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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Review of After Dark

If you’re interested in being a writer, every now and then it’s good to go ahead and read, watch, or listen to something you’re pretty sure you aren’t going to like. First,  you might be surprised and actually like it. Second, even if you don’t like it, there might be things about it that you do like and you can use them in your own writing. Finally, if you still don’t like it, you can try to figure out why you don’t like it so you can make sure never to do those things yourself.

Along these lines I recently listened to an unabridged audiobook of After Dark by Phillip Margolin. The story is about a wealthy female prosecutor, named Abby. She’s accused of killing her soon to be ex husband  and pinning it on a serial killer she had failed to keep in prison.

I got the audiobook at a garage sale because of the reasons I’ve outlined above, and because I thought it would be something to listen to while I was cleaning and what not. Although you might think it was a horror novel from the title, it’s actually a courtroom thriller. I’m not particularly fond of those, which is why I wasn’t very excited about it. But there are a few examples of the genre that I have enjoyed, or at least, I’ve enjoyed the movies inspired by examples of the genre. Anyway, the book wasn’t that bad. There have been novels I actually haven’t been able to listen to because of their terrible-ness and this was not one of them. With four tapes comprising the audiobook and two sides to a tape, I had seven golden opportunities to stop listening, but I kept going, and not out of any bloody minded determination to continue to the end, but simply because I wanted to know what would happen next.

Why was this? Well part of it was, of course, that I didn’t know what was going to happen next. The other part was that I cared about what happened next. I would say the first part is relatively easy to recreate in a story: you just don’t tell the reader everything all at once. I say it’s relatively easy, because it can be hard to remember to be coy about exciting details when you’re chomping at the bit to let them all come out in a gush of exposition. The second part is harder, though. It revolves around creating sympathetic characters, or at least characters who are interesting.

The most interesting character in After Dark is the serial killer Charlie Daniels, with his charmingly evil demeanor and love of game shows. You pretty much know he has had something to do with all the deaths, the question is more about how Abby and her attorney, Mathew Reynolds can prove it. Matthew has a quiet intensity and a desire to not let any of his clients get the death penalty. The title of the book, After Dark refers to what defense attorneys have to do when their clients get the death penalty. They have to go to a court house after dark the night they are executed. It is the thing Matthew is most keen on avoiding. The title phrase is used perhaps over much throughout the last part of the book, but I am glad when an author chooses a title for a reason, rather than on a whim.Tracy, Matthew’s competent assistant, is arguably the main protagonist, as she discovers some secrets that provide many of the twists and that move the plot forward, but oddly, I found her to be one of the least fleshed out characters. In fact for half the book I kept confusing her with Abby. Abby is probably the second most interesting character. At least in the beginning, she shows herself to be very resourceful and assertive, but she has to deal with a very difficult situation.

These characters were just interesting enough to make me worry about them and how their stories panned out. Why, though, wasn’t I more interested?

It’s tempting for me to say the story was clichéd, because it felt like a lot of other crime dramas. Even though my experience with the genre is limited to the few Grisham novels I’ve read, I feel like I sort of know the drill. But while it seemed like old ground, it wasn’t predictable. Yes I knew all the way through it that Charlie was up to no good, but the main thrust of the story is proving Abby’s innocence, if she is in fact innocent. All of which left me guessing. So if it’s not predictable, what about the story makes me feel as if it is?

I think perhaps it’s the way the new information is presented. Although I don’t know what exactly a character might reveal in After Dark, I can tell, simply by context, that they’re going to reveal something surprising. It’s unpredictable, but it’s predictably unpredictable. The feeling is a little like watching a soap opera. When the camera comes in for a close up, you know something emotional is going to be said, even if you don’t know for sure what that might be.

The take away of this for me is that although having plot twists may be enough for some readers (Margolin did, after all, get his book published and made into an audio book, which suggests that a good number of people must have read and enjoyed his work), it’s not quite enough to make a work seem fresh. You have to vary the way the twists are presented too. In other words, you don’t want the plot to feel like a mad libs game, where there are surprising moments in a cookie cutter frame work.

I think following a character’s natural motivations will tend to keep the cookie cutter feeling from coming up. I’ve never read any interviews or anything from Margolin, but my guess is that he’s a plot first kind of guy. The characters in his stories are colorful, but they seem a little animatronic, tied to the things they must do to get to the next scene rather than free to do as they really wish.

