The Lost City of the Monkey God

by Douglas Preston

  At the end of my tour, a lab assistant brought out two bottles of live leishmania parasites for me to look at under the microscope. They were living in a cloudy, reddish-orange nutrient broth. I peered into one of the bottles with a binocular microscope. As I focused the eyepieces, the parasites sprang into view, thousands of them in ceaseless motion, bumping into each other and going this way and that. They had elongated, pointy-headed bodies and whiplike flagellae, which are on the front of the cell and draw it forward instead of pushing it along from behind. For a while I watched the wriggling little buggers go about their business, thinking of the havoc they had wreaked on us.

  The lab’s chief is Dr. David Sacks, a lean, handsome, plain-talking scientist who occupies a cluttered office in the basement. “These flies are just desperate for blood,” he told me. “They’re seeking any source and you folks just happened to be in the right place at the right time.”

  Why, I asked, didn’t we all get sick? Why only half of us?

  “I think all of you were bitten and infected,” he said. “I wouldn’t be surprised if a hundred percent of you were exposed, given the frequency of bites you seem to have had. So it’s actually more interesting why some of you didn’t develop lesions.”

  He explained that one of medicine’s greatest mysteries is why some people get sick and others do not, given the same exposure. Environment and nutrition play a role in infection, but genetics are paramount. This is the very question at the heart of why so many New World people died of Old World disease. What was the actual genetic machinery that made some more susceptible than others?

  With gene sequencing, Sacks said, we finally have the tools to figure out why some people are more vulnerable than others. Scientists are sequencing people’s entire genomes and comparing them, one against the other, to see what genetic differences pop out between those who, exposed to an infection, got sick and those who didn’t. We finally have the tools to understand the biology behind the great die-off and how such pandemics might be prevented in the future, but the research is still in its infancy.

  During our exchange, when I made an offhand comment about how disgusting the flies were, he chided me: “Of course we don’t think they are disgusting at all. We love our flies.”

  The leish lab, Sacks said, has been working for years on charting every stage in the life cycle of leishmania, looking for chinks in its armor that could be exploited by a vaccine. It’s harder to design a vaccine against a protozoan than against a simpler virus or bacterium; in fact, not one major parasitic disease has a reliable vaccine yet. Leish is very sophisticated in how it infects the body. It is, as one parasitologist said, “the royalty of the disease world.” Instead of wreaking carnage like many viral and bacterial diseases, and thus triggering a massive immune response, the parasites “try to have tea with your immune system.” Sacks and his team have identified the essential proteins the parasite uses during its life cycle inside the sand fly—and they’ve created mutant forms of those proteins that might block development. But figuring out how to exploit those vulnerabilities is hard, and getting from there to a vaccine is even harder.

  As is too often true, the biggest hurdle is money. Vaccines cost hundreds of millions of dollars to develop, test, and bring to market. Human trials involve thousands of subjects. “It’s difficult to get companies to partner in trials,” Sacks told me. “They don’t see any market in it, because the people who have leishmaniasis have no money.”

  Over the past decade the World Health Organization sponsored a series of clinical trials to test a simple leish vaccine, in which parasites were heat-killed and injected into people. Doctors hoped the dead parasites would prime the immune system to attack live parasites when they arrived. The trials failed, but it is unclear why. Other possible vaccines are in the early stages of testing.

  One of the biggest discoveries Sacks and his team made was that the leish parasites have sex inside the sand fly. Previously it was thought the parasite could only reproduce by division—clonal reproduction. By having sex they can recombine their genes. This gives them a way to hybridize and adapt. It explains why there are dozens of leish species and why, even within a species, there are so many different strains. The ability to have sex gives leishmania a tremendous evolutionary advantage. It is the main reason it has thrived and spread for a hundred million years, infecting dinosaurs and people, becoming one of the most successful diseases (from its own point of view) in the world.

  With leishmaniasis so prevalent in the valley of T1, I wondered how ancient people might have coped with the disease. Could they have controlled it by clearing vegetation or killing the animals that acted as hosts? I posed the questions to Sacks. He pointed out it would have been difficult for the people of T1 to identify the sand fly as the vector and certainly impossible for them to know a host animal was necessary; assailed daily by biting insects, they probably would not have made the link between a sand fly bite and a lesion that developed weeks later. (The link between mosquitoes and malaria, for example, wasn’t made until 1897. Previously, malaria was thought to be caused by the “bad air” of nighttime—which is what mal aria means in Italian.)

