show about the Walking Dead hosted by Chris Hardwick. He had a segment where he went over the death toll in the show and it was depressingly low. I think it was one human and three zombies. By contrast, in the last episode of Death Valley alone, a whole elevator full of zombies (about 8 of them maybe) was mowed down by automatic rifle fire and a grenade. Then, later on, one zombie with an incendiary device attached to it blew up in a dumpster. A higher death toll doesn’t make a show better, of course, but it does give a coarse reading of the amount of action that takes place. More stuff happens in Death Valley. There are emotional scenes, but they last only as long as they have to and then it’s on to more humor, horror, or violence.

The season isn’t over yet, but I would say so far that Death Valley gets a 8/10 from me, while this season of Walking Dead gets a 6/10.

How to Make a Mutant: Transgenesis

(this creature does not exist)

Even though at some level, we’ve been making mutants for hundreds, even thousands of years through selective breeding and agriculture, these aren’t the kind of mutants we think of. We usually expect something bizarre and alarming that happens almost immediately. Like the Incredible Hulk turning green, or turtles becoming sentient, bipedal, and proficient in martial arts. We get a little closer to that sort of thing with environment sensitive genes.

Biologists usually first learn about these genes in bacteria, with the lac-operon system. The lac-operon system is an arrangement of proteins and DNA that essentially lets bacteria adapt to their environment. Bacteria like to eat sugar, and they survive the best on glucose, the simplest of the sugars. If glucose isn’t available, they can eat other sugars, like galactose or lactose, but that requires more machinery and the bacteria don’t want to rev up those machines until they know they have to. How the lac-operon transcription system works involves the use of two proteins, one that blocks the expression of the lactose-eating gene lac-x and one that amps up the expression. When lactose is present, the blocker protein can’t work, and the amp-up protein only binds if there isn’t any glucose. So with this system, a bacterium can shift to eating different sugars like a car shift gears.  This is something of a simplification of the process, but the upshot is that while the bacterium’s DNA remains the same, it’s expression is altered significantly by the environment.

Similar situations occur in more complex animals. Researchers often make use of temperature sensitive genes in fruitflies to create flies that are genetically identical to a control group, but have a protein that works differently due to being exposed to higher temperatures while forming inside the egg. In nature, this happens with many cold blooded animals whose sex is determined by the temperature where their eggs are kept.

These environmental affects control the expression of genes, and not necessarily the genes themselves, still, this isn’t as trivial as it may seem. The well-known statistic that our genes are 96% similar to chimpanzees’ is only true when we don’t count the so-called junk DNA that doesn’t seem to directly code for anything. But while this DNA doesn’t seem to make anything, recent evidence has shown that it may have an effect on how things are made or when they’re made. In other words the obvious difference between us and other animals may have more to do with how our genes are expressed rather than what genes we have in the first place.

”]Scientists can also insert known genes into the genomes of animals to create transgenic creatures. For example the gene that produces the fluorescent protein GFP in jelly fish can be inserted into the DNA of bacteria using electroporation, a technique where a electric field is used to create pores in the cell membrane of bacteria, which allows foreign DNA to enter. This can also be done through abruptly increasing the temperature, which forces the bacteria to open pores in their membranes to adapt to the situation.

Bacteria will incorporate DNA into their genome, and as long as the new DNA doesn’t interfere with their ability to survive and reproduce, the bacteria will quickly grow in number, providing a way of naturally increasing the amount of foreign DNA available. Scientists can then use  enzymes to cut out the gene that they want from the bacteria and insert it into the genome of a more complicated organism through several methods

Lab workers can insert DNA directly into the nucleus of a stem cell, for example, or simply allow the cell to take in the DNA on its own. Alternatively, scientist might use a virus that has had all its DNA replaced with the foreign DNA so that it can be injected into the cell without direct human supervision.