One place where I feel this most acutely is when Abby is supposed to fall in love with Matthew. At this stage doubt has been placed on Abby’s innocence, and the seductive manner in which she addresses Matthew lends credence to the idea of her guilt, but it doesn’t quite mesh with how she acted in earlier scenes. This isn’t the only problem with Abby. Before her trial starts, she seems like a competent and intelligent woman, but once the trial starts she seems passive and confused about everything. She’s a lawyer, but there are times where she seems ignorant of courtroom procedure.

In one of the Amazon reviews, someone has complained about not knowing whose story the book is telling. I agree with this, but I also know that there are books without a definite singular main character that still work. I think if I have to put my finger on what is wrong with After Dark, it’s that the characters aren’t given enough freedom to act appropriately.

Overall I give the book a 6 out of 10.

Reading your Blueprint: Genome Sequencing

Logo of the human genome project

In this post I’ll go over the third and most recent method of identifying people through DNA:  looking at their genome. A genome is the sum total of all of the genetic information of an individual organism. If using electrophoresis and PCR is DNA fingerprinting, determining someone’s Genome is writing their DNA biography. It took some ten years for the human genome project to be successful in producing the genome of a human,  a testament to just how much information the genome contains.  Nowadays, of course, scientists and technicians can determine someone’s genome in much less time (about 4 weeks with one machine in 2009), due to the incredible advances in technology we’ve enjoyed, but how did we even get started?  DNA fingerprinting is great if you already know what you’re looking for, or if you want to compare samples of something to something else, but how do you get from that to figuring out every piece of genetic information about that thing?

Well the place it starts is with DNA sequencing. DNA is made up of nucleotides that code for various proteins. About the best thing we could hope for then is to know the sequence of these nucleotides on a sample of DNA so we can know which proteins it will code for. DNA sequencing is the process of determining this sequence.

You might recall that with DNA fingerprinting, restriction enzymes cut up DNA into fragments at specific nucleotide patterns. Those fragments split and replicate again and again through PCR, then a researcher will push them through a gel by electrophoresis, which forms bands on the gel at different levels. The closer the band is to the other end of the gel, the smaller the fragments of DNA are inside that band, and you can compare different samples by seeing where the bands show up when you subject them to the same restriction enzymes.

DNA sequencing takes this a step further. The nucleotides that make up DNA can be in two forms, deoxynucletide-tri-phosphate (dNTP) which is the usual version, and DIdeoxynucleotide-tri-phosphate (ddNTP) which has an extra hydrogen on it that keeps any more peptide bonds from forming. This means that if a DNA strand is elongating, and a ddNTP attaches, instead of a dNTP, the DNA can’t elongate any more. It’s done, terminated, its story is over.

Okay, so what? How does this get us to DNA sequencing? The way we get the sequence of a piece of DNA is  by labeling the DNA fragments by attaching a fluorescent or radioactive marker to either the ddNTP, the primer (which starts the elongation of a piece of DNA) or the dNTPs that make up the rest of the DNA.  Then you can separate each sample into four separate containers, and in each container you add in a different kind of ddNTP. Remember there are four nucleotides found in DNA, Adenine (A), Cytosine (C), Guanine (G), and Thymine (T). Each of these has a terminating, ddNTP form that we can add to a sample. So now you have four samples and each one has a different terminating nucleotide added to it. What this means is that wherever that nucleotide normally appears in the DNA sequence, the DNA well stop elongating there. So for example, lets say we have a piece of DNA with the sequence

CACGATTCGA(10 NTPs)

In the first sample we add the adenine ddNTP so in that sample we’ll have DNA fragments that look like this:

CA*(2NTPs)

CACGA* (5NTPs)

CACGATTCGA*(10NTPs)

Because the ddNTP will attach at different points as the DNA elongates during PCR and each possible fragment size will be amplified equally, all of these fragment sizes will be available in the amplified sample that is put through electrophoresis. These different fragment sizes will then form different bands based on how large they are.