  Nor could leishmaniasis have been a reason for the abandonment of T1, since the disease in pre-Columbian times was too widespread; there was nowhere the people of T1 could escape to. They would have lived with the disease, just as hundreds of millions do today.

  When our team members were diagnosed, biopsies were taken from our lesions and sent to another lab at NIH, called the Molecular Parasitology Section, where the lab’s director, Michael Grigg, had originally identified the parasite as L. braziliensis by sequencing part of its genome. I called up Grigg to find out if he had found out anything unusual.

  “The type of leish you have was very hard to grow,” he recalled. In fact, like some difficult strains, it wouldn’t grow at all. He smeared tissue samples from our biopsies on blood agar plates, but the parasites refused to multiply. Because of that, his lab wasn’t able to tease enough parasites clear of human tissue to sequence the entire genome at the time—there was too much human DNA mucking up the works.

  Instead, he explained, they initially sequenced one gene or marker: a characteristic one that reveals the species. That marker matched braziliensis. But later, Grigg sequenced five markers—which he described as “five little windows into the parasite.” He got a big surprise. In two “windows” he found genetic sequences different from any known species of leish. In another window, he found that the DNA resembled another species called L. panamensis, an equally bad mucosal strain. But that gene also had a couple of mutations.

  Our parasite, he said, might have been a hybrid between panamensis and braziliensis, in which the two species mingled in a sand fly gut, mated, and produced hybrid offspring. That hybrid was then isolated and began to evolve into a new strain or possibly even a new species. There were enough mutations, called “snips,” at the five sites to indicate that this particular species had been isolated for a period of time.

  How long? I asked.

  “That’s a tough one. There are not a lot of snips, so I’d say it’s been hundreds of years, not thousands or tens of thousands.”

  I had a sudden idea. I explained to Grigg that the valley had once been the site of a bustling city with active trade networks. But about five hundred years ago, the city had been abandoned and the valley suddenly cut off from the rest of the world, with people no longer coming and going to spread the disease. Could that abandonment be the moment when the parasite was isolated? And if so, could the parasite’s molecular clock be used to date the time of abandonment?

  He thought about it and declared it a reasonable hypothesis. “When you get rates of change of one or two snips, we’re looking at an isolate of hundreds of years. It’s relatively recent. It’s consistent with your theory.”

  All species have what is known as a molecular clock. This clock measures how fast random mutations accumulate over the generations. Some species, li
ke cold viruses, have fast clocks, while some, like humans, have slow. By counting the number of mutations, the molecular clock will tell how long that species has been isolated. It’s like the game of telephone; you can tell how far you are from the original message by hearing how garbled it has become.

  Later I sketched out to Sacks the same idea about dating the death of T1 by using the parasite’s molecular clock.

  “That would make sense to me,” he said. “These phylogenetic trees are published, so when you find a new species you stick it on that tree to find the genetic distance.” And that would give you the time period of isolation.

  If true, this might be the first instance in which an archaeological site could be dated by molecular clock; our disease might actually hold clues to the fate of T1. The research, however, has yet to be done.

  CHAPTER 26

  La Ciudad del Jaguar

  After our expedition departed the valley of T1 in February 2015, the ruins lay undisturbed for almost a year. A rotating contingent of Honduran soldiers remained in our old campsite, guarding the city. Within weeks, soldiers began coming down with leishmaniasis, something that the Honduran military had not experienced elsewhere in the country. The military considered pulling them out, but in the end it dealt with the problem by rotating the soldiers frequently in hopes that would minimize exposure. The soldiers cleared the brush and vegetation in the camp area, leaving only the trees, in an effort to reduce the habitat for sand flies. To make the rotations simpler and quicker, the military built a barracks at the Aguacate airstrip.

  The excavation of the artifact cache at T1 became a priority. Even Chris understood that leaving everything in the ground was not a long-term option. With archaeological looting a widespread problem in Honduras, and the cache worth millions of dollars, it would have to be guarded indefinitely by the military. That was not realistic, given the expense, the frequent changes in government, and the raging leishmaniasis that made a permanent human presence in the valley problematic.

  At the same time he fought his grueling battle with leish, Chris prepared a plan of work and began assembling an expert team of archaeologists and technicians to excavate the cache. The idea wasn’t to remove the entire offering, but only to take out artifacts that were sticking out of the ground and in danger of being disturbed. He planned to leave the rest of the site covered and hidden so the material remaining underground would be safe. He hoped a partial excavation would help us begin to understand the meaning of the cache and any answers it held to the many mysteries surrounding this culture. (Later, Honduran archaeologists continued the excavation and have at the time of writing recovered over five hundred artifacts.)

