Life Imitates Art: Portable DNA Sequencers

FuturePundit points to a NYT article describing something very similar to a piece of technology readers might recognize from the Oasis scene of In the Shadow of AresTaking DNA Sequencing to the Masses:

Dr. Rothberg is the founder of Ion Torrent, which last month began selling a sequencer it calls the Personal Genome Machine. While most sequencers cost hundreds of thousands of dollars and are at least the size of small refrigerators, this machine sells for just under $50,000 and is the size of a largish desktop printer.

While not intended for the general public, the machine could expand the use of DNA sequencing from specialized centers to smaller university and industrial labs, and into hospitals and doctors’ offices, helping make DNA sequencing a standard part of medical practice…

Rather than culturing a bug to identify what is infecting a patient, for instance, a hospital might determine its DNA sequence. Massachusetts General Hospital is already sequencing 130 genes from patient tumor samples, looking for mutations that might predict which drugs will work best. It has won an Ion Torrent machine in a contest and hopes to put it to that use…

While most experts agree that sequencing will become commonplace in medicine, some say they think Dr. Rothberg is overselling his machine. Like the early Apple II of Mr. Jobs, it is too puny for many tasks, including sequencing the entire genome of a person…

Dr. Rothberg acknowledged that the existing model was good for sequencing a virus or bacterium or a handful of genes, and indicated that future models would be more powerful.

Indeed. Just imagine what forty more years of technological evolution might do to this device, in terms of cost, power, speed, and size.

On the Radio

I’ll be on 850KNUS here in Denver on Sunday, talking about In the Shadow of Ares with my PPC co-blogger Ross “Rossputin” Kaminsky.

The show is on from 5 PM to 8 PM on 710 AM KNUS in Denver and 1460 AM KZNT in Colorado Springs. I will be on between 7:00 and 7:30PM. For those outside the Denver area, you can listen to the show online by clicking HERE.

Science fiction fans might want to tune in a little earlier, as one of Ross’ other guests this weekend is SF author and Tea Party figure Andrew Ian Dodge.

McDonald’s on Mars

One theme running through In the Shadow of Ares is the economics of early human settlements on Mars, and one way in which we explore this theme is through the contrast between the entrepreneurial independent settlements and those subject to the meddling of the Mars Development Authority.

Readers of MarsBlog may find familiar the following passage, which sets up the first major illustration of this theme and is based on a blog post from almost exactly five years ago:

Aaron halted the rover near the base of the huge sculpture.

“Why are we stopping?” Lindsay asked.

He leaned forward, looking at the nearly complete monument rising before them.  “Look.  Can you see it?”  From this angle the third arch was hidden behind the central axis, so that the Gate appeared to be only a pair of arches.

“See what?”  Amber asked.  She and her mother both craned their necks, trying to see what it was that Aaron was seeing, besides the obvious.

Aaron traced an “M” across the rover’s window with his index finger.  “McGate,” he grinned.

Lindsay chuckled.  “Ha…you’re right!”

“Mick what?” Amber asked.  She had heard the project referred to as “Gate-gate”, by critics of the MDA’s waste of funds and materials.  The controversy had been surprisingly short-lived in the Martian media, with Quipu and the smaller news aggregators alike quickly losing interest in it and not following up on the occasional revelations of mismanagement and overspending.  The rumor among the independents was that MDA pressure squelched the reporting of any controversy.  It was easy to believe such a rumor — the Gate was, after all, Administrator Poissant’s pet project.

“McGate,” he repeated.  “You know, like McDonalds.”

“The Earth restaurant?  Are we getting one?”

“No, no, no,” he shook his head.  “But isn’t it ironic that the new ‘signature’ of Port Lowell should look so much like an ‘evil corporate logo’?”

“Evil?” Lindsay frowned.  “McDonalds isn’t evil.”

“No, of course not,” Aaron laughed.  “It’s just that the MDA resents successful private enterprise.  Look at the independent settlements — the better they do, the less power the MDA has over them.  A Martian McDonalds would be MDA’s worst nightmare:  it would mean Mars had reached a high level of economic development.  Private development, exactly the kind they don’t like.”

“What do you mean?” Amber asked, confused.

“Well, shipping all the ingredients in from Earth would be prohibitively expensive, so they would have to be produced right here.”

“So?  How hard can it be to make a hamburger?  I mean, aside from the fact we don’t have cattle on Mars.”

“Yet…” Lindsay amended.

“Yet.  Well, it’s not just about burgers.  The meat, cheese, pickles, onions, buns, and other things have to come from somewhere.  That means a whole range of other complex economic activities.  Things like meat synthesis facilities that go way beyond what we have on Mars today, bakeries for the buns, and plants making soft-drink concentrate and condiments.  Not to mention all the necessary transportation and construction elements, or a manufacturing industry able to produce the specialized machinery needed to turn all the raw materials into the final product and deliver them to customers — freezers, refrigerators, fry vats, grills, microwave ovens, cooker ‘bots, soft-drink dispensers, and more.”

“And don’t forget customers,” Lindsay added.  “You need enough customers to keep the restaurant profitable.”