If you put all the ddNTP additions together on a gel , the example above would look something like this:

|——A—–|—-T—-|—-C—-|—-G—-|

10–BAND-|—-0—-|—-0—-|—-0—-|

9—–0—-|—-0—-|—-0—-|–BAND—|

8—–0—-|—-0—-|–BAND—|—-0—-|

7—–0—-|–BAND—|—-0—-|—-0—-|

6—–0—-|–BAND—|—-0—-|—-0—-|

5—BAND—|—-0—-|—-0—-|—-0—-|

4—–0—-|—-0—-|—-0—-|–BAND—|

3—–0—-|—-0—-|–BAND—|—-0—-|

2—BAND—|—-0—-|—-0—-|—-0—-|

1—–0—-|—-0—-|–BAND—|—-0—-|

 

Looking at this result, a technician can tell the exact sequence of the DNA by simply putting the nucleotide where it’s base shows up in the sequence: 1:C,2:A,3:C… and so on.

This is pretty nifty, but this example only deals with a DNA fragment ten NTPs in length. A human genome has DNA that is billions of NTPs long. How in the world can a genome get sequenced in any reasonable amount of time?

The answer comes in three parts. The first trick is to automate the process, so that a researcher doesn’t have to guide each process along by hand. The next trick, related to the first, is to conduct sequencing experiments in parallel. In other words, you want to have several sequencing experiments going on at the same time. The reason why this second technique is related to the first is that the way to do this is to have an array of wells with samples and the required chemicals inside them, then have a machine which deposits a controlled amount of required enzymes or other materials to each sample at the same time. The machine can then heat each well and allow it to cool as needed for PCR.  The final trick is to break apart a long strand of DNA into much smaller fragments and then sequence those fragments randomly, rather than try to do fragments in the order they appear naturally this technique is called shotgun sequencing.

You might wonder how, after all these random fragments are sequenced, can researcher’s put them back together in the proper order. The way this works is similar to a jigsaw puzzle. In a puzzle you may have several pieces that are obviously part of the sky, say and other pieces that are part of other separate areas. If you have several sequences, some of which overlap each other, you can put them together by recognizing that some of them are part of a recognizable pattern. You can put the sequences from fragments with the same pattern together and proceed through the whole genome that way. Obviously, if you were to try to do this by eye, it might be very time consuming, but with the help of computers the situation becomes manageable. So much so that the newest forms of genome sequencing use much smaller fragments that are only few base pairs long, allowing them to sequence all of them in parallel very quickly. A computer can then use statistics to predict where each fragment would show up. This method produces more errors, but makes up for it by the amount of usable information it gives, similar to how Wikipedia makes more errors than an encyclopedia, but makes up for it by being so convenient and covering such a vast array of topics.

Switchblade Pisces: Pt.6

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 At this point, I feel hopelessly lost. How could all of this stuff be going on without me hearing about it on the news or something? “They can make brain cells that fire when you shine light on them?”

“Yes, this is the fundamental technology behind the optogenetic interface. The fiber optics provide an input into the brain, and EEG can be used as an output.

I know about EEG.  It stands for electroencephalogram, and it’s what a lot of the video game console makers are working on. Basically it’s where you put sensors all around your head to measure the slight electrical impulses your brain gives off. The EEG reads your thoughts and the character does what you want it to. It’s the latest thing, but it’s still a little slow. “How do you deal with the lag?”

“The lag? I am guessing you mean the lag you experience in video games that use EEG? The version we use is more invasive. The electrodes have almost direct contact with the brain. They are also more sensitive than what is commercially available. This significantly reduces the lag we experience.”

Jazz has exited off the highway and we are now on road going through the woods. When we pass by a visitor’s center I realize we must be in a national park. Jazz drives into an empty cove for RV enthusiasts that has a fire pit in the center.  “Are you okay?” I ask Janis.

“I am better. I am not yet ideal though.” Janis takes a few deep breaths. “I should be able to walk.”

Jazz gets out of the car and invites us to follow him. “I hope you have made a decision by now. We really do not have much time.” Janis and I both get out of the car and lean against the door.

“I haven’t even had a chance to think about it, yet! Just give me five minutes okay?”

“I will comply, but I would prefer to keep moving.”

I try to go over everything in my mind while Jazz and Janet are silent. Here I have two highly trained cyborg assassins sitting here waiting for me to give them an order and all I can do is make them wait! What is my problem exactly?

“I do not understand why I am so upset,” Janis says suddenly. “My prosthetic cortex affects my speech and decision making, but my memories and emotions are completely biological. Can you explain my feelings to me, Ethan?”

The purple irises of her eyes pull me in as she asks this. Something about the way she says my name makes me want to hold her. I swallow. “I don’t know. Usually I just know what I’m feeling without really thinking about it. Do you have any clues?”

