The Atlantis Gene

“The research team had become her family, and the research participants her children.”

Early on, Riddle hints at the loss of Warner’s mother, the mysterious disappearance of her father, her adoption by Martin Grey, and a cryptic reference to a traumatic event in San Francisco. Riddle doles out his information sparingly, leaving hints like a trail of breadcrumbs. What he eventually reveals to be Warner’s haunted past—a miscarriage and an affair with Dorian Sloane who absconds the moment she becomes pregnant—justifies her maternal protectiveness for her test subjects, especially for the two kidnapped boys, Adi and Satya.

“What a mess. Find out if she has any money. If so, bring her to the station. If not, dump her at the hospital.”

Jakarta Police Chief Eddi Kusnadi is a corrupt cop. When he finds Warner unconscious on the floor of her lab, he violates basic procedural protocols without batting an eye. Instead of leaving the crime scene untarnished, he searches the victim for money to find out if she is worth extorting. Riddle plays upon Indonesia’s history of corruption dating back centuries, and that history—combined with some Western stereotypes—is embodied in the character of Kusnadi. Riddle also employs a clever rhetorical strategy, using the word “dump” instead of, say, “deliver” or “leave her at.” Kusnadi is blunt and ruthless, and readers can intuit that from his choice of words.

“Clocktower was the world’s secret answer to state-less terror: a state-less counterterrorism agency. No red tape. No bureaucracy. Just good guys killing bad guys.”

Riddle’s description of his fictional secret counterterrorism organization is the stuff of libertarian nightmares. Seemingly accountable to only itself and armed with vast arsenals and espionage equipment, Clocktower nonetheless enjoys the sanction—official or not—of governments across the globe. It is not hard to imagine the existence of an organization like Clocktower in real life, assuming one doesn’t already exist, given the fear terrorist cells spread and the willingness with which citizens surrender their rights in the name of security.

“You use different words. So did the Dutch East India Corporation. Do you know of it? I am sure you do. They used the word colony, but they owned Indonesia for over two hundred years.”

To intimidate Warner, her interrogator suggests that she will never get a fair trial due to Indonesians’ distrust of foreigners, especially Westerners. He cites his country’s collective memory of colonization under the Dutch, implying that resentment still exists long after independence. It is a brief but resonant moment one, giving the Indonesian people a voice even if that moment passes quickly. Some have theorized that the country’s long history of corruption is a direct result of that colonization and of outside economic pressures.

“Jin was scared to death. They were paying him a fortune, an absolute fortune. And he had no other options.”

While Jin’s lifestyle seems luxurious compared to his brother’s, it is a distinctly low bar. Despite his comparatively exorbitant wages, Jin is treated little better than a prisoner. Ironically, he will never live to spend those wages as he and his fellow test subjects are just fodder to be sacrificed in the name of badly practiced science. Jin’s predicament speaks to the ability of those with resources to extort the poor into a life-or-death gamble.

“At their feet, a small child, a gaunt child, was tied to a wooden beam that held the roof up. He was gagged, but she could hear low rhythmic noises coming from his mouth as he rocked back and forth, hitting his head on the beam.”

When Warner is forced to explain why her research study has legal custody of its test subjects, she relates a story of a child with autism she finds in a rural village. The villagers don’t understand autism or neurodivergence. They only see behavior that disturbs them, and they shun the children, relegating them to a hut in the forest where many of them die of malnutrition. With therapy, many people on the spectrum learn to navigate social relationships with little problem.

“Whatever Toba is, I believe that’s the goal: to drastically reduce the total human population.”

Although details are still sketchy, Vale has an inkling that the Toba Protocol’s endgame is massive genocide. He doesn’t understand the purpose yet, but this is the first hint at the magnitude of the Immari plot. The revelation comes as a shockwave to readers who have not imagined the stakes to be so high.

“Situation changed. Clock tower will fall. Reply if still alive. Trust no one.”

Using a standard decryption method, Cohen finally decodes the hidden message masquerading as a Craigslist post. The message confirms Cohen’s worst fears: All Clocktower cells have been overrun, leaving Jakarta station as the only uncompromised cell. Cohen knows it is only a matter of time before turncoat operatives come after him. Cohen must race to wipe clean the station’s hard drive, and from here on, the pacing shifts into high gear. Also, Riddle’s use of the phrase “Trust no one” is a sly nod to The X-Files, a show to which the novel owes a debt of inspiration.