“Certainly.  They’d also need unskilled and surly teenagers to staff the counter.”  He winked at Amber.  “And all these industrial capabilities — machine fabrication, transportation, specialty materials — would support many other industries, besides food production.  All of that together implies economic self-sufficiency.”

“Which means the MDA is no longer needed,” Amber said.  “We could petition for full sovereignty.”

“Exactly.”

Kindle and Nook

The Kindle version of In the Shadow of Ares is now available at Amazon.com. Thank you to everyone who has already purchased the book — plus the helpful feedback from  sharp-eyed Ari, who discovered an editorial comment left behind like a bad surgeon’s forgotten scalpel. The mistake has been corrected and the text republished, but it may take 24 hours to propagate to the product page.

We’ve had multiple requests to publish to the Nook platform, which I just so happen to be doing. It is a little bit more involved than publishing to Kindle — Kindle merely involved entering payment information, a cover image and description, and uploading the .doc file. Smashwords (the site used for Nook and many other e-reader platforms) is a little more particular about formatting and metadata, but in return it includes assignment of an ISBN number and listing in major book catalogs. This means publishing through Smashwords will not only get us onto multiple additional readers but into libraries and other outlets.

In the Shadow of Ares – Story Synopsis

To kick things off, here’s the description we used for the Amazon Breakthrough Novel Award contest entry:

The world was shocked and saddened by the Space Shuttle Challenger and Columbia disasters.  But after the memorials, recovery efforts, and detailed investigations were over and the hard lessons were learned, we moved on.

But what if a spacecraft and its crew simply vanished, with no explanation?  What if, years later, you had an opportunity to solve the mystery of this disappearance?  And what if someone else knew what happened – and would do anything to stop you?

This is the challenge facing 14-year-old Amber Jacobsen in “Labyrinth of Night”, a mystery set on frontier Mars.  Amber is an interplanetary celebrity: ‘the First Kid on Mars’…and so far, the only one.  Pioneering on Mars is hardly glamorous, though, and Amber secretly wishes she were an ordinary girl living on Earth.

When their homestead is destroyed in an apparent accident, the Jacobsens relocate to a new settlement located on the northern fringes of Noctis Labyrinthus, a vast and largely unexplored network of canyons.  Their new home promises new opportunities, and Amber looks forward to being accepted as a regular member of the community rather than a celebrity.  Instead, the settlers treat her as a burdensome child and not the responsible young adult she is.

In order to prove herself, Amber vows to uncover the fate of the Ares III mission, which vanished near Noctis Labyrinthus.  As she digs into the disappearance, however, she discovers that those who destroyed her family’s homestead want power over the settlement she now calls home — and ultimately the entire planet.  By solving the mystery, she could hand them the tools to destroy a free and prosperous Mars.

Labyrinth: Excerpt from Chapter 19

After a minor catastrophe forces the Jacobsen family to move to a new settlement, Amber and her mother get a tour of the place. Having spent her whole young life within the cozy spaces of habs, settlement tunnels, rovers, and suits, Amber finds certain parts of her new environment a bit unnerving at first. Margolis […]

After a minor catastrophe forces the Jacobsen family to move to a new settlement, Amber and her mother get a tour of the place. Having spent her whole young life within the cozy spaces of habs, settlement tunnels, rovers, and suits, Amber finds certain parts of her new environment a bit unnerving at first.

Margolis led them down a set of steps to floor level, then to another large bulkhead door.  Inside the door was the chamber of an  airlock, one large enough to drive a small rover through.

As they entered the airlock into Bubble 1, Margolis muttered something into the small object strapped like a watch to her wrist.  Amber only caught a quick glimpse, but was sure Margolis’ MA was a new Holst Informatics Onyx 3.  She could only hope her new job paid enough for her to buy one of those.

The door behind them swung shut, and the one in front of them immediately opened — it was pressurized on both sides, so there was no need to pump down or suit up here, but the small difference in pressure made her ears pop.  Like the emergency bulkhead at the entrance to Main Street, the airlock was a safety feature against catastrophic depressurization of the bubble above.

Walking up the long ramp into the bubble, Amber thought she knew what to expect.  After all, they had had a greenhouse at home…arguably the prototype for this one.  This one was bigger, of course, but how much different could it be?

She looked up at the narrow slot of sky visible between the walls lining the ramp.  The tint of the translucent membrane overhead gave the sky an alien hue, a pale red-blue, not quite Martian or terrestrial, but somewhere in between.  It was far enough above that she didn’t notice at first that anything was there at all — it just appeared to be a strange-colored sky.

But it wasn’t the size or the color of the dome that made Amber look around, slack-jawed.  As she reached “ground” level, she stepped into a world she had only imagined before, based on pictures, vids, and her parents’ descriptions.  She stopped, astonished.  Is this what Earth is like?

The openness made her stomach knot.  She had no problem with open spaces while out on the surface, suited, but this was very different.  Here she stood unprotected at the edge of a grassy field a hundred meters on a side — larger than any open place she had ever been without a suit.  Worse, there was much, much more volume beyond the end of the ramp, where instead of grass there were long ranks of trees and assorted crops stretching into the distance.