Janis looks down. “Images keep playing through my mind. I see my father in the moments after the accident, when he is trying to get me out of the car, just before I black out. I see my mother saying goodbye to me after visiting me here. I see the two secret service operatives just before the explosion from the grenade I threw. I do not know what these images have in common, but when they cycle through my mind like this it is worse than confronting any one image by itself.”

“What happened when your mother came to visit, Janis?”

“I do not kn…I…I do not know!”

I think the exclamation startles Janis as much as it does me. She blinks slowly and the fans on her prosthetic cortex whirr loudly for a second.

“Mr. Yates,” Jazz says, “It has been five minutes. We can deal with Janis’s malfunctioning later if we must.”

“I am n…I..am not malfunctioning!” Janis takes a few short breaths. New tears come from her eyes. “I am not a robot, and neither are you, Jazz. Our guardian told us we should train ourselves not to rely on the prosthetic cortex.”

“Dr. Eklund is an optimist. Realistically, there is no way we can regain what we have lost. We should learn to work synergistically with our optogenetic interface. We should adapt to what we are.”

I hold my hand up. “Let her speak.”

“Very well. I will comply.” Jazz crosses his arms. I notice the fans of his prosthetic cortex whirr a little more than usual.

“It was my mother who signed over her guardianship of me to Dr. Eklund so he could give me the prosthetic cortex. A year after I awoke with the prosthesis, he invited her to visit me. He told her not to expect too much. I greeted her politely. When she asked me questions I answered them truthfully. But she started crying. I started having problems with my prosthesis about that time, but I managed to maintain equanimity. It was when she said goodbye that I had the worst reaction.”

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. “Janis,” I ask, “have you ever killed anyone before today?”

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My Own Back Yard

Passion flower. Image from http://www.neoninc.org/budburst/resources_plant.php?Species_ID=27

For the last six months or so I’ve been walking the dogs around the field behind my house, and I’ve noticed there is a great diversity of plants there. I got into to plant identification for a while, and it was fun figuring out what everything was, but I had slacked off the last couple of months because I started teaching more classes and other things came up. Last week though, I started reading Evil Genes by Barbara Oakley, an interesting book about the genetic and environmental causes of evil. Oakley writes the book in a conversational yet journalistic style and she often describes the area where scientists live or where their labs are situated by talking about what kind of plants are there. She’ll say things like “The lab is nestled amidst hills of wild barley and bluegrass.” This gave me another reason to look into plant identification: it can help with my writing.

Another factor is that Fall is beginning to influence things. Plants that were unremarkable before now have flowers and color. There’s an area in the back of the field where you can walk between two copses of evergreens. And there, almost hidden in the nettles that the dogs were sniffing through, was a very strange and awesome looking flower. It looked almost like something you’d expect on an alien world. It was pink and purple and had some very prominent stamens or something sticking out of it, and it was on a vine. There were a bunch of them, so I cut one off and brought it inside and showed it to my mom. “Oh,” she said rather matter-of-factly, “That’s a passion flower.”

“A passion flower?”

“Yes. It becomes passion fruit later on.”

Well, this blew my mind. I thought passion fruit was from some exotic place like Hawaii or Madagascar or something. Turns out it’s native to Tennessee. In fact the passion flower is Tennessee’s state flower. The natives in the area called it ocoee and it’s the namesake of the Ocoee river.

Ironweed

After this, I found a strange purple flower along the edge of the field where some dogwoods and honeysuckle separate the field from the road and determined that it was Ironweed, so called because it has a hardy root system that’s difficult to dig out. The Indians supposedly used some part of it to ease stomach aches. There were also several large plants that looked a little like wild carrot, except they were larger and the flowers were much more sparse and not in a true umbel but more of a branched system. I thought that these were cow parsnips until I did some further research for this blog. There’s another plant that looks a little like a thistle mixed with an aster that I haven’t been able to identify, but these set backs if anything, make me want to know more.

All this is very exciting, but civilization places pressures on the situation that I didn’t quite expect. Yesterday a man came by the house to work on the tractor, which has lain more or less dormant since the beginning of spring. Weeds and grasses pushed through its mechanisms, the back left tire had gone flat. When the man got the thing to start by replacing the battery and shorting the starting circuit with a screwdriver, it seemed to be asking us to please leave it alone to die in peace. The man said that he would come back and do some more repairs on it, but that we ought to be able to use it to mow the field if we didn’t care that none of the gauges worked and the screwdriver method was the only way to start it.

