by Neil Clarke
I stayed on at the house on the island for a few months. Fran and Penny said to come and join them, but they were in Paris and I wanted to be somewhere colder. The time had passed and they hadn’t been there and I didn’t want to be their little girl any more. Like I’d never wanted to be their ambassador, or Callie’s lapdog, or the Banvilles’ charity case. Besides, I had access to the trust now and while I didn’t know yet what I wanted to do with it, it was like Anila had said, that sometimes it’s more about having the choice than making it. I got a really great haircut, and some expensive clothes. I’ve been thinking of setting up scholarships—I could buy whole schools if I wanted, and run them however I liked. If I knew the best way. I might go and study myself, although I don’t know what. I might just get my eyes tinted instead.
As for Anila—she did travel. I didn’t expect anything, but I get a message, now and then, from all over. The last one came after what happened to Beijing—she’s often there, in the wake of disasters, clearing up. Her note is always short and exactly the same: To Em—wherever you are now in your brave new world.
First published in Foundation, #100, Summer 2007.
About the Author
Una McCormack is a New York Times bestselling author of novels based on Star Trek and Doctor Who. Her most recent novel, The Baba Yaga, is in the Weird Space universe created by Eric Brown. Her audio plays based on Doctor Who and Blake’s 7 have been produced by Big Finish. She has a doctorate in sociology and teaches creative writing at Anglia Ruskin University, Cambridge.
The Next Generation of DNA Sequencing
Dan Kobolt
In 2001, an international team of researchers led by the NIH announced the completion of the Human Genome Project. Sequencing all 3.2 billion base pairs of our genetic code had cost ten million dollars and taken almost a decade. Now, just fourteen years later, we can sequence a human genome in four days, at cost of about twelve thousand dollars.
This rapid advance was fueled by the development of a single disruptive technology called massively parallel DNA sequencing. A company called Illumina (San Diego, CA) has emerged as the market leader. Their approach first breaks up the long DNA molecules into short fragments (a process called fragmentation), and then loads them to be sequenced simultaneously on a high-density microscopic array called a flowcell. Going from tissue sample to DNA sequence essentially involves four steps:
Isolation of DNA from a tissue sample. This is usually a blood sample, but could also be a small piece of a tumor, a skin punch, or other tissues of interest.
Creating a sequencing library. The long molecules are sheared into fragments of a few hundred base pairs by a sonicator, an instrument that uses high-amplitude sound waves to break DNA. At each end, we attach (by ligation) a sequencing adapter that allows DNA polymerase to attach and do its thing.
Loading the library onto the flowcell. It contains millions of tiny wells, each of which will host a single DNA fragment. Usually, that fragment is duplicated (by PCR) in the well so that there are many identical copies to boost the “signal strength” in the next step.
Sequencing by DNA synthesis. A complementary DNA strand for each fragment is synthesized in a base-by-base reaction called a cycle. Each cycle adds one base to the growing DNA strand. A very sensitive (and expensive) camera records which base (one of the nucleotides A, C, G, or T) was incorporated.
After one hundred fifty cycles, we have “read” one hundred fifty bases from each end of the DNA fragment. This may not seem like much, given the size of a human genome, but each flowcell produces millions of these short reads for a given sample. On average, we sequence each base in the genome about thirty times, from thirty different unique fragments.
It might seem counter-intuitive that we can sequence one genome so many times in a single experiment. True, almost every cell in the body has just two copies of each chromosome—one from mom, and one from dad—but the DNA samples we use comes from a tissue sample that contains thousands of cells. All of those DNA molecules are randomly fragmented when we create a library (step 2 above), which means that any position in the genome is represented on numerous different fragments.
The Computational Challenge
Once all of the short sequencing reads are generated, the lab work is essentially complete. Next, we turn to computers and software to help us assemble and make sense of the genetic data. The first step is to identify, for each sequencing read, the region of the genome from which it came. Here, we benefit from knowing the sequence of the human genome already. Rather than trying to reconstruct the entire genome sequence from scratch, we can use the short DNA sequence like a search query. Once we know where it came from, we line up the read sequence to the reference and compare them one base at a time.
Typically, 99.9% of the sequenced bases will match the known reference. The other 0.01% might represent either sequencing errors, or genetic variants in the individual’s genome. Each of us has around three million such variations, which are most commonly a single base substitution, but can also be insertions or deletions of bases or even large-scale structural rearrangements.
Applications of Next-Generation DNA Sequencing
This “next-generation” sequencing technology makes it possible to sequence entire genomes quickly and at a reasonable cost. Rapid, inexpensive genome sequencing provides many avenues of important research. For example, sequencing can be used:
In cancer treatment, to compare the genomes of a patient and his or her tumor. This not only reveals the mutations that caused the disease, but may identify possible drug targets for personalized cancer therapy.