She gulped and squeezed her eyes shut.  The nausea and unease gradually passed.

Looking up again, she could see the sky for what it was:  a multilayered translucent membrane some thirty meters above her, curving down to the waist-high anchorage wall.  Just inside the anchorage was a deep recess where the windows of the residential area below were located.  Construction details  — crisscrossed tension-stay wires, broad light panels, small clusters of sensors here and there — brought the bubble into a manageable but still unsettling scale.

Towards the near end of the bubble, the grassy field was bounded by a concrete trough filled with assorted bushes and flowering plants, sunflowers mostly, carefully arranged and meticulously manicured.  Amber looked at the dark green carpet stretched out in front of her.  “Is it real?”

Margolis giggled. “The grass?  Of course.  Try it out.”

She hesitated.  “I’m not going to hurt it, am I?”

“No,” her mother laughed, giving her a playful nudge forward.

Amber took a few cautious steps. Even through her slippers, the ground felt strange, spongy.  The floor is actually alive! She pulled her slippers off and ran her toes through the soft, slightly moist blades.  Imagine a whole planet like this…so full of life you can’t go anywhere without seeing it, touching it…or stepping on it. She closed her eyes as she walked gingerly into the field, imagining she was on that lush planet, instead of a world carved with great effort from a cold, dead wasteland.  Opening her eyes again, she felt a fleeting twinge of disappointment.  True, the Green was a little spot of paradise in the middle of the barren Martian desert, but no matter how real it looked, it was still only a simulation of the real Earth.  The thought tempered her delight…but only slightly.

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Labyrinth: Excerpt from Chapter 6

For those unfamiliar with the novel, or who may have forgotten the synopsis from the Amazon Breakthrough Novel Award entry some time back, Labyrinth of Night is a young adult science fiction novel following the struggles of Amber Jacobsen — the first and so far only child on Mars — to prove her value to […]

For those unfamiliar with the novel, or who may have forgotten the synopsis from the Amazon Breakthrough Novel Award entry some time back, Labyrinth of Night is a young adult science fiction novel following the struggles of Amber Jacobsen — the first and so far only child on Mars — to prove her value to the other settlers by (among other things) resolving an old and largely forgotten mystery.

In this short excerpt, Amber and her parents are camping out in their beat-up rover, as they travel from their home (one of the old tuna-can habs left behind by the early exploratory missions) to the main settlement, Port Lowell. Amber, having just turned 14 a few days earlier, is finding herself increasingly bored with life on the frontier:

Amber awoke with a start, feeling dangerously exposed under the transparent curve of the rover’s front window.  She had lived all her life surrounded by walls or a suit, seeing the surface only through a small viewport or a helmet visor.  This broad, clear view of the sky always made her feel vulnerable.

She wondered what time it was — just above the horizon was one of the morning stars, which the daily astronomy report said would rise about an hour before the sun.  Dawn was near.

She reached out both hands towards the faintly blue star, touching her wrists together and forming a cup as if to cradle a precious jewel.  “Earth”, she whispered.

Aaron, lying on his reclined seat with his back to Amber, stirred.

“Dad?”

“Unh?”

“You awake?”

“I am now.”

Amber paused and collected her thoughts, feeling about her throat for the Earth pendant and remembering that she’d left her necklace behind at the hab.  “Why are we here?”

Aaron rolled onto his back.  “We’re going to Port Lowell.  You know…”

“No, not here here.  Mars.  Why are we on Mars?  Earth has everything.  Mars has nothing.  Why would anyone want to come here?”

He stretched, crossed his arms behind his head, and stared silently out the window for a time.  “Because we’re explorers.  That’s who we are.  That’s what we do.  From the time we are babies, able to crawl, we—”

“Right, right, okay, I know all that,” she interrupted.  “I’ve heard that speech a hundred times.  I’ve given that speech a hundred times, in my class videos.  I mean us:  you and me and Mom.  Why do we have to stay on Mars?  The planet’s being explored, and permanently settled — that’s what you wanted, why you stayed behind.  Right?”  She let the question hang for an instant, but her father didn’t take the bait.  “So why stay?  Don’t you want to go back to Earth now?”

“No,” he said simply.  “I used to think we’d go back some day, but now?  No.  There’s nothing back there for us — our lives are on Mars now.”  He sighed.  “Look, sweetheart…I know life on Mars isn’t everything we would like it to be.  But this world is growing and things will change for you.  Maybe sooner than you think.  You just need to tough it out for a while longer — Mars is bound to get a whole lot more interesting in the near future.”

“Yeah.  Sure, Dad.”

“Goodnight, sweetheart.”

“Goodnight.”

She drifted off to sleep, but Aaron sat awake, mulling over what to tell her, and when.  He knew Lindsay would be upset if he told Amber about the offer — there was no point bringing it up yet, when there might be no need.

It’ll all work out, he thought.  He checked the hab’s status on his MA before nodding off again, as the sky began to lighten in the east.


Excerpted from “Labyrinth of Night”, © Thomas L. James and Carl C. Carlsson

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