Our tractor sitting in our field after Tractor Man looked at it.

We could mow the field.

And I felt a surge of panic. Mow the field? But that’s where all the plants are! You can’t just mow them down! Sure there are snakes and ticks and chiggers and what not that breed and stalk their prey in the tall weeds and grasses, but I still haven’t figured out what all the weeds and grasses are.

Crazily I thought of maybe just asking my brother, who operates the tractor usually, to just mow part of the field. Or maybe leave a circle untouched, but I know the field is going to be mowed eventually. All the plants will grow back next year, just as they have this year, and it someways maybe they are there in the first place because we mow the field. Still, it’s a little disheartening.

Switchblade Pisces: Pt.5

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“I don’t understand. Why is she crying all of a sudden?”

Janis tries to speak “I…I…I…”

The male Pisces shakes his head. “Her speech centers are controlled through her optogenetic interface. You need to wait for her to cool down before you can talk with her.”

“Alright, what the hell is an optogenetic interface?”

“I will comply with your request for information, but may I be permitted to take you to Eklund as I do so?”

“No. I don’t want to go there.” I grit my teeth as I try to figure out what to do. “I need to think. Can you take us somewhere safe?”

“Safety is relative. I can take you somewhere that is hard to find, but I am afraid the FBI will still reach us eventually. I urge you to make a decision quickly.”

“I know, okay? I suck at decisions! Just… give me some more time to think.”

“I will comply as best I can.”

 “What’s your name by the way?” I ask to distract myself from Janis. It’s uncomfortably warm next to her, and she looks so vulnerable and hurt. Despite myself, I’m kind of worried.

The male Pisces turns on to the road and drives back toward the highway as talks. “My name is Jazz. That is the music I like the best. I don’t prefer any artist in particular, so I simply chose Jazz as my name. I am told that I enjoyed jazz before I became a Pisces as well. Has Janis told you how we came to be this way?”

I shake my head no, then I realize Jazz can’t see me so I say the word. Janis is taking shuddering breaths, but she is sitting unaided now, her elbows on her knees as she holds her head in her hands.

Jazz stops at a red light and takes the opportunity to pat Janis on the knee again. “Love will find a way,” he says, “time heals all wounds.”

It strikes me that despite the awkward mechanical way Jazz does this, he is still doing a better job at consoling Janis than I probably would, even if I weren’t upset with the Pisces woman for killing two people. Looking ahead to watch the light, Jazz continues his explanation. “Janis and I both suffered severe trauma to our brains, which left us comatose. Although our bodies were capable of autonomic functions, breathing, digestion, et cetera, we had no activity in our frontal lobes. We were vegetables. I was a police officer who got shot in the temple. Janis was a twelve-year-old girl who was in a car accident while sitting in the passenger seat. The air bag deployed too quickly for her. She was in a coma for ten years before Dr. Eklund found her.”

The light turns and Jazz drives onto the highway as he continues. “Optogenetics refers to the way Janis and I were rehabilitated. The computers you see attached to our heads control lasers which are guided through fiber optic cables to special genetically modified neurons grown in our frontal lobes. Using cells from our skin, Eklund’s laboratories were able to create neural progenitor cells. That is, cells that are able to create new neurons.”

“They can do that?” Sitting next to two people with computers attached to their brains my question seems hopelessly naïve.

“My guardian is the only one who has been able to create a working prosthetic cortex, but many of these technologies have been available since the beginning of this century.”

“How come I never heard about them?”

“The information has been available in many respected scientific journals and news magazines.”

“Oh,” I say. I guess this is what I get for reading nothing but sci-fi novels and video game reviews.

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Reading your Blueprint: DNA Fingerprinting

Who are you? That’s the question asked repeatedly in the song by The Who that CSI uses as it’s theme song. The answer, it seems, is found in the various pieces of evidence the Crime Scene Investigators find. Sometimes it’s pieces of fiber or pollen that eventually lead to the answer, but by far the most common method of determining identity is analyzing DNA evidence. What you see in the show is attractive people in lab coats taking samples of tissue, sticking them into some machine and then looking at a bunch of bars on a lit screen and saying things about what they mean. How is this any different from the old methods of reading patterns in tea leaves or goat entrails?