Optogenetics Experiment in Mouse (Source: MIT)

One of the most dramatic examples of transgenic research involves the use of a protein called channel rhodopsin. This protein is related to the protein that detects light in the cells of our eyes. When the gene that produces the protein is introduced into the neurons of a mouse, and a light of a certain color is show on the neuron through LEDs or  fiberoptic cable implanted in the mouse’s skull, it can cause the neurons to fire, directly affecting the behavior of the mouse. Not only that, but the channel rhodopsin can be altered to respond differently to different types of light so that blue light might cause a neuron to fire, while orange light might cause it to stop firing. This system has opened up an entirely new field of biology called optogenetics and researchers are currently finding ways to use the techniques to help sufferers of all sorts of brain diseases from Parkinson’s to Alzheimer’s.

So real mutants might not fly or shoot laser beams out of their eyes, but in many ways they’re even cooler than that.

Book Festival and Margot’s

http://bit.ly/pgPk3L

The Friday before last, I went to the Southern Festival of Books, which is thrown every year by Humanities Tennessee next to the courthouses of Nashville. I like this convention more and more each time I go. The first time I went, it was actually held in Memphis and it seemed to be just a string of tents with some vendors selling books there. Then some years later I ran into it again in Nashville and learned that there were talks given,  just like in the sci-fi conventions that I was more familiar with. And what talks! The first one I went to was hosted by Susan Orlean who wrote the Orchid Thief, the novel that one of my favorite movies, Adaptation, was based on. Since then I’ve learned at least one new thing each time I’ve gone. I learned about the history of beef, about the southern gothic genre of books, how dependent we are on utilities, and how networks propagate over time.

At the book festival the emphasis is on books, rather than a specific genre. At this point in my life I find I like to read a lot of nonfiction; so I appreciate the relaxation of the guidelines. There is an emphasis on the south, which those of us who grew up here knowing how to speak correctly usually have something of an ambivalence about, but because the people at the festival can read and in fact do so avidly, you get to see all the interesting parts of Southern culture without lamenting the fall of civilization quite so much.

This year I went to the festival with my father and saw an interview between a host of a podcast and Tom Piazza, who among other things, is one of the writers that work on Treme. He mainly talked about music and some of the stories he wrote about the characters he met while reporting on the subject. They were entertaining stories, and I got his book, Devil Sent the Rain, because of them, but I’ve got to say that I’m more impressed that I got to shake the hand of a guy who works with David Simon. Homicide was good enough. The Wire made me rethink how a crime drama could be made, and Treme…well I don’t like Treme as much but a lot of people do like it and anything that allows Lucia Micarelli to make her awesomeness more apparent is good.

Anyway, after I got Piazza’s autograph, I asked him a couple questions about the show. One question was whether he was on board with the death of John Goodman’s character and  he said that he was against it originally, but that he warmed to the idea eventually.

Dad later asked him something to the effect of why do people in New Orleans blame Bush for Hurricane Katrina when the real problem was that the levees weren’t adequately maintained. While I agree with Dad that blaming Bush for that situation is something of an oversimplification, I didn’t think that that particular moment was the best time to engage in a political discussion.

Thankfully a friend of Piazza’s showed up and he had to go. After his panel, Dad and I went to the last half of another panel about the biographies of people that no one remembers, which was actually kind of interesting. The idea was that you can get an idea of the atmosphere of a time by knowing about the lives of people who were influential, but stayed more or less in the background.

The front of Margot's Cafe and Bar

After that, Dad and I wanted to sit at a bar and talk about things, so I looked at the map function on my phone and found Margot Café and Bar. It was rated highly and it said “bar” in the name so I figured it would be good. It was. It was great. But it was a little classier than I had thought from the name. Dad was dressed well, but I had just worn a t-shirt and cargos that day and felt a little scruffy. We were both wearing our Irish hats, so maybe that masked some of my uncouthness, but we were seated in the far corner, so maybe it didn’t. They didn’t cast any overt aspersions, and the service was excellent. So I can’t complain.

I got to try a few dishes I had heard about on cooking shows. Margot’s had scallops that tasted great and seemed to melt on the tongue. Dad got the mushroom risotto and found that very enjoyable. Good food, great service; it was an excellent cap to the day.

 

Switchblade Pisces: Pt.8

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“I’m glad you could make it, Ethan,” the man says, “I’m Baxter. Let me show you around.”

Eklund sounds older; he’s maybe in his sixties, but his voice has a manic energy that makes me wonder if maybe he’s my age, only he has bronchial pneumonia or something.

He leads me, Janis, and Jazz through a bulkhead door and into a brightly lit expanse lined on either side with doors and glass partitions. The floor is covered in white tile, and the aisle way is as large as a two-lane road. The wet stone smell of the cave is still there in the background, but now there’s a strong scent of antiseptic. It’s like a hospital, an airport, and a mall all had an orgy and left this place in their wake.

“Impressive, eh?” Baxter says. In the light I can see the lines in his face. He has more crow’s feet than I would have thought possible around his eyes. He has thick laugh lines too, and some nice forehead creases. The man is a prune. His eyes are sharp though. Light green and piercing. His hair is bright white, but thick and dynamic. I hope I look as good as this guy when I’m his age. I hope I’m as energetic too. “Four wings of a hospital all the way down, with multiple ORs, elevators, stairwells, and bathrooms spaced evenly in case of emergencies. Easier to dig forward than down, you know.” He hopped into the driver’s seat of a golf cart that was sitting by the door. “Well, get on. The offices are at the very end.”

I sit next to him uneasily while Jazz and Janis sit behind us. I keep on thinking I should do something, but I have no idea what that might be. Looking at the long corridor ahead with labcoated people walking busily down and up its length I ask, “How are you paying for all of this?”

Eklund raises a bushy white eyebrow at me as he keys the engine. It’s electric, so there’s only a somewhat disappointing hum when he does this. “This is the Baxter Eklund Cognitive Trauma Ward. You have a loved one in a coma? We take care of them for you. The place would practically pay for itself if it weren’t for the goddamned government regulators.”

I raise my own eyebrow at this.

“We take on a few pro bono cases as a charity. But the government wants all of our cases to be pro bono.”

I’m starting to get that desperate, queasy feeling I always get when people talk politics around me, so I attempt to change the subject: “Why am I here, Dr. Eklund? Why is the FBI after me?”

Eklund doesn’t answer right away. He drives past a bathroom, and a small group of people in lab coats pointing their tablet computers at each other and nodding. Finally, he says, “You’re a curiosity to me, Ethan. Unfortunately, the government has learned to be a little suspicious of the people I’m curious about.”

“Why would they care?”

Jazz speaks from behind me in his deep baritone. “Dr. Eklund has been trying to solve the problem of free will.”

“Yes, thank you, Jazz. I tried to find people who seemed to have a lot of free will first. People who followed their own path regardless of the consequences. After I contacted two people the FBI had under surveillance, they got leery. When I found the third they started to get violent.

“They used some strong arm tactics. Some of my staff were beaten when they refused to cooperate. I had to let them see this part of the ward, so they could see I wasn’t heading some sort of paramilitary boot camp back here or anything. Thankfully they didn’t know what all the equipment was for.”

The golf cart is finally reaching the end of the hallway, where a comically innocuous looking wooden office door stands inset in the wall. Eklund steers the cart into a space by the door and turns off the ignition. I don’t feel like getting off yet, though. I’m feeling a little sick. “Why couldn’t you have just told the FBI what you were doing?”

Eklund lets out a rasping laugh that turns into a cough before he gets control of it. “For one thing, they wouldn’t have believed me, and for another, I don’t exactly want the FBI to know what I’m doing.”

“Why did you program Janis to kill those people?”

Eklund’s expression turns serious. “Why didn’t you order her not to?” He turns away and gets off the cart.

“There, there,” Jazz pats me mechanically on my shoulder. “You did what you thought was right.”

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Review: Ring of Fire

Last Saturday I got the chance to see a production of Ring of Fire performed by the Gaslight Dinner Theater at the Renaissance Center in Dickson, Tennessee.  The show plays until October 15th and features excellent performances of songs by Johnny Cash as well as scenes depicting times in his life. I wasn’t sure what to expect when I sat down to watch it, but the sheer amount of talent on the stage was mind blowing. Every one of the twelve cast members acted, sang, AND played a musical instrument as good or better than anyone I’ve seen on the stage, and I’ve seen several Broadway musicals.

The show is really more of a concert than a musical. In fact, I felt that some of the acted out scenes took away from rather than added to a few of the performances, but the blocking and musical-style frame work did allow each performer to showcase their considerable talent and it prevented the scenery from seeming stale as it can with a standard concert.

I would caution that the show is a PG or PG-13 affair, as they do go into the time Cash spent in prison. If you are familiar with Cash’s oeuvre, though, this isn’t a surprise, and it provides a nice contrast to the other songs in the show.

Overall, I’d highly recommend this to anyone who enjoys Cash’s music. I give it an 8 out of 10, which is a high mark for me (I would have to have a quasi-religious experience to rate something a 10 out of 10). I’m a Johnny Cash fan by way of U2 and Nine Inch Nails, so I’d say you don’t have to be a country music person to enjoy the show. On the other hand, don’t be expecting Walk the Line in musical format. Although the show does dip into the darkness a little with a few somber set ups, it doesn’t have the sturm and drang of the movie. That’s a good thing, though, as far as I’m concerned. Ring of Fire is a fun, feel-good showcase of the songs and life of Johnny Cash. The feeling I got from watching it is actually similar to watching a good show at at Opryland: A friendly atmosphere punctuated by explosions of talent.

How to Make a Mutant: Mutagens

http://bit.ly/p2fCgl

The term “mutant” gets bandied about quite a bit in popular culture. It can mean some freakishly deformed animal or person, or, more recently someone with magical, almost god-like powers (if you think that the X-men stories are completely scientifically accurate, then you have a disturbingly unrealistic understanding of the universe). But the reality is that mutants are all around us. The word comes from the Latin mutantem which means to change. In some sense, then, we are all mutants, as our genes are naturally a mix between the genes of our parents and therefore are always changing. Usually though, by “mutant” we mean some organism that has had their DNA altered by artificial means. Even this more focused definition still applies to an astounding number of the things we look at every day.

There are basically two ways of making a mutant: using a mutagen, or specifically targeting  an organism’s genome. We’ll talk about mutagens first. A mutagen can be anything from nuclear radiation to insecticide. Anything that’s a labeled carcinogen is also mutagen, as cancer is perhaps the most common form of mutation. Since cancer happens naturally, it’s perhaps a little  incorrect to put  it under the heading of “mutation,” but as some unfortunate people are intimately aware, cancer can be caused by man made materials, so it does fit.

Before we get too ahead of ourselves, we should first go over how a mutagen might make a mutant. The way it works is this: every living thing starts out as a single cell. How this cell behaves is determined by the genetic information in the DNA of the cell. This behavior includes how it divides, what structures it makes, whether it moves around, how it connects to other cells, you name it. If this cell is exposed to a mutagen, then this DNA might be altered. For instance, if the cell is subjected to ionizing radiation,  subatomic particles will scour through all the material of the cell including DNA, knocking electrons and possibly even whole atoms off the molecules that make up each material. If the intensity of the radiation is low enough, most cells can repair this damage, but some damage might be too severe to repair, or might be missed by the repairing processes, and if this happens to DNA, a mutant can result.

Ionizing radiation, as you might imagine, is a rather ruthless mutagen. It’s a bit like trying to hit the bull’s-eye of a target with a shotgun. You might get lucky and hit the area you want, but even in the best case scenario you’re going to have collateral damage. So while this type of mutagen is the most commonly found in nature, it isn’t something you want to use to find a beneficial mutation.

A slightly more nuanced approach is to inject material that looks like a section of DNA into the originating cell while it’s dividing. This approach only affects the DNA, and so you don’t have to worry about killing the cell outright, but it’s still random and so it could cause changes that an organism won’t be able to survive. There is a more sophisticated version of this involving actual foreign DNA, but we’ll get to that in the next post.

One of the mutagens most commonly used in labs is a chemical called EMS (Ethyl MethaneSulfonate). This chemical will affect the DNA of a cell by affecting  only a single nucleotide base pair. This allows much more of the mutants to divide and develop fully into adult organisms.

