Junk DNA

By Sean Brandywine

It came as a flash of inspiration. All that “junk DNA” in human genes that seems to serve no purpose; suppose parts of it were activated? What changes would that make? That question compels research scientist Dr Maya Robbins set about awakening that unused DNA. What would that do? Was there a purpose behind it that evolution has lost in the mists of time or, perhaps, not yet developed. How would the procedure affect a human? New physical features? New powers? Unique mental abilities? Or changes for the worse?

In fact, the result goes far beyond anything Dr Robbins could have anticipated. The unique powers it gives her test subject are, without a doubt, awesome.

But, as a wise man once said, all power tends to corrupt – and absolute power...

• Language: English
• Publisher: Running Wolf Books
• Release date: Jan 14, 2020
• ISBN: 9780463343586

Sean Brandywine

Sean Brandywine was born in 1943 of a Russian father and Irish mother. Most of his professional life was spent working with computers, ranging from programmer to systems analyst and project leader. His BS and MS are in Computer Science. He began programming computers in 1961 and still enjoys writing code occasionally, and designing his own websites.In addition to science fiction, he also writes juveniles under the pseudonym of Shiloh Garnett, and adventure/horror as John Savage.He has been married to the same woman for over forty years and claims to love her more now than ever. He has two children, named Talon and Melody, and three grandchildren (so far). He lives in Solana Beach, California where he enjoys watching his grandchildren growing up, astronomy, fishing, fast sports cars, and, of course, writing.

Book preview

Look What the Subconscious Dragged In

It came as a flash out of the dark. Literally. Maya Robbins had just retired and was in that half-awake, half-asleep state just before sinking deeply into Morpheus’s arms. All day she had been abusing her sixty-five year old brain, trying to make sense of a complex problem in human DNA structure, until late that night she finally gave it up as an exercise in how to become brain-dead. Her empty apartment greeted her with silence, the answering machine told her she had five calls – which she ignored – and her bed called to her. Divesting herself of clothing, dragging on a nightgown, she slipped between the cold sheets and dragged the covers up to her chin.

Sleep, however, was elusive. Her mind, having churned away all day on proteins, RNA, DNA and enzymes and such, refused to totally shut down, forcing her to toss and turn in an effort to find a position comfortable enough to relax her body. Of course, the problem was not with her body – it was tired enough. It was all in her head.

Eventually the overactive consciousness began to fade away. At that point, the subconscious, which had been teasing her all day with hints that might solve her problem, burst forth with the answer. The Solution. The breakthrough that could well enable her to make the next major step forward in the field of DNA research.

She sat up in bed, sleep forgotten in the urgent need for pen and paper. She scrambled to her desk, blinked as the desk lamp blinded her, fumbled to get her reading glasses on, then pulled a pen out of the dinosaur shaped pencil cup and dragged a pad of paper out of the lower left corner drawer. The pen danced across the lined paper surface, imparting almost magical insight into the complexities of DNA chemistry onto the paper. The rapidly applied scribbling continued onto the next page before halting. She sat back in her chair and stared at what she had written. It was all so simple, so easy once you understood the exact mechanism that allowed the enzyme helicase to split DNA molecules at exactly the right point!

So long did she stare at the writing that her eyelids lowered of their own accord and, before she was aware, she was claimed by slumber.

In the morning, she awoke with a stiff neck, sore back and that horrid not-quite-right feeling you get when you sleep with insufficient covers to keep you really warm. Stretching, she started to rise from the chair when her eyes fell upon the pad with its hastily scribbled notes. Like a bucket of cold water poured over her head, it came back to her. The answer! Quickly she reviewed what she had written, made a couple corrections, then hugged the pad to her chest with a joy that almost came out as a squeal of delight. She felt like giggling.

A quick shower and a hasty breakfast, and she was off for the lab where she and a small team of others worked on the secrets of life. The two pages of precious notes were carefully folded and stored away in her briefcase.