“So many illusions had died today: Clocktower couldn’t be compromised, Clocktower couldn’t fall, David couldn’t be killed, the good guys always won.”

War often marks the death of idealism. Far from being the heart-stirring and honorable enterprise of the movies, war is pain, death, and chaos, and rarely is it as clear-cut as a John Wayne film. Facing what he assumes is Vale’s death, Cohen has the same moral reckoning about war as did countless patriotic men and women who enlisted to fight in Vietnam, only to discover the “enemy” was often villagers and farmers, not the purportedly evil Communists of government propaganda. Like life, war is not a simple duality, and the “good guys”—if such an objective assessment can be made—do not always defeat the “bad guys.”

“The human race is the biggest mass murderer of all time…We attack whatever is different, anything we don’t understand, anything that might change our world, our environment, reduce our chances of survival.”

Riddle does not hesitate to point out humanity’s brutal track record when it comes to other species, as well as its own environment. Once Homo Sapiens developed an evolutionary advantage, they used their superior cognitive skills to kill off the competition. That tendency to view with distrust anything foreign persists to this day. Witness the violence against trans people, the genocide against the Tutsi minority in Rwanda, or Hitler’s Holocaust, or America’s mass extermination of Indigenous Americans. The common thread among all these is the fear of difference and the assumption that the different group is dangerous and must be extinguished in the name of self-preservation. Sloane makes the same assumption about the Atlanteans: that they are a threat and must be eradicated.

“We were animals, just like them, fifty thousand years ago. But some Great Leap Forward gave us an advantage we still don’t understand.”

One of the most fascinating historical tidbits in the novel is the Great Leap Forward. Those with only a passing knowledge of evolutionary history may assume that biologists have figured out the timeline of the transition from one subspecies to another. The fact that such a vital question remains unanswered gives rise to all sorts of untested theories, including the book’s narrative that a technologically superior race once populated the Earth in advanced cities, before Mother Nature sunk them to the bottom of the ocean.

“Sometimes you had to be a bad guy to save the good guys.”

As Vale uses a booby-trapped Immari security agent to gain access to a research facility, he claims that the end justifies the means. Again, Vale retreats into his “good-guy/bad-guy” reductive morality, a rationale that may solve this particular ethical dilemma but doesn’t work so well for most cases which are not so black and white.

“Entertainment is the future.”

In exchange for his help, Vale gives Harto, the Indonesian fisherman, a 60-foot “mini-yacht.” Rather than use it to fish, he plans to start a fishing business, taking wealthy tourists out into the Sea of Java. Even a simple fisherman, Riddle implies, can see the entrepreneurial value of entertainment.

“The woman, Dr. Katherine Warner, has been identified as a genetics researcher performing unauthorized experiments on impoverished children from rural villages outside Jakarta.”

An Al-Jazeera wire release, reporting on the kidnapped children and the firefight in the streets of Jakarta, pegs Warner as a prime suspect and a key player in a “child-trafficking ring” (150). For a supposedly reputable news outlet, the misinformation and lack of context is stunning. For starters, there is no evidence of child-trafficking. For another, the headline “connects” two Americans to the terror attack even though Vale was the victim of the attacks. The headline not-so-subtly evokes an anti-Western bias prevalent in Indonesia after centuries of Dutch colonization. Lastly, the rhetoric of the article is clearly meant to demonize Warner; “unauthorized experiments” conjures images of unwilling victims being subject to torturous tests. Perhaps Riddle is commenting on the news media’s penchant for sensationalism over truth, but one hopes this kind of sloppy reporting is pure fiction like the rest of the story.

“‘Relax. Apart from the gratuitous violence, it was a very PG evening. Is it safe for kids again?’

Kate pulled the shirt on. ‘And immature soldiers.’”

 After a restless night in Vale’s bomb shelter, Warner and Vale plan their next move. Her memory of the past night is sketchy, clouded by the drugs she was given in the Immari research facility. Sleeping close to one other—after some slowly percolating sexual tension—creates an awkward chemistry between the two protagonists, and they compensate for it with a bit of Hollywood-style romantic banter. This is a recurring motif in the novel, particularly with Vale and Warner. When things get stressful, Riddle gives them some playful dialogue to defuse the tension.

“Humans began using language and thinking critically, solving problems rather than acting on instinct. Essentially, the brain started acting more like a computer than a processing center for impulses.”

Hiking through the Indonesian jungle, Warner explains a key moment in evolutionary biology, a subtle change in brain wiring which had a “huge impact.” Trying to understand why Immari would want her two test subjects, she dwells on a theory that the brains of people with autism may represent the next evolutionary leap in cognitive development. One of the pleasures of The Atlantis Gene is the fascinating history of human brain evolution, mass extinction events, and unsolved scientific mysteries. The information serves as a cerebral respite from the gunfights and explosions, much like The Da Vinci Code’s intriguing exposition on the history of the Catholic Church.

“Our genes might control the possibilities, but epigenetics determines our destiny.”

As Dr. Chang attempts to explain the boys’ resistance to the Bell, he suggests that Warner’s treatment may have worked on the epigenetic level, activating a dormant gene that the boys already possessed. Riddle again displays his grasp of technically complex material. Epigenetics, Chang explains, works at a level beyond mere genetics. Genes may give humans the possibility of certain traits or behavior, but those traits may lay dormant until something at the epigenetic level turns those genes on.

“Kate reached out for them, but a man pinned her arms. Another man rushed to her, and she saw the butt of a rifle coming at her face.”

Much of The Atlantis Gene has a very cinematic style, almost as if Riddle saw the movie playing in his head while writing it. From bodies flying through the air after an explosion to Vale and Warner parachuting from a skyscraper, the novel reads like a film treatment. Here is a perfect example: As Warner reaches for the children who have been taken from her, a guard slams a rifle butt into her face. It is a classic movie shot, the gun thrusting toward the camera (the actor’s point-of-view) followed by a blackout as the victim is rendered unconscious.

“Immari is a family. We don’t leave anyone behind.”

As Sloane and Chang evacuate the burning research facility, Sloane orders all the bodies from the Bell tests to be loaded onto cargo trains. He claims to be doing this out of respect for the victims’ families, but spreading the virus is all part of the Toba Protocol. His generous façade masks a sinister motive, and Riddle takes a pointed jab at corporate rhetoric that labels employees “team members” and their uncompensated contributions “buy-in,” phrases that have little real meaning beyond their attempt to create a feel-good atmosphere.

“We have known for almost a hundred years that a day would come when we had to battle this enemy. That day has arrived. Each one of you is a soldier in the army that will stop this coming apocalypse.”

Like in the previous quote, Sloane attempts to rally his troops—mostly data analysts—to his cause. His speech is notable for what he doesn’t tell them: that they are participating in a mass genocide. No matter, however, because Sloane employs the time-tested rhetoric of fear and heroism: manufacture an enemy and convince the foot soldiers that they are serving a noble cause. George W. Bush’s now famous “Axis of Evil” speech led directly to the US invasion of Iraq. Hitler’s rhetoric of fear and purification convinced millions of Germans to conveniently look the other way as six million Jews were exterminated.

“You overestimate her. But if that’s your price, you can have it, and the two thousand dollars per week.”

As Pierce and Lord Barton haggle over terms of his employment, Barton dangles his daughter’s hand in marriage as an incentive. Pierce argues that Helena will defy her father for love, but Barton scoffs at the notion. His world is a traditional patriarchy, in which young women have no autonomy or personal choice except that which is granted by a man. It is unsettling to witness a man bargaining with his daughter’s future like he would a beast of burden or a bushel of wheat.

“It’s always the same war. Only the names of the dead change.”

With his own father’s experience in the Civil War as a reference point, Pierce’s father attempts to dissuade his son from enlisting in World War I. Despite his son’s protestations that “[t]his is a different war” (303), his father argues that, where war is concerned, nothing is ever different. The only variables are the men who die and the men who collect the spoils. It is a prescient—and accurate—bit of persuasion. When it comes to who benefits from war, one needs to simply heed the advice of Washington Post reporter Bob Woodward’s covert source Deep Throat and “follow the money.”

“The world is dying. And we killed it.”

After Pierce emerges from the tunnels and unleashes the 1918 flu pandemic on the world, he articulates his guilt in the simplest, most direct way possible. The guilt, however, is not his alone; these killing sprees have been going on for tens of thousands of years and arguably show no sign of slowing down. In truth, the world itself will likely survive, but humans may not.