All these methods will produce mutants, and this is far from a complete list, but scientists usually have a specific mutant in mind. For example, a scientist might be interested in muscle growth and wants to find an animal mutant that will mimic a known human disease.

http://bit.ly/pLanTO

The first step for this is to find the right animal model. Animal models are used in many kinds of research genetic and otherwise. A human model wears fashions or tries different products so that we can see how they supposed look or work in an idealized environment. In a similar way, an animal model is given different ailments so that scientists can see how the animal responds to different treatments and other situations, with the hope that a human might have the same result. Humans are not all that different from other animals, as even Aristotle was aware, (We should venture on the study of every kind of animal without distaste; for each and all will reveal to us something natural and something beautiful. -Parts of Animals I.645a21)  but certain animals are better for studying different systems. If you want to study the higher functions of the brain, for instance, you probably want to work with mice, or chimpanzees. If you are interested in the steps involved with development from a single cell to an embryo, however, you might use zebrafish, as zebrafish embryos are transparent, allowing you to see many processes hidden in other animals.

One thing that is common for most animal models is that they tend to have faster life cycles, and produce more young. If you are a graduate student hoping to get your PhD in two years, you don’t want to have to wait ten months for an animal to get born, just to find out it doesn’t have the right genetic make up and you have to start all over again. In lectures, scientists often talk about how expensive each animal is. In other words, how much grant money goes into studying each individual animal. If a study is supposed to follow the entire lifespan of a rat, then it’s going to take four to seven years, and so that rat is going to be very expensive. If a scientist does a similar study with a fly, on the other hand, it will only take a few months and therefore be only a fraction of the cost. Also, while there maybe eight to twelve rats born from a mother, which is a good number in comparison to a chimpanzee, there still may not be enough chances for the pups (baby rats) to have the right genetic make up. If one of the pups needed for the study dies, it can be devastating, while if a fruit fly dies, there might be forty other flies to take its place. This is one reason why fruit flies are used often in genetic studies.

Two fruitflies contributing to research -http://bit.ly/oy62XW

Let’s look into how to make a fruit fly mutant. The procedure is typically to subject fertile, male flies to a mutagen (EMS for example) for a period of time, and then allow them to reproduce with normal female flies. Some degree of care must be taken to ensure that the female flies are virgins, so that there isn’t any chance of another fly’s genetic material getting involved. Thankfully virgin females are paler and a black dot is visible on their abdomens. They are therefore distinguishable from older females, which don’t have the black dot, and males, which have darker coloring and a reddish structure at the ends of their abdomens. To examine these features, a researcher can take flies and subject them to CO2 gas, which knocks them out. They can then manipulate them using tweezers and a low magnification microscope. The virgin female flies are sequestered in a separate vial with a mutagen-treated male and allowed to mate. The female will lay mutant eggs, which will eventually become mutant larvae, and then mutant flies. Depending on what trait a researcher is looking for, they will analyze either the larvae or the flies for altered behavior or health.

Wild banana -http://bit.ly/l1jut6

This method  of producing mutants has been around for decades. You might think that they are science fiction things, but if you walk into any sophisticated biology lab and talk to somebody there, you’ll find that mutants are not only studied a lot, but they are almost taken for granted.  Furthermore if you take away the use of mutagen, this kind of directed evolution has been around for ages.Without human intervention bananas are, fat, green, cumbersome things that are difficult to work with. By cultivating the trees that produced the tastiest, easiest to eat fruits, however, humans managed to breed the trees to produce the banana we know and love today, a fruit that fits so nicely in the hand, and opens so easily it seems like it was designed for us. It seems that way because we designed it.

This also has happened with animals. Geneticist Dmitri Belyaev managed to domesticate foxes, by breeding the ones that were the most tame. The breeding program was successful, but oddly the tame foxes began to look an awful lot like dogs.  Belyaev’s research suggests that many of the same genes that control physical attributes, also control behavioral ones. Just as he domesticated foxes within his life time, wolves must have at one time been domesticated by early humans. In other words, when you look at a dog, you’re probably looking at a mutant wolf.

Switchblade Pisces Pt.7

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I’m beginning to get a picture of things, but I’m not sure how much of it I’m making up. Filling in the spaces, I ask, “Janis,have you ever killed anyone before today?”

Her cortex fans are whirring more now. “In simulations. I have been training for three years now.”