Chapter 2

Explaining What We Do

DynGenRes was the name given to a research project funded by the Chronodyne Company. It stood for Dynamic Genetic Research, and was located in a peaceful valley on the outskirts of Tucson, Arizona, an area noted for its hot desert climate. The project’s facility was a single story building, around four thousand square feet, bare concrete walls with few windows, a nest of air conditioning units on the roof, and an interior which was one quarter offices and the rest biological laboratories. The area around it contained half a dozen similar units and was labeled East Tucson Research Park.

While a small group of scientists and lab technicians worked in air conditioned comfort, their cars sat in the parking lot, accumulating heat from the bright sun, 100 degree plus desert air and the greenhouse effect until, when the door was opened, the air rushed out to hit you in the face like a blast furnace. Steering wheels were usually too hot to touch with the bare hand.

Even though it was only eight o’clock in the morning, the air was already in the eighties and promising to be another typical desert day in which you could fry eggs on the pavement. Maya Robbins pulled her five year old Toyota Camry into her assigned parking slot and locked it up. Once inside, she found the air conditioning already humming away and the air refreshingly cooler. She hurried to her office, bypassed the usual cup of coffee from the machine in the small lunchroom, and switched on the computer. Immediately she began checking data from the last dozen runs of the latest experiment in gene therapy. They were as she remembered them. Then she began feeding parameters into a simulation program. So intent upon the numbers was she that the Project Director, Dr. Stryker had to clear his throat loudly three times to get her attention.

The Director was middle aged, with a receding hairline, about half gray, and a bit of a double chin. All in all, he looked like a businessman going to pot slowly as the years drifted by. Perhaps a banker, but not the classic image of an award-winning physicist that he was.

Dr. Robbins, I have someone I want you to meet, he told her when she finally looked up from her computer terminal. This is Barbara Winters. She’ll be writing an article about our research here. I’d like you to give her some background on what we do.

Maya was about to snap at him for interrupting important work, but she held it back with an effort. Of course, Dr. Stryker, she said with a forced smile.

Good. Miss Winters, I’m sure you’re in good hands now. Dr. Robbins is one of the foremost scientists in the area of gene research, Stryker told her before turning and leaving.

Maya sighed and looked to the visitor. For a moment she only stared in silent shock. Then she shook her head and told herself that it was only a coincidence that this young woman looked almost exactly like her daughter Stella, a daughter who died twenty years before.

Please, she managed to get out, come on in. Turning to the computer, she saved the simulation status and shut down the program. Now then, what can I do for you? It was not easy to be polite when you have just been jerked away from an important piece of research that might even earn you a Nobel Prize.

Hello. I’m from Research News magazine. I’m here to find out what you do here so I can write it up in an article for our readers.

The young woman could not have been a day over twenty. She was dressed casually in jeans and a pale blue blouse, wore her long dirty-blonde hair in a ponytail, and looked like she might have been on the cheer leading squad.

Maya sighed again and pushed her chair away from the desk. Would you like to get a cup of coffee before we talk? she asked.

I don’t drink coffee, Barbara told her. But thank you.

Well, I drink it, and I need a cup right now. We also have tea, hot chocolate and soft drinks.

Without waiting for a response, she led the young woman down the hall to the lunchroom. From a rack of cups she took hers and filled it with French blend, adding creamer and sugar. Barbara found a dispenser of apple juice next to the coffee maker and took a Styrofoam cup of that, mostly to be polite.

Back in her office, Maya bid the young woman to sit down. Feeling calmer now, she mentally prepared herself to spend an hour or so lecturing a non-scientist on the principles of genetic research. The facts would, of course, be mixed up when the article came out, but that would not be her fault.

What do you know about genes and DNA? she asked.

Not much, I’m afraid.

Well then... She paused while Barbara took out a small recorder from her purse. "To begin with, in every cell there are large molecules called DNA. That stands for Deoxyribonucleic acid. This is the molecule that defines what we are. This incredibly complex molecule is wrapped around itself and twisted so that it is so small you cannot see it. Coded into that ribbon of organic chemicals are the blueprints for what we are. Encoded therein are the genetic instructions used in the development and functioning of all known living organisms.

"The DNA is made up of repeated groups of small base units called nucleotides attached to a backbone of sugars. There are only four of these: guanine, adenine, thymine, and cytosine. Don’t worry about the names; usually we use the letters GATC instead of names. In a strand of human DNA there can be approximately 220 million base pairs and, if stretched out, would be 85 millimeters long. That’s about three and a half inches. Of course, it is not stretched out but wrapped around itself and twisted into a small shape. That shape is where the term Double Helix came from. You can think of this as a repeating string of those letters: GATC. A very long string.

"Sections of that string function together to define some characteristic of the organism. Those small sections are called genes. Humans have about 23,000 of these genes encoded into their DNA. These genes provide the code needed to create proteins of different types.

Now here is where it gets interesting. Originally, scientists thought that humans would have around 100,000 genes because we are the most complex organism on the planet. However, a massive international effort called the Human Genome Project mapped out the sequence of base pairs that make up the human DNA and identified the total genes. It was quite an undertaking, and gives us a base to work from to really understand the DNA structure and what it does.

Like most scientists, she began warming to her subject and spoke more animatedly.

"However, while doing this, they found that the number of genes was only about 20,500! That’s about the same count as with mice. By the way, that’s far from the largest number for life on this planet. Grape plants have approximately 30,440 genes.

"Probably the most accurate estimate of the human gene count is the RefSeq database maintained by the U.S. National Institutes of Health. That count is 22,333 genes. But another government database lists 38,621, and a different project called Gencode currently recognizes 21,671.

Why so much variation in the number? Barbara asked.

"It isn’t as easy as counting cattle in a stockyard. A good part of the problem is the fact that genes comprise only about one percent of the three billion A’s, T’s, G’s and C’s that make up the human genetic code. And the genes aren’t conveniently laid out as a single, continuous strand of code. Instead, human genes are found in protein-encoded pieces called exons, interspersed with stretches of DNA that doesn’t form protein. Those spacers are called introns.

"But what is more important is that a surprisingly large amount of the DNA string is not part of a gene. These are bases that are not used to create proteins, and are called non-coding DNA.

"Now here’s the really surprising part. The Human Genome Project found that only about 2 percent of the human is coding DNA. In other words, genes. Research since the project was completed suggests that some of that non-coding DNA does serve a purpose. There is a lot of debate about that percentage that is, but it could be as high as 80 percent, according to ENCODE. Others feel that figure is far too high. Still, even taking that figure, this leaves 20 percent of the DNA that does not serve any known purpose. That’s ten times the amount of DNA material in known genes.

"Some scientists contend that this junk DNA, as it is called, is simply biochemical noise. In other words, just random, useless garbage that accumulated in the DNA over millions of years.

"But... What if it is not? What if this junk DNA is really as functional as genes and can produce proteins? Think of it as additional genes that simply aren’t being used but that could be, if triggered somehow.

"That’s what this project is doing. We’re trying to find out if this junk DNA does serve any purpose, and, if so, what is that purpose?

You following along, or have I gone too fast?

I think I follow you, Barbara said. There is some part of our DNA that is not used but could be.

I couldn’t say it better myself, Maya exclaimed.

Are you finding out what this extra DNA does?

"Some, but very little. It was a major and very difficult task to figure out which genes do what in the human body. Some genes define how we are built, how cells are made, and how they function. These genes are the blueprints that are used to make a human, to define how he or she will grow, and for our bodies to do every function needed for life. We have been able to take a great deal of the DNA code and relate it to parts of the body or functions. But there we have both sides of the equation. With this junk DNA we have only the code but don’t know the result.

Will you ever be able to learn what it does? Barbara asked.

Maya sighed. Maybe. I am of the opinion that the only way we will succeed is to activate regions of this junk DNA and see what it does. Then we’ll have both sides of the equation.

What it does? You mean to...

To test it on a human. Yes. Do you know what gene therapy is?

No.

"Well, gene therapy is an attempt to alter the genes in our DNA with the intent of correcting a malfunctioning or bad gene. We can take a small portion of a DNA and separate it from the rest. Then we attach it to a virus, a small piece of protein itself, and inject it into the human body. Eventually it enters the cells where the new DNA will replace or augment the cell’s DNA to correct the problem.