In genetic research, to uncover the genetic architecture of inherited diseases and possibly find ways to treat them.
In agriculture, to identify the genetic variation underlying favorable traits like drought resistance, pest resistance, and better yields.
In forensics, to rapidly identify human/animal remains, match DNA from crime scenes to suspects, etc.
In archaeology, to learn about human history, migration, and speciation from the clues left in ancient DNA samples.
These are just a few of the potential applications for the current state of next-generation DNA sequencing technology. But the evolution of that technology is still under way.
Next-Next Generation Sequencing Technologies
One of my favorite emerging technologies for DNA sequencing is made by a company in the United Kingdom called Oxford Nanopore Technologies. Their technology relies on feeding a single molecule of DNA through a very tiny hole (a nanopore) and inferring the sequence from fluctuations in electric charge. They’ve developed a prototype instrument called the MinION that’s about the size of a thumb drive and plugs into the USB port of your computer. I’ve got to get me one of those, mostly so I can walk around with a DNA sequencer in my pocket.
Another company called Pacific Biosciences has developed a technique to sequence single DNA molecules several thousand base pairs at a time (in contrast to the one hundred fifty base pairs). This is advantageous in certain regions of the human genome that contain highly variable sequences, such as the “human leukocyte antigen” (HLA) region on chromosome six, which is important for matching organ donors to recipients. Very long reads also help us improve the accuracy of the human genome reference in “repetitive” regions of the genome that are difficult to sequence with short read technologies.
Clinical Sequencing
One of the major near-term goals for DNA sequencing is to get it into the clinic, where genetic information could be used to improve patient diagnosis, prognosis, and treatment. There are a number of practical and ethical hurdles that must be overcome to do this. First, we need to establish that next-generation sequencing can provide consistent, accurate results on par with current genetic tests. Given the random processes on which the technology relies, this may be one of the most difficult tests to pass.
There are ethical concerns, too. Because of the discovery power of sequencing, it’s also import
ant to establish guidelines about the results that may be returned to a patient after sequencing. Genome sequencing may uncover predisposition to late-onset diseases (like Huntington’s disease) that are unrelated to the reason a patient is in the hospital. Routine DNA sequencing of multiple family members may also reveal unexpected results, such as “non-paternity events” (you can guess what those are) or two parents who turn out to be second cousins. Whether or not to return such “secondary findings” is an area of contentious debate among researchers and clinicians.
The Future of DNA Sequencing
It’s impossible to look at a technology like DNA sequencing and not speculate about the possibilities for the near or distant future. In the short term, I think that DNA sequencing will become a routine part of healthcare for many people, especially those affected by genetic diseases. As our knowledge of the human genome grows, this information will have more and more predictive power, too. In other words, based on an individual’s genome sequence along with clinical and environmental information, it should become possible to estimate his or her lifetime risk for various diseases like cancer, heart disease, diabetes, and Alzheimer’s disease. These will probably be reported in terms of probabilities: twenty-one percent chance of stroke, fifteen percent chance of prostate cancer, etc. It might resemble that baby-is-born scene from Gattaca, though I doubt we’ll be able to deliver the information in seconds, or predict the manner of a person’s death. On the bright side, legislation like the Genetic Information Non-discrimination Act (GINA) in the United States will hopefully prevent employers and other organizations from discriminating against people based on their genetic makeup (as they do in the movie).
In many cases, these assessments will only be informational in nature. Even if lifestyle changes could reduce the risk of a certain disease, I wonder whether that will be enough motivation for many people to do them. Just look at how many people use tobacco products in spite of their scientifically proven links to cancer, heart disease, and other problems.
What if we could instead use genetic information to correct “defects” that are likely to have a negative impact on an individual’s health? For example, there are more than three thousand genetic disorders for which the responsible gene is known. In theory, if we knew the mutations that gave individuals a severe disorder, correcting that genetic defect might be the only way to prevent the disease. Numerous “gene therapy” clinical trials are under way to accomplish this by, say, using an engineered virus to deliver a fully functioning copy of a gene to individuals who are sick because they don’t have one.
Even better would be to permanently correct the genetic variant in a patient’s genome. A new technique that enables precise “genome editing” in living organisms—called CRISPR/Cas9—might one day provide this capability. Yet that would also be a tremendous responsibility to undertake, even for healthcare providers. It’s messing with nature, and not everyone is going to be on board with that. Case in point: earlier this year, to the alarm and distress of the larger biomedical research community, a group in China used CRISPR/Cas9 to modify the genome of human embryos as a “proof-of-principle” experiment.
Although their success rate was abysmal, and their work widely criticized by the rest of the research community, the Chinese group brought forth a discussion that we need to have about the capabilities of genetic technology and what it means for our future.
About the Author
Dan Koboldt is a genetics researcher who has co-authored more than sixty publications in Nature, Science, The New England Journal of Medicine, and other journals. Every fall, he disappears into Missouri’s dense hardwood forests to pursue whitetail deer bow and arrow. He lives with his wife and three children in St. Louis, where the deer take their revenge by eating all of the plants in his backyard.
Dan also writes fantasy and science fiction. His debut novel The Rogue Retrieval, about a Vegas magician who infiltrates a medieval world, will be published by Harper Voyager on January 19th, 2016.
Traitors and Tough Decisions:
A Conversation with Seth Dickinson
Chris Urie
The first story I ever read by Seth Dickinson was published right here in Clarkesworld. With “Morrigan in the Sunglare,” I was introduced to an author concerned with complexities and subtleties, power, and hate. His stories dive deep under the emotional and societal surface to explore the more challenging parts of being human.
The Traitor Baru Cormorant, his debut fantasy novel, comes out from Tor Books September fifteenth and is a fascinating look at someone bringing down a tyrannical government from the inside. Through the eyes of Baru Cormorant, we see the conquest and cultural subjection of an entire society as it is assimilated into the larger empire of the Masquerade. Baru’s life, her family, her home, and her sexuality are all under attack and she must use her sharp mind to use the systems in place to save herself and her people.
Seth is a graduate of University of Chicago, a lapsed PhD candidate at NYU, an alum and instructor at the Alpha Workshop for Young Writers, and used to write item descriptions for video games at Bungie studios. His work has been published in Clarkesworld, Shimmer, Lightspeed, Analog, Strange Horizons, and Beneath Ceaseless Skies.
For a time, you studied social neuroscience as a doctoral student at NYU. Has that influenced your writing?
Oh, man, right to the heart of things. Yeah! Behavioral science colors everything I write. My time in academia ripped up a lot of my assumptions about people and the world. We used brain imaging, eye-tracking, and a lot of behavioral measures to study how decisions can be swayed by invisible social forces.
My project involved millisecond-level simulations of the role of racial bias in police shootings. We were trying to create a firearms training program that would lead officers to make fair choices. My colleagues worked on a huge range of experiments studying prejudice, power, and implicit attitudes.
I guess I’d point to three big takeaways—
People don’t understand their own behavior. Every day, we make choices driven by social cues and weird heuristics that we don’t notice. That’s okay. It doesn’t take away our agency. But we do have a responsibility to look at our own behavioral outcomes and try to understand what drives them.
Prejudice is real, powerful, and endemic. Certain mechanisms in our brain soak up subtle (and unsubtle) prejudice from the cultural bath. And it sways key decisions—hiring policy, shoot/don’t shoot choices, even our facial microexpressions. But at the same time, many things we think of as biological facts are actually cultural constructs! That suggests we may be able to reprogram ourselves.
Last (and greatest) is my love of really tough moral dilemmas. I grew up on the Milgram experiment, Hannah Arendt, the Robber’s Cave, and the Asch paradigm—scary, cutting insight into human moral behavior. I want to know how people behave in extreme circumstances. I want to look at evil rationalized as good, good dressed up as evil, territories where ethical systems break down, the clash between utilitarian and deontological ethics, and—in the end—the human, emotional cost of making impossible choices.
The Traitor Baru Cormorant is about a woman who will do anything to achieve her goal of world liberation, because she believes the goal is so good it justifies any sacrifice. And it’s about how much that hurts.
I also picked up a bunch of cognitive tricks to keep readers engaged, but I’m pretty sure writers already know them!
“Morrigan in the Sunglare” appeared in the March 2014 issue of Clarkesworld. While a very different story, I think it has some similar themes to your novel. Have you found a common thread running through your work?
I think it’s this idea of the necessary, monstrous choice, the Sophie’s Choice. Back as a teenager writing embarrassing fanfiction, my heroine had to blow up a space station to save the universe, which became the blood calculus in “Anna Saves Them All”; in “Worth of Crows” the necromancer chooses to mercy-kill the man; in “Never Dreaming (In Four Burns)” (here in Clark
esworld!) Nur Zaleha has to choose between death and losing what she believes in. In ‘Morrigan’, Laporte and Simms struggle with the psychology of combat, and they each find their own way to justify violence.
But I’m not necessarily interested in worshipping or valorizing that choice. The Hard Choice often sees use as a justification for atrocity—torture, murder, breach of due process. I want to look at the cost of it. Sometimes it’s important to stick to your principles. Sometimes that makes for a better, warmer world.
And I want to look at the space after the choice. My favorite structure operates in two parts—the first part pushes the protagonist out, away, into lonely ruthless spaces, and the second part asks them to come back, mend their wounds, and accept a world of human compassion and solidarity, if they can. If you’ve put away trust, love, and the possibility of redemption, can you get them back? Will that jeopardize your victory? Maybe community and compassion are a better way to get what you want.
That’s the driving tension of the ‘Morrigan’ sequel, and the next Baru Cormorant novel.