I cover my forehead with my hand. “Janis, you’ve been playing video games. Real life is different. Ending someone’s life is not anywhere near the same as making some mass of pixels go away. That’s what your brain is telling you. What happened to your father and you, when you saw him lose you, and then when your mother visited you and you saw her realize that you will never be who you were again, that’s what those FBI agent’s families are going through right now. Maybe one of them is at this moment in coma just like you were. Or maybe all them are dead and their loved ones don’t even have a body to cry over.”

“If they were agents, then she did the right thing. They would imprison Eklund and without him, many would die and quality of life would diminish worldwide. They wanted your information to get more control over people. That would diminish freedom. The negative of their death is less severe than the negative of letting them have what they want.”

I shake my head, “Jazz, it doesn’t matter whether what she did was right or not. They were people. Whenever people die, it’s sad. That’s just the way it is.”

“Would you like me to believe this?” Jazz asks.

“Believe whatever you like!”

“I only believe what I am told to believe. I am a Pisces.”

I’m about to argue the point when Janis grabs my free hand. “Thank you, Ethan. I think I understand now.” She releases my hand suddenly and stares at it for a little while. Then, slowly, she wraps her fingers around my hand again. “It is not only me. I see myself in other people. I…feel a little of what they feel because I can imagine myself in their position.”

Janis’s hand is so warm against mine. She looks so beautiful. I close my eyes and swallow. I can’t be thinking about things like that!

“You do not have to be…afraid, Ethan.” I open my eyes and there is Janis looking up at me. “I will not hurt you.”

“Unless she is ordered to,” Jazz adds, his cortex whirring, “Have you made your decision yet?”

Oddly, when I look at the fans on Janis’s prosthetic cortex, they don’t seem to be spinning much at all.

“I’ll go see Eklund,” I say, almost without realizing it.

Jazz nods and takes an exit onto a highway.

~~~~~*~~~~~

After the highway, we travel through several back roads until Jazz pulls over at a fairly nondescript area where the road widens a little for cars that need to turn around. The road here cuts into the hill so I can see the sedimentary layers underneath the soil. There’s a sign that says to watch out for falling rocks.

Jazz puts the car in park and gets out.

I look at Janis, but she’s just sitting, rubbing her wrists, looking distant.

Through the side window, I can see Jazz touch an area of the shorn off hill with his large hand. The surface moves inward and up, revealing a rectangular space not unlike a garage.

Jazz walks back and folds his large body back behind the steering wheel.

As he drives us inside, I feel like I should say something but I have no idea what would be appropriate. Wow? Cool? Nice place you’ve got here? That last might be good, but the moment’s gone by now and I don’t think either Jazz or Janis are in a position to appreciate sarcasm. It bothers me that I’ve driven by so many areas just like this one and never really noticed them. Somehow I’ve always had the feeling that if I drove past a secret hideout I would know it if I saw it.

After we’re inside, Jazz turns off the engine and the door —rock face? Portcullis?— falls back into place with a reverberating thud. There’s an uncomfortable time when nothing seems to be happening, but just as I’m about to mention this, there’s the sound of hydraulics and we’re being lowered down below the floor.

Once again I get to see the sedimentary layers of the rocks through the car window, but now they’re lit by sparse, artificial light and covered over with algae blooms where the light is brightest. We keep going lower and lower, down past older and older sedimentary layers. I’m just beginning to worry irrationally about possibly going through the crust into the mantle of the Earth… when we stop.

Jazz and Janis get out of the car immediately. I take a moment to think about how I got to be where I am and whether I really want to be here. I wonder if perhaps I might be safer staying in the car. But then I realize that I’d be staying in a car several stories beneath the surface of the Earth on a hydraulic elevator operated by someone I can only assume is some kind of mad scientist.

Might as well see if I can figure out where the controls are.

When I get out, the scenery reminds me a little of those caves they have at tourist traps. Stalactites and stalagmites dramatically lit by strategically placed lights. Dominating the scene is a man wearing a linen suit that was probably white at one time. He has a white fedora on and glasses with flashlights embedded in the rims so that looking at his head is like seeing a car coming at you in the night. Because of this, I can’t make out his face too well, but judging by the martini and olive he’s holding jauntily in his left hand, I don’t get the impression that the conversation I’m about to have with him is going to be dull.

“I’m glad you could make it, Ethan,” the man says, “I’m Baxter. Let me show you around.”

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