"The first time that was successfully performed was in 1990 when a four year old girl, Ashanti DeSilva was treated for ADA deficiency. That’s a genetic disease that prevents your immune system from functioning properly. It made her vulnerable to even the mildest infections. If nothing was done, she was likely to die a premature death. Researchers collected samples of her blood, isolated the white blood cells, and used a virus to insert healthy adenosine deaminase gene into them. The cells were then injected back into her body.

"The treatment proved safe, and the treated cells did produce the enzyme needed, but new, healthy cells did not grow as was hoped for. The upside is that Ashanti is still alive today and is relatively healthy.

So gene therapy is an attempt to insert new genetic material into a person’s genes.

That’s fascinating! Barbara said brightly.

Well, it’s still got a long way to go before it will become a cure for many genetic diseases, but we’re working on it.

Are you working on any particular disease now?

Not really. Here at DynGenRes, we are focusing more on basic research. You might say that we’re developing the techniques to dig into the DNA, find out what’s there, and then use it.

There were a few more questions and it was, indeed, an hour before Maya was able to get back to her computer.

If I’m right, we do have a way to activate sections of the unused DNA as if they were genes, was one of the last things she told the young reporter.

She went back to running simulations.

That afternoon, two of the simulations showed positive results.

Chapter 3

You Can’t Do That

Okay, why did you dump that reporter on me?

It was the next morning during a coffee break after the morning’s staff meeting. Stryker made the mistake of not retreating back to his office and was cornered by Maya as he stood next to the coffee machine.

Well, I wanted to have someone knowledgeable give her the straight scoop.

Karen, the lowest lab tech here could have told her what I did. Why not have her or Ted waste their time instead of me?

Good public relations are important, he responded.

Even if it is a small magazine with a readership of a few hundred? was her comeback.

Yes, he said, but had the decency to look embarrassed, if not ashamed. Anyway, it didn’t take too long, did it?

Maya only grunted and added sugar to her coffee.

You interrupted me in the middle of something important, she told him as she blew on the hot coffee.

Oh, and what was that?

I think I’ve figured out a way to combine sections of junk DNA into viable genes.

But even if you could do that, how would you know what sections to combine? There is a lot of non-coding DNA. The number of permutations in combining the nucleotides would be damned near infinite!

Not really. I believe that there are large segments of potential genetic material that are whole, almost complete. And there are patterns in existing coding DNA that serve as guidelines. I think I’m on the verge of putting some of those sequences together.

Make new genes? Human genes? He harrumphed. Even if you could, what would those genes do? Most likely nothing, or something detrimental.

She paused at the door before returning to her office. I’m certain that some of the sequences I’m looking at will create genes involved with bodily functions.

But you’re not sure what functions?

No, not sure.

Dr. Robbins, I may not be a geneticist but I do know that you won’t be able to learn what the function would be.

True. Unless... she frowned before adding, unless it would be by experimental insertion.

You mean as in gene therapy? he said.

Something like that.

Dr. Robbins, our only purpose on this project is to map the junk DNA – if we can. There is no way we could ever get permission to run human experimentation. You know how difficult it is to get FDA clearance for most anything. Besides, Chronodyne, our parent company, would never allow it.

Yes, I’m sure you’re right, she said, then threw him a smile. The smile faded the moment he turned to leave. ‘A bloody shame we can’t,’ she told herself as he walked away.

Before leaving the room, he turned back to her. "By the way, I’ll be gone for a while, probably a number of weeks. You can get in contact with me via my secretary at Chronodyne.

"Oh, and another thing. The Weeks project will be relocating to our Des Moines facility because there is some test equipment they need there that is too big to move down here. And Robert is finishing up his project here, so I guess that will leave you as the only researcher in this facility. Well, I’m sure that won’t last too long. Chronodyne is buying biotech companies right and left, and some will probably be assigned here. Maybe one of those small companies up in Minneapolis. They love to relocate down to a warmer climate. Then they find out how damned hot it is down here and wish they were back up north.

Well, good luck with your research.

Then he was gone.

When she got back to her desk, the computer screen displayed the results of three simulations she had been running. She sat down, put her coffee cup aside, and began reviewing the results. An hour later, her coffee cold and untouched, she sat back in the chair and felt like laughing. Her technique for assembling genes