Book Festival and Margot’s

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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

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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

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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

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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

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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

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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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