First off, I should probably point out that tv shows don’t always get things right. It usually takes much longer to get a result from a DNA sample, and if you recall the Casey Anthony trial and the OJ Simpson trial, DNA evidence does not always lead to a sure result. Well, what good is it, then? It’s not that DNA evidence isn’t useful, it’s just that there are circumstances where it isn’t available or isn’t clear. Similar to fingerprints.

So how do they analyze the samples they gather? They can’t use karyotyping usually, because they need living cells in order to do that. Thankfully, technicians don’t need to have DNA in chromosomes in order to be able to analyze it. As long as all they are looking for is straight DNA, they can get it from almost anything biological. Hair, skin, saliva, blood, and other fluids all contain viable DNA.  You still have to get it out of the sample first.

Close up of polymer gel structure. Water and small molecules can pass through spaces in the mesh. Image adapted from http://bit.ly/qvsOix

One way to do this is to crush and dissolve the sample using proteases. Proteases are enzymes that eat up proteins. They are present in a lot of different cells and even in some of the food we eat. If you’ve ever eaten a lot of pineapple and found your mouth sore afterwards, the reason is because of the proteases in the pineapple. This is also the reason why it is very difficult to make pineapple jello. Jello is a type of gel, a substance made up of proteins that form a mesh that traps water inside. If there is too much protease present, that mesh can’t form, and the Jello mix stays syrupy. The materials that keep your body’s cells from moving all over the place are also a mesh of proteins, and so if there is enough protease, some of this mesh will be dissolved. This is why pineapple can make your mouth sore. It is also why a strong protease can eat away the proteins that surround a DNA sample. Hair samples, in particular, have a lot of protein surrounding the DNA, so there needs to be a lot of protease to get to it.

Another way to get at the DNA is by using a detergent. Laundry detergents clean clothes by breaking up the oily materials that trap stains in the fabric. The membranes of cells are also made of oily material, so by using a detergent, we can wash away the cell membranes and get to the DNA inside.

Often both a protease and a detergent is used just to be sure the DNA is accessible. After this, the sample is put through a centrifuge to remove the lighter, non DNA molecules from the heavier DNA. Once the DNA is free, chemicals or heat is used to separate the two strands of DNA into single strands. This allows the restriction enzymes to work on the DNA. Restriction enzymes cut the DNA at specific areas that a technician can determine ahead of time. DNA is formed of four different bases: Adenine, Guanine, Cytosine, and Thymine, Each enzyme attaches to a certain sequence of these bases and cuts the DNA where ever that pattern shows up. DNA from different individuals will have different lengths between each recognized pattern and so will be cut up into differently sized sections after the restriction enzymes do their work.

Image from http://bit.ly/9h7sIW

The cut up DNA is then poured into a gel, usually made out of agarose or polyacrylamide. Just like Jello, these gels are made of long molecules connected together to form a mesh that partially traps water. The DNA fragments can travel through the spaces in the mesh, but not very easily. Lab workers apply an electric field to the gel using a tray with exposed electrodes that holds the gel immersed in a bath of mostly water mixed with some chemicals to help pass the electricity to the sample.  DNA is made of sugar molecules, and like most things made of sugar, it becomes negatively charged very easily.  In fact, unless DNA is in a solution with a high pH, it will have a slight negative charge, and so the electric field made by the tray device  pushes DNA down the gel toward the positive electrode in a process called electrophoresis.

http://www.biologyreference.com/Dn-Ep/Electrophoresis.html

The larger the piece of DNA, the harder it is for it to pass through the mesh of the gel. Smaller strands will therefore travel farther along the gel in a given period of time.Fragments of DNA that are the same size will be in the same area of the gel after they’ve been pulled through it, forming bands in those areas. These bands are still not visible, however, until the lab worker applies some kind of label to the DNA. This could be a chemical dye that binds to DNA, or DNA fragments with radioactive isotopes attached. The most common chemical dye is ethidium bromide, which is only visible under a black light. The lab worker can place a gel stained with ethidium bromide on a scanner attached to a black light to record the bands in the gel. In the case of radioactive isotopes, a film sensitive to x-rays can be placed on the gel which will turn dark where ever the radioactivity is.

Gels fall apart very easily, so many lab workers will transfer the DNA from the gel to a sheet of filter paper by pressing the paper to the gel and passing a current through it for some time. Then they can apply a label as before to see the bands of DNA.  These bands are what you usually see on tv shows where they compare DNA. By looking at where the bands from different samples show up, a lab worker can tell which samples are from the same source and which ones aren’t.