  The academic controversy about the expedition did not die down, as many on the team had hoped it would. Many months after the 2015 expedition, Juan Carlos gave a talk in Tegucigalpa about the expedition’s lidar work, and a group of protestors showed up to heckle. Their leader, Gloria Lara Pinto, a professor at Universidad Pedagógica Nacional Francisco Morazán in Tegucigalpa, arrived late. She stood up during the question-and-answer period and challenged Juan Carlos, saying that he was not an archaeologist and had no business passing himself off as one, and that his talk (which was for a general audience) lacked scientific rigor. Juan Carlos pointed out that he had made precisely those disclaimers at the beginning of his lecture and that it was a shame she had arrived late and missed them. “I acknowledged,” he told me later, “that I was not an archaeologist or an anthropologist, but as a Honduran I do have the right and the obligation to understand more of my country’s geography and history, and as a PhD researcher I do have the basic tools to do historical research.” After his response, he said, the audience booed Professor Pinto and her group of hecklers.

  The cost of the return trip and the excavation amounted to almost a million dollars, much of it again due to the expense of operating helicopters. With Chris’s help, Steve Elkins and Bill Benenson worked to raise the funds, receiving contributions from the Honduran government and the National Geographic Society. National Geographic magazine once again hired me to cover the team’s work. I was apprehensive about going back but intensely curious to see what was in the cache. Wisely or not, I was no longer worried about leish: I was, in fact, far more concerned about poisonous snakes and dengue fever. The size, power, and lethality of that first fer-de-lance we encountered had been an experience I would never forget. Instead of reusing my old Kevlar snake gaiters, I went online and bought a $200 pair of snake guards said to be the finest made. The manufacturer had posted a video of the snake guards repelling repeated strikes from a big diamondback rattler. I called and asked if they’d ever tested them against a fer-de-lance, and I was told they had not, nor would they guarantee them against that kind of snake. I bought them anyway.

  I also had a plan about dengue: I would spray my clothes with DEET inside and out, strip twice a day and cover myself with DEET, and I would take refuge in my tent at sunset, before the mosquitoes came out, and not emerge until after sunrise.

  In early January 2016, Chris Fisher and his team of archaeologists, Honduran and American, arrived at the site, set up a base camp, and flew in their supplies. They were working with the latest high-tech archaeological equipment, including tablet computers reinforced and cased to withstand the rigors of the jungle, state-of-the-art GPS units, and a portable lidar machine operated by Juan Carlos. Remarkably, neither Juan Carlos nor anyone else who had been struck by disease on the original expedition was deterred from coming back, except Oscar Neil, who (for understandable reasons) informed the IHAH that he would not set foot in the jungle again.

  Within a week, Fisher and his team were ready to begin work at the cache. Breaking ground in the lost city generated much excitement in the Honduran press, although so far, the location had successfully remained under wraps—a surprise, given how many people now knew about it. President Hernández announced to the country that he, personally, would fly in to the site to remove the first two artifacts and carry them to the new laboratory being built at the Aguacate airstrip. Aside from taking a deep personal interest in the project, the president wanted to put out some good news for the country.

  As was perhaps to be expected, the flurry of news stories about the excavation revived the academic quarrel and also inflamed a segment of Honduras’s indigenous community. The project’s critics once again took to the blogs and complained to the press. The former head of the IHAH, Dario Euraque, told the website Vice.com that the archaeologists were taking credit for a discovery that was “not theirs” and that they had offended indigenous groups by engaging in “racist dialogue.” He said that the publicity had left the ruins open to looting and that he was very sad to see Honduras turned “into a reality show.” Some archaeologists and others accused President Hernández of exploiting the find to distract public attention from corruption, human rights abuses, and the murder of environmental activists. They condemned the expedition for cooperating with such a government.*

  On January 13, a group of indigenous Honduran leaders, los hijos de la Muskitia or the Children of Mosquitia, wrote an open letter criticizing the government and claiming the excavation of T1 violated Indian treaties. The communiqué had a long list of demands, and it objected to the use of the term “Monkey God,” which the writers considered “denigrating, discriminatory, and racist.” The letter concluded, “We, the sons of the Indigenous Miskitu Community… demand the immediate return of all artifacts looted from our sacred site called the White City.” The letter included a map of Miskