Monthly Archives: August 2011

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

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

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.

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.

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.

Switchblade Pisces Pt. 4

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We’re at a gas station, because apparently even motorcycles driven by crazy robot girls need gas occasionally. I’m leaning on one of the support columns, and Janis is filling the tank when I realize I have a way out of this situation.  I call to Janis to get her attention. She looks up, her purple irises regarding me with the same focus that she had previously applied to filling the tank. “Yes?”

“I’m not going to see this Eklund character of yours. I order you to take me to the cops or whoever you’re supposed to call in this situation, and for you to confess what you’ve done.”

“I will comply. This is not ideal, however.”

“I don’t care if it’s ideal! That’s what we’re doing.”

“You understand that you will be arrested if I do this?”

“I don’t believe you about that. All I know right now is you just killed two people and I just helped you blow up my apartment after you tried to kill me.”

Janis hangs up the nozzle, but she pauses just as she’s lifting her leg above the seat of the motorcycle. She shudders and starts to collapse. Without thinking I find myself diving forward to catch her. She is burning hot, her face is beet red. She opens her eyes and they look blood shot. “I need to rest. I don’t feel well. I think. I…think I am upset about something.” She closes her eyes and a droplet of moisture falls out of a corner of one of them.

Is she crying?

She’s running a high fever, and the fans on the boxes on her head are whirring like crazy. I feel the side of one of them and involuntarily jerk it away. Feeling again more carefully I estimate that it’s running about fifty degrees Celsius. That’s not too bad for a processor, but for something attached to a human?

I consider my options. I could just get on her bike and leave her, but that doesn’t seem like the right thing to do. Even though she did kill some people.

Just then a black sedan pulls up in front of us. A man who looks to be in his forties rolls down his window and addresses me. “Ethan Yates?”


“Please get in the car. Janis is overheating. She needs rest. You are only a few miles from Eklund’s compound. I’ve been tracking her on GPS.”

Crap. Reinforcements. He’ll probably kill me if I don’t go with him. “Janis. Go ahead into the car, alright? You don’t have to follow that last order I gave you.”

“Th…Th…” Janis tried. I could barely hear her over her fans. Damn it!

The guy in the car gets out. He’s wearing a shiny silver suit. It looks expensive, but I’m not an expert. I’ve been wearing jeans and t-shirt for most my life. The guy in the suit opens the back door and I help him get Janis inside.

“She’s burning up,” I say to the guy. “You have a hospital or something in this place?”

“She will be fine. She just needs to rest.”

I sit next to Janis feeling the temperature of her skin. Before I realize it, the car door is closed and the guy in the suit is in the driver’s seat again. ”I will take you both to Eklund now.” That’s when I see the two boxes on back of his head.

“You’re like her? You’re a Pisces?”

“Yes,” he says as he drives out of the gas station. “I will follow any order given to me. I lost more of my brain tissue before reconstruction, so I suffer less from emotional stress when compared with Janis. She has been like this before, when her birth mother came to visit. I believe that if you give her physical contact and say meaningless optimistic statements, it will accelerate her recovery.”

Janis sobs involuntarily. She is definitely crying now.

The man stops to wait for traffic at the entrance and reaches back to Janis while he’s stopped. “There. There.” He says as he pats her mechanically on the knee. “It will all be alright.”

Janis sobs again.

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Reading Your Blueprint: Karyotyping

DNA is  what makes us who we are. It identifies us. The government uses it to control us. Well, that last one isn’t quite true…yet. Still most of us, even those of us who should know better, treat DNA as if it were magical fairy dust that wizards in lab coats use to answer questions. But the only difference between the wizards and you is some knowledge and equipment. This blog will help with the knowledge part.

There are three main ways to use DNA to tell something about an individual: Karyotyping, DNA fingerprinting, and Genome sequencing. I’ll go over Karyotyping in this post and tackle the other methods later.  Karyotyping is basically looking at the chromosomes of a cell as it’s dividing. Cells divide to make new cells, but in order to make sure each new cell has everything it needs, everything has to be copied, including the genetic information. Unless the cell is a bacterium (or an archeum), it will keep its genetic information in a sort of ball of denser material called a nucleus. Most of the time this ball is all we see of the cell’s DNA, but if we add a dye and watch the cell divide, we can see several strange, threadlike structures, or bodies, that are colored by the dye. These “colored bodies” are the chromosomes, named after the Greek “chromo” for colored and “soma” for body. A chromosome is actually DNA wound up around proteins and then wound up again and again until it becomes a tight tangled mess, similar to what happens if you twist a coiled telephone cord.

As you look at  chromosomes under a microscope, in other words, you are actually looking almost directly at DNA.  Normally the chromosomes are haphazardly arranged around the nucleus of the cell, but after taking a picture of them, you can rearrange them so that they’re aligned the same way and in order from largest to smallest. This is a Karyotype.

Usually a lab worker who wants to karyotype a person’s blood, will look at some white blood cells, which are easier to work with for a variety of reasons, and wait for themto start dividing. Then, he or she will use a drug such as colchicine or vinblastin to stop the cell from dividing completely. This allows the technician to look at all the chromosomes under the microscope and analyze them using dyes that bind to different genes. The lab worker or another scientist or technician can then compare the karyotype of one individual to another to see what differences they are in where the dye shows up.

The drugs used to stop the cells from dividing have interesting histories. Colchicine started out as the active ingredient in an herbal remedy extracted from autumn crocuses to treat gout and inflammatory arthritis. Crocus extract was used as such as far back as 1500 BCE though it was only isolated from crocus extract in the late 1800’s. Colchicine is still used to treat severe cases of gout today, however, the difference between an effective dose and a toxic one is rather small, so takers of the drug have to be careful.

Chromosomes of a cell. Vinblastin or colchicine used to keep them from separating.

Vinblastin also comes from a plant extract, this time from the madagascar periwinkle plant. The plant was originally crushed into a tea, and researchers noted that people who drank the tea had a lower white blood cell count, leading researchers to look into the active ingredient as a possible treatment for diseases that affect white blood cells.

White blood cells are primarily responsible for the body’s immune response, which causes inflammation, the primary complaint of gout and arthritis sufferers. These cells also  affect a number of diseases, including cancer. White blood cells use microtubules to initiate movement, and all cells use microtubules to separate chromosomes as they divide. Cochicine and vinblastin both inhibit the production of microtubules, which is why the drugs are useful in karyotyping as well as a number of other diseases.

The easiest thing you can do with karyotyping, after determining species, is determining sex. A normal human being has 23 pairs of chromosomes and sex is determined from the 23rd pair. Genetic females have two longer chromosomes, called “X” chromosomes here, while for genetic males one of the chromosomes is shorter and called a “Y” chromosome. Sometimes a person might have two or more X chromosomes along with a Y chromosome in a condition called Klinefelter’s syndrome. There are also a number of other possibilities, such as XXX or even XXXY. All these scenarios usually result in learning disabilities, and regardless of how many X chromosomes there are, if there is a Y chromosome the person will be physically male. These situations where there are more than two sex chromosomes are examples of aneuploidy.

Karyotype of a normal male. From

The word “aneuploid” comes from four Greek words mashed together: “an-” for not, “eu” for good,”ploos” for fold, and “oidis,” which means form or type. So all together you have “not good fold type,” a set of chromosomes that is not correctly paired. This sort of situation can occur in other chromosomes as well, such as in the case of Down syndrome, the second most common inherited  form of mental retardation, where there is an extra copy of chromosome 21.

In biological terms, “-ploid” refers to how many complete sets of chromosomes there are. The normal number of copies for a set of chromosomes is two, so most cells are called diploid. Sperm and eggs only have half the normal amount of chromosomes, so they are haploid. Plants and some other organisms can have more than two sets of chromosomes, making them polyploid. While polyploidy can occur in human fetuses, it never results in birth. In fact no vertebrate animal can be polyploid.

A normal x chromosome on left, fragile x on right.

Fragile X is the most common inherited form of mental retardation, and while it is not a aneuploidy disorder, diagnosticians can also identify it using a karyotype. In fragile X one of the x chromosomes looks thinner in an area that has a long string of the same DNA sequence. Because of this repeated sequence, a protein required for normal development can’t be produced properly and the neurons of the brain cannot form the proper connections as a result.

Diagnosticians can tell that someone has Fragile X from the way a certain area of a chromosome is affected naturally, however they can also tell other genetic attributes by how the chromosome is affected by the dye they use. Giemsa, the most common dye used for karyotyping, will concentrate in different bands on the chromosome, which you can see in the picture of the normal male karyotype above. By comparing where these bands show up between different karyotypes, researchers can begin to find abnormalities and differences that may have something to do with how a person looks, acts, or feels.

Other labeling techniques have also been used to get more information from chromosomes. Especially exciting is the work done on telomeres, which can be labeled using a protein attached to a fluorescent marker. These are the ends of the chromosomes, which are made up of repeating patterns of DNA that act like the aglets of shoelaces, keeping the chromosome from shortening prematurely. Telomeres have been found to be  linked with the aging process. Although the telomeres will shorten and lengthen throughout life, various stresses can cause them to shorten more than usual. It seems the older we are, the shorter our telomeres get. If we can figure out how to lessen the shortening process, we may find a cure for aging itself.


Suggestions? Corrections? Questions? Observations? I’m trying to cover a lot of ground here without letting things get too complicated, so I’m bound to make some mistakes. Please feel free to comment on this post or email me at zorknot (at) about what I’ve written.

Switchblade Pisces Pt.3

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“Please do not attempt to have sex with me.”

I hold my hands up and back off a little. “Okay, you got it. Can you tell me why you were about to kill me?” I walk over to the kitchen area of my apartment and open the refrigerator for a beer.


I pull the tab on the beer and take a swig, waiting for Janis to tell me what she knows.

“Well?” I ask finally.

“Oh. I was not aware that was a request. I am still learning intonations and intention monitoring. My neuroplasticity has been heightened, but learning is still difficult as I am no longer in the growth phase of my development. I was about to kill you because I was ordered to kill you. I do not know why I was ordered to kill you. I suspect however, that it is for the same reason the FBI wants to kill you.”


“I do not know. Only that you have recently appeared on their most wanted list without any information describing your crime.”

My apartment is on the first floor of a two story complex. I have two windows looking out on the parking lot. One of those windows has my air conditioner in it and I usually have black out curtains on the other one to keep the sun from making the place hotter than it already is, but the curtains are parted now to keep the place from seeming too gloomy.

That’s how we know when the FBI arrives. Well, it’s either the FBI or a black sedan got separated from a funeral procession. “Shit!”After taking a precious second to weigh my options,  I run out of the door. Of course the black sedan has my Tracer blocked, and the two guys in black suits and sunglasses are getting out and pulling out their pistols and giving me conflicting orders.

I’m standing there, trying to decide whether to freeze or put my hands up when I hear Janis.

“Please run to my motorcycle,” she requests loudly, “And hurry.”

“But… they have guns…”

Just then, Janis moves in front of me as one of the agents shoots.

Janis’s arms become a blur. There is a rush of wind and a clang. Something hits a car window, causing it to shatter. “I am aware of their weaponry,” she says holding her blades in her hands. The fans in the black boxes she has on her head are whirring loudly now. “Please run to my motorcycle. It is at the South exit.”

I swallow and do my best to follow her advice. Her motorcycle, looks a bit larger than the ones I’ve seen before, while still seeming utilitarian. I notice as I’m climbing onto it that the license plate has a single letter on it. H. The Feds are shooting at me now, but Janis seems to be able to knock out their bullets. It’s getting difficult for her though. And I start to worry until Janis throws a small, dark object at them that arcs onto the ground at the men’s feet, bouncing a little metallically.

There’s an almost comical moment when they look down and realize what it is.  Then I’m temporarily blinded and deafened as the grenade explodes me.

“Holy crap!” I yell. Janis just killed those guys! Four men paid with taxpayer money, and this crazy girl with boxes on her head just blew them up!

Janis gets sits on the driver seat of the motorcycle. I get off immediately not wanting to go wherever this psychopath is going. The floating colors in my vision are slowly fading away. I can smell the smoke from the grenade. Smells like fireworks and burnt plastic.

“The apartment is about to explode. We are in the blast radius. Please get back on.”

I move mechanically, sitting behind Janis and grabbing the hand rails beside me. She speeds away from the apartment just as the window without the air conditioner in it blows out and orange flames reach out to the heavens.  It isn’t that large of an explosion, really but what if someone gets caught in the fire?

And what about those four FBI agents? They weren’t bad people, were they? They were just doing their jobs, serving their country. And here I am sitting behind the woman that killed them, as everything else that I own goes up in smoke.

I could jump off right now even while the road is speeding underneath me. I’d get a few broken bones, but I’d get away from her.

We zoom past a white mustang on one of the wider city roads. The wind is tugging at my clothes with alarming strength. We’re going too fast. I’m stuck.

Might as well relax and enjoy the misery.

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Switchblade Pisces Pt. 2

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“I am a Pisces,” the woman says as if that explains everything.

“You’re kidding me. So am I.” I laugh.

“When were you made?” the Pisces girl asks with a tilt of her head.

“I was born February twenty first. I just missed being an Aquarius by two days,” I tell her. Not that I believe in all that mumbo jumbo, but it’s always bothered me that I was a Pisces. I mean Scorpios are supposed to be the worst I think, but whenever I see a description of Pisces it seems like the most wishy washy of signs. Worse, it fits me pretty good in some places.

The girl closes her eyes and turns her head back and forth in three movements. “You are not a Pisces in the way that I am a Pisces.” She opened her eyes. “I was ordered to kill you. In the event of my failure, I was ordered to tell you that your services are requested by Baxter Eklund and to take you to his base of operations. Would you like me to repeat the message?”

“Who is Baxter Eklund?”

“He is my guardian.”

“Oh.Did you grow up in a mental institution or something? That would explain a lot.”

The girl looks down and rubs her right wrist with the thumb of her left hand. “The AI of my prosthetic cortex was developed in an institution of learning, a laboratory. Also, I have been training with my optogenetic interface for three years in the same environment. In this sense it can be said that I grew up in a mental institution. However, I did not grow up in a mental institution in the derogatory sense you seem to suggest.”

Although she doesn’t have a discernable accent, she says all the syllables of the word “laboratory.” La-bo-ra-to-ry. It’s kind of cute and creepy at the same time. Like a levitating puppy.

“Are you supposed to be a robot or something?”

“I told you. I am a Pisces.” She’s taken to rubbing her other wrist now.

I rub the bridge of my nose. “Just so we’re clear, you don’t mean Pisces as in the astrological sign, you mean something else?”

“I am a human female, partially controlled by computer through an optogenetic interface. I am distinguished from other human females from my programming, which requires me to answer any question truthfully and to follow any order that I can physically obey. Humans with this programming are called Pisces.”

I don’t know what an “optogenetic” interface is, but there are things I’m more concerned about at the moment.“Okay. So you aren’t going to kill me if I turn my back to you or something?”

“Not unless you want me to,” the Pisces girl releases her blades and tilts her head.

“Thanks, but no. I think I’ll pass.” I look around my apartment, trying to think of what to do now. I should probably phone the police, but, well look at it another way, I’ve got a beautiful girl in my apartment. Sure she’s a psychotic nutjob who might kill me anyway no matter what she says, but that kind of adds to her mystique. “So, uh what’s your name?”

“Janis” She says, retracting her blades once again into her smooth, lightly tanned wrists.

That’s a neat trick she’s got. “Janus? As in the two faced Roman god of doorways and financial fortune?”

“No. My name is Janis because Janis Joplin’s name was Janis. I admire the passion she exhibits in her music, perhaps because I do not understand it. I hope to someday.”

I nod and get up from the floor. “Nice to meet you, Janis.” I hold out my hand. “My name is Ethan. Ethan Yates.”

She extends her hand and grasps mine. Her hand is unexpectedly warm. Almost too warm. Her grip is firm for a woman, but not unnaturally so. I release her hand and she seems to look me over. “You are attracted to me, yes?”

I feel a little heat rise to my cheeks. “Yeah…uh sorry.”

“Please do not attempt to have sex with me.”

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A Story of Glowing Maps

The Japanese didn’t have GPS during World War II, at least not in the form that we’re familiar with today.  If ground troops in the Pacific wanted to look at a map, they had to shine a light on it, and that was rather detrimental to their survival prospects if they needed to know where they were while conducting a secret night time operation.

Luckily for the Japanese soldiers, one thing the Japanese knew a good deal about was ocean life. In particular, a crustacean they call an umi hotaru or “sea firefly”  has the unique property that if you prod it, it glows. If you crush a bunch of these little guys up, and pour water on them, you can create a glowing sludge that you can put on your hands. A glow that is dim enough to not be noticed in the field, but bright enough to read a map by.

When the atomic bombs fell on Hiroshima and Nagasaki, it effectively ended the Japanese soldiers’ need for glowing maps. But a young man who had been working at a factory only 15 miles away from Nagasaki when the bombs dropped, would ensure the sea firefly retained its place in human history. A decade and a lustrum after the war, this man, Osamu Shimomura, was studying at Nagoya University when his mentor,  Yoshimasa Hirata, gave him the task of figuring out how the sea firefly glowed.

Sea fireflies. Image from

Sea fireflies, similarly to the fireflies we’re more used to, glow, in part, because of a protein named luciferin.  When oxygen binds to luciferin in the presence of another protein, an enzyme called luciferase, the molecule glows. Even though the sea firefly had been studied for a number of years, no one had been able to purify its luciferin because it was so unstable. If you’ve ever had a firefly splat on your windshield, you’ve observed this instability first hand. The firefly guts glow, but they quickly fade to nothing. When the firefly splats, its luciferin binds with oxygen in the air, causing it to glow as it degrades, but it’s used up after only a few moments. In order to purify the luciferin from the sea fireflies, Shimomura had to take powder from the crushed creatures and distill it using a complicated apparatus (pictured at right), then get it to crystallize in a special solvent, all before too much of it degraded into uselessness. It was tough work, but Shimomura finally did it, and published his results in a scientific journal that got the attention of Frank Johnson, a professor at Princeton University in the U.S.

At Princeton, Johnson and Shimomura worked on figuring out how jellyfish glowed. At the time, the popular theory was that every living thing that glowed used some form of luciferin and luciferase, but try as they might to purify luciferin  from the jellyfish, they weren’t able to do it. The problem was that the jellyfish they were looking at didn’t use luciferin at all, but a completely different protein.

Jellyfish glowing mechanism. Image from

Shimomura suspected this might be the case and looked into the possibility on his own even while Johnson obsessively pursued the luciferin angle. After a tense period of disagreement, Shimomura discovered that the glowing was actually caused by two different proteins: one, which Shimomura and Johnson named after the jellyfish they were studying, (aequorin) and another, present only in trace amounts, which they called simply “Green protein,” because it glowed green when placed under an ultraviolet light.

Thing was, although the green protein was present in only trace amounts, it had a dramatic effect on the bioluminescence of the jelly fish. Aequorin, the more numerous protein, glows blue in the presence of calcium ions, but instead of glowing blue, as one might expect, the jellyfish glow green.  What is happening here is that the blue glow from the aequorin was making the green protein fluoresce green. This was a very interesting property for a lot of researchers and so the green protein was studied in several other labs, and was soon officially renamed “Green Fluorescent Protein” or GFP.

Shimomura and his colleagues spent many years gathering enough of the protein from the jellyfish near Princeton to properly analyze GFP, isolating  the part of the protein (the peptide) that was responsible for its fluorescence. Such fluorescent peptides are called chromophores.

GFP is unique among fluorescent proteins in that its chromophore is within the actual protein, as opposed to being in a compound attached to the protein. This means that if you can copy the DNA that’s responsible for making the protein, you can recreate the protein in all its glowing glory in just about any animal you care to genetically modify , and indeed,  Douglas Prashar and his colleagues  managed to do  just this in 1985, “cloning” the protein so that other, animals could produce the protein. This allowed research on GFP to continue, even as  the jellyfish it originally came from became much harder to work with due to decreased populations.

The nematode worm C. Elegans

In 1989, a marine biologist who spent many of his summers studying at the same research facility that Shimomura worked at, was giving a lecture on fluorescent proteins and bioluminescence when one of the scientists in attendance, Martin Chalfie, had the idea that he could maybe use GFP in his research on nematode worms.

Nematodes have bristles on their bodies, which normally make them very touch sensitive. The system that allows them to feel touch is governed by a very fast molecular motor, operating at least ten times faster than the molecules responsible for vision in humans and other animals. Chalfie was studying how this touch system worked by comparing normal worms with worm mutants that lacked the gene that produced the molecular motor. The problem was that the only way to distinguish between the mutant worms and the regular worms was to either kill them, which would make it impossible to check their touch sensitivity, or to tickle them with a hair, which kind of defeated the purpose.  He wanted to know which worms were touch sensitive, not just that some were and some weren’t.

One thing that nematodes have going for them is that they are transparent. Chalfie realized that if he could get a fluorescent protein to show up wherever the molecular motor was produced, he could easily distinguish between the mutants and the normal worms without having to kill them, because the worms that had the fluorescent protein would glow.

In 1992  when Chalfie and a graduate student of his found out that Prasher had been successful in cloning the gene for GFP,  they contacted him and worked out how to express the GFP gene in bacteria. To their delight, GFP didn’t require any other molecules to get it to glow after it was produced from the gene. All Chalfie had to do was insert the gene into the bacteria, and it made the bacteria fluorescent. That meant that GFP could be used in other organisms easily.

Chalfie’s wife, Tulle Hazelrigg, gave the next contribution to the study of GFP by showing that fusing the molecule to another protein causes that other protein to be fluorescent as well. This meant that rather than simply labeling mutants versus normal animals, researchers could see exactly where the proteins showed up in the animals they studied.

Finally, Roger Y. Tsien, a Chinese-American biochemist working at Berkeley, California improved the GFP molecule by mutating the gene so that the GFP that was produced was brighter and could be seen with the fluorescent scopes that were already widely available in many different labs. He also was able to make GFP mutants that glowed red or yellow instead of green, allowing several different proteins to be viewed at the same time. This gives scientists a glowing map of where all the proteins they want to look at are showing up in their samples.

One of the most remarkable uses of this technology is in the Brainbow technique, developed by Jean Livet, Joshua R. Sanes, and Jeff W. Lichtman, which labels each neuron in the brain of a research animal individually with a separate color formed by a combination of fluorescence molecules.

An image of a rodent brain using the brainbow technique

So we’ve gone from glowing maps of battle grounds, to glowing maps of the brain all in the span of some sixty years.

Osamu Shimomura, Martin Chalfie, and Roger Y. Tsien all received the Nobel prize in chemistry in 2008 for their work on GFP. Shimomura has retired to emeritus status, but Chalfie still works on worms, and Tsien still works on sub-microscopic molecules. They have all changed the world.

My information for Osamu Shimomura came primarily from his 2008 Nobel Prize lecture.I got Martin Chalfie’s story from an interview conducted with him on the podcast Futures in Biotech. I left quite a bit out for simplicity’s sake, so I suggest giving these sources a look if you’re interested.All other sources are available through the hyperlinks I have provided in text.

Big Dumb Aliens

The alien Mo-Ron from the show Freakazoid

Last night I watched yet another movie with big dumb aliens in it, Cowboys and Aliens. Don’t get me wrong, C&A was a pretty good movie. I’d give it a 7/10. It’s fun, and it turns out Olivia Wilde is a sexy alien, which I always kind of suspected. But it seems that if an alien isn’t humanoid, they have to be some kind of horrible beast that kills people for some inadequately explored reason. Just listing some recent ones there’s Cowboys and Aliens, Super 8 (7/10 I’ve downgraded it from a previous score), Battle: Los Angeles (6.5/10), and the tv-series Falling Skies (4/10). Not so recently there was Independence day, and who can forget the aquaphobic aliens in Signs. Basically ever since the movie Alien, there’s this trope of big dumb aliens attacking us, that kind of has me peeved.

In Alien it made sense. The Giger alien monster didn’t come to us, we came to it. It was a creature, not an intelligent being, at least not in the first movie or so. But in all the movies I listed, to a greater or lesser extent, all the aliens come from innumerable light years away using technology we can only dream of, and when we see them we are distracted by how coldly they are separating our heads from our torsos using their serrated appendages.

There are other cases where this makes sense. I included Battle: Los Angeles because the aliens are big and burly and are attacking us, but in that movie they were just the soldiers sent to Earth by the weaker, presumably nerdier ruler aliens. In fact for all we know in the movie the soldiers might even be another species conscripted into battle by their previous conquerors.  I still call Big Dumb Alien in B:LA, though,  because there’s something missing in it that’s missing in all of them. Communication. You can’t really develop any advanced level of technology without communicating. You can’t organize the concerted invasion of a planet without it either. And yet we hardly see the aliens communicating at all in Big Dumb Alien movies. Not to themselves, and certainly not to the humans.

Super 8 is a little bit of an exception here. The alien does eventually communicate with a human and vice versa, but, I still include it, because the alien acts like a savage animal throughout most the movie. It can make people understand it if it touches them. Fine, but as my brother asked after he watched it, why doesn’t it just touch everybody then? Why not do that instead of killing people, or tying them up in some cocoon thing?

The aliens in Falling Skies might also be considered an exception because some humans eventually find out they communicate on radio frequencies. And they can also use children as cyranoids, speaking through them against their will. But why not do this all the time from the start? Their goal is to rape the Earth of its resources, fine. But it isn’t exactly working out that well if your operations keep getting attacked by the indigenous population. The idea is that they’re supposed to act like European colonists, but the European colonists had Indian guides. They didn’t start out mindlessly attacking natives. They ate with them, traded with them, gave them small pox that decimated their population, and THEN they killed them.

The other thing I don’t like about Big Dumb Aliens is that they aren’t just dumb, but big too. It just seems to me that any creature that can kill other creatures easily probably has little incentive to develop an advanced civilization. We humans have got opposable thumbs and our brains and that’s pretty much it as far as physical advantages go out in the wild. We have martial arts, but that’s a developed skill requiring technology. We have weapons, but that’s already technology right there. Just us, by ourselves, we ain’t much. That’s why we had to use our heads and work together to survive.

I just have a hard time believing that something with razorblades coming out of its armpits would ever try using a rock to kill something. The whole premise of these naked creatures being intelligent enough to travel through space seems off to me. It’s possible, but it just doesn’t seem likely. The whole reason we wear clothes is because we’re vulnerable. I just tend to think that if we didn’t have to wear clothes, we would have never invented the internet.

One of the best things about Cowboys and Aliens is the alien technology. There’s a nifty alien gadget that melts gold and floats it, dripping, up to receptacles that move it to the core of their ships, presumably giving them power somehow. Their ships aren’t just slightly tweaked versions of our aircraft, they look completely different and yet move how you might expect them to move. There’s a strange feeling I got while watching where I forgot that what I was watching was impossible. The mother ship is buried in the earth (which also seems to be a running theme in these movies now that I think about it) with a large part sticking out of the ground that looks similar to the rock mesas around it in the desert. When the camera first showed it, my eye just sort of took it in with everything else. There’s the plain, the sun, part of a mesa, an alien space craft, another mesa, a horse…wait what? The arm band thingy too, was different, yet it worked so naturally I wouldn’t have been that surprised to find out Steve Jobs or somebody designed it.

But all that care that went into the tech is rather wasted on the big dumb aliens that use it. A human gets a hold of one of their arm guns. Do they organize a group to go after that human and retrieve the weapon? Nope! They just carry on, tra la la, business as usual, kidnapping humans, making them watch television until they forget who they are and then cut them up and kill them for no real reason.

Of course in the movie, the humans are equally stupid. Okay, you know the aliens have these nifty arm guns that are the only things that seem to do them any noticeable harm. You manage to kill a few of the aliens that have the arm guns by luck and guile. What do you do? Keep shooting bullets so you can watch them ricochet off their impenetrable armor… WRONG! Cut their arms off and get their freaking arm guns! What’s wrong with you people!

…But I digress.

Basically the point I’m trying to make here is that if you’re going to write a movie where aliens are going to invade earth, take a few moments to think on things from the aliens’ perspectives. Yes, having a smaller alien body part come out of a larger alien body part is creepy, but how does that help the alien? Is it being creepy on purpose? Is that the alien’s way of saying hello? How about showing that the alien uses the smaller body parts for sophisticated tasks requiring a lot of dexterity or something? Anything. If you can let us know something about where the aliens come from and especially if you can show them working out some form of counter strategy to what the humans dish out instead of them just being evil, that will make the story so much better.

Just a thought.

Switchblade Pisces pt1


There’s a beautiful woman in my apartment. Unfortunately, she’s about to kill me. I suppose you got to take the good with the bad. The only reason I’m not already dead is that the floors of my crappy efficiency apartment are so squeaky they’re pretty much ninja proof. The woman’s on the other side of the room right now wearing khaki shorts and a light blue sleeveless top. She has a utility belt and her milky blonde hair is in a braid. The odd thing is that she’s got these two small, black boxes on the top of her head. That and she’s wielding two knives in her hands.

I’m probably going to die.

She advances on me slowly. I’m still sitting in my swivel desk chair, turned around from my laptop. I wonder what James Bond would do in this situation. He’d grab the girl’s wrists and seduce her into a kiss, and then she’d tell him everything as she languished beside him on silk sheets. And in the next morning she’d be conveniently dead.

Well that sounds nice, even if it seems a little like retroactive necrophilia. I stand up, my hands out like I’m about to catch a beach ball, and I clear my throat, preparing my best Bond impression. “Um…could you stop please?”

Yes, I’m afraid that was more or less entirely unlike James Bond. Particularly the “um.” I’m pretty sure he never ever said “um” in his whole made up life. Then again, whatever I said seems to be working.

The beautiful woman has stopped.

Her skin is perfect, except for a thin, barely visible scar across her right cheek. Her eyes are an enchanting shade of purple, and they are dilated. I read somewhere that if a girl’s eyes are dilated, it means she likes you.

What does it mean if a girl has purple irises? Oh yeah, that she wears contacts. I haven’t seen colored contacts much since the late nineties though, and while I’ve heard of platinum blondes before, the girl’s hair seems more soft and liquid than shiny. I’ve never seen hair like that. It definitely isn’t bleached, or at least I don’t think it is. Who knows maybe there’s some new product out there that I don’t know about.

I’m not sure what to make of the two black boxes protruding out of her skull on either side of her braid. I could almost convince myself they were decorative bows, except for the blinking LEDs and the little computer fans whirring on the sides of them.

“Could you, ah, drop those knives?”

“No,” the girl says in a melodious soprano, “I cannot.” There’s an uncomfortable pause. Then the girl says. “They are surgically attached to my body.”

“Huh?” I ask, intelligently.

By way of answering my question, the girl straightens and lowers her weapons. Then, in a motion so quick I almost don’t catch it, she retracts the blades and the handles into her wrists.  “What the… who the hell are you?”

“I am a Pisces,” the woman says as if that explains everything.