Debbie Knight at biologyze gives an excellent  detailed accounting of the process of gel electrophoresis here if you’re interested. She uses it to analyze proteins, but the idea is very similar.

Sometimes there isn’t enough DNA in a sample to get visible bands, in fact, this is usually the case. For these situations, there is PCR. PCR stands for Polymerase Chain Reaction. Polymerase is an enzyme that replicates DNA, but it’s more complicated than that. In order for the DNA to be replicated, it has has to be separated into single strands from its usual two stranded arrangement. This is called denaturing the DNA. In nature, this task is performed by proteins called helicases, however in the lab, heat or other chemicals can do the job.  Chemicals are somewhat difficult to work with, because they have to be washed out of a sample every time they are used. Heat is a much better denaturing agent, but most polymerase molecules can’t stand the heat needed to separated the DNA.

http://users.ugent.be/~avierstr/principles/pcr.html

Thankfully scientists found the molecule Taq, a DNA polymerase found in bacteria that can withstand the heat.  So what happens during PCR is that after Taq is added, the samples are first heated to a temperature high enough for the DNA to denature. Then the temperatures lowers, letting initiating sections of DNA called primers to attach or anneal to the fragments. Then the temperature raises again to a temperature that is ideal for Taq to replicate the DNA. Finally the samples are heated once more, so that the new DNA fragments separate again with twice as many fragments as before. This reaction is performed again and again, so that first two new strands are made, then four, then eight and so on, the amount of DNA increasing exponentially with every cycle. This way even with a miniscule amount of DNA you can have enough of a sample to work with.

 

Canoeing on the Harpeth

A couple of weeks ago I went canoeing with my friend David and some of his friends and family on the Harpeth river. It’s really more of a stream than a proper river, but it’s a pleasant stream with lots of bends and plenty of wildlife to see along the way, so it makes for good canoeing.

The Harpeth river forms the Harpeth valley, sometimes called the Harper valley, and for a while the area reached a certain level of fame from a country song by Jeannie C. Riley called Harper Valley PTA that came out in 1968. It’s a very simple song (there’s two points where the key changes slightly and that’s as exciting as it gets musically), but it deals with a mother refusing to bend to the will of a semi-theocratic quasi-socialist regime (the Parent Teacher Association) and so the lyrics give it a little punch.

It had been some fifteen years since I went canoeing. I had gone a few times in the scouts, and what I remembered from that was

  • I was going to get sunburnt
  • I was going to get wet
  • I was going to need water
  • Either my posterior or my knees were going to hurt
  • And at some point the canoe would tip over.

Bearing this in mind, in the hour or so I had to prepare before I showed up to the meeting place I rushed through the house looking for swimshoes that I haven’t worn since the Clinton administration, knee pads that were marginally more comfortable than cardboard, a completely dorky fanny pack for putting snacks in, and a few bottles of water, which I completely forgot about when I eventually showed up.

My brother Shane was up as I was searching through the house and he asked me where I was going. When I told him he said, “Ew,” and asked why I would ever want to do that. I said something to the effect that it would be fun and I’d be able to hang out with some friends. Shane asked me if I had ever seen the movie “Deliverance.”

Ignoring his warnings, I got everything I needed from home, put it in the car, and left.

cell phone dry box and dry pouch

My chief concern was that my cell phone and wallet might get wet when my canoe tipped over. So after I drove the twenty minutes into town I went into Walmart and got a water proof cell phone box and a water proof pouch for my wallet. The makers of these items had an interesting sales strategy. They said that their waterproof containers were not intended to be submerged. Now I understand the idea. Basically I can’t go scuba diving and expect them to work, but “submerged” can mean a large range of things, and what I want when I’m purchasing water proof containers is some assurance that they are, in fact, waterproof. So I don’t know, maybe do what watch makers do and say that they’re waterproof up to ten feet or something?

Anyway I showed up at David’s father’s house to meet everyone on the trip. It was Me, David, David’s father Tom, David’s wife Kristi, a girl visiting from China named Nicole, and another friend of David’s named Gray. Gray was the only other person wearing swim shoes, which made me feel slightly less like a dork. David was wearing long jeans and army boots, almost daring the river to try to mess with him.

Tom provided us all with Ziploc bags for our cell phones, which I used along with my dry box, because I was pretty sure my canoe was going to tip over. After having a nice chat about our previous canoeing exploits, most of which were variations on the terrible things that could happen if you got tipped over in the rapids, we all got into our vehicles and went down to the company that was going to rent our canoes. The company’s name was Tip-a-Canoe.

It was me, Nicole, and Tom in one boat, David, Kristi, and Gray, in the other. The girls weren’t terribly keen on rowing, so they sat in the middle. The way canoes work is that the person in the back does most of the steering, the person in the front provides thrust and helps with the steering, and the people in the middle try to make themselves feel useful with varying levels of success. Kristi took several pictures on the river, and both she and Nicole helped during some of the trickier areas of the course, so everyone participated.

I was glad to have knee pads as the seats on the canoes are amazingly uncomfortable. I also like paddling better on my knees because of the lower center of gravity, or maybe it make me feel like I’m going faster. Unfortunately the knee pads I was using weren’t intended for extended use. I eventually fell into a rhythm of alternating between sitting on my rear and sitting on my knees as each area got more painful. I like to think that I was better off than my friends, who just sat, but I’m not entirely sure.

I had of course forgotten to put sun tan lotion on, but thankfully the weather was mostly cloudy that day so I only got slightly sun burnt on my arms. It wasn’t too hot either, and there were several relaxing tranquil moments as we let ourselves be pushed by the current and admired the profundity of the nature around us. There were several turtles along the river. Often just as we spotted them, they would slide into the water, making us wonder if we had seen them at all. Tom shared a story with us about how David once had been conscripted to move a turtle off a road. I won’t go into any details, suffice it to say the moral of the story was: “Don’t ever try to pick up a turtle, unless you are sure it’s not a snapping turtle.”

We saw a heron or two launch gracefully into the sky, and at one point we came across a flock of ducks. David shared with us a little song at this point that described the behavior of one of the ducks perfectly: “Shake your butt / Shake your butt / Poop!”

That wasn’t the only singing that took place. Gray revealed that he had quite a good singing voice and belted out a few lines from some of his favorite songs. He mentioned one of his favorite singers was John Denver, which I found a bit odd. The only thing I really know about John Denver is that he died in a plane crash and one of his songs was used to ominous effect in the first Final Destination movie. I couldn’t figure out a way to leverage this into conversation, so I just let it go.

At some point during the trip I started quoting Monty Python, as I am wont to do. This prompted Nicole to ask me how to speak in an English accent. Not being from the UK myself, I had to inform her that I was far from an expert in the subject. Next I told her what my father always said about the accent, which was that the best way to imitate it was to imagine there was a bumble bee in your mouth while you were talking.

Nicole knew a great deal of English, so I was surprised when she asked what a bumblebee was. Tom and I explained it several different ways, describing how it buzzed, how it could sting you, but only once, which was a little sad. How wasps had chemical stingers and could sting you several times and were nasty little things… I got the impression that Nicole figured it out after a few seconds, but let us carry on for the entertainment value.

We all stopped for lunch halfway through. Tom had made a plethora of chicken for us to eat, and we did our best to consume as much of it as we could. It was at this point however that I learned there wasn’t any water in the cooler. There was only diet soda, diet tea, fresca, and Pepsi. The Pepsi was the only thing that didn’t have aspartame in it, and aspartame tastes nasty to me, so I had that. It reawakened my love of high fructose corn syrup. David and I had a discussion about corn syrup’s deleterious effects. He lauded a number of brands of soda that used sugar instead . I said that I kind of preferred the corn syrup to sugar. My main problem with sugar soda is that for some reason it’s almost always flat. It sometimes doesn’t taste quite right either. Maybe I’m just a victim of consumer culture.

At one point we came to a hole dug into the rock on one side of the river, and Tom told us how it had been carved by slaves under orders from Montgomery Bell. I didn’t realize it at the time, but we were canoeing around the Narrows of the Harpeth, near Mound Bottom an archeological site where artifacts have been found from as early 900 CE. I’m definitely going to want to check the area out on foot sometime. It looks pretty interesting.

Once we reached our end point, we took pictures of each other while we waited for the canoe truck to come by to take us and the canoes we rented back to the starting point. It was a good trip over all. Nobody tipped their canoes over, which I was a little sad about after all the anticipation. We did have to get out quite a few times to carry our canoes over the shallow regions, but it was no substitute. I still have an unfinished feeling about the trip as a result. Still glad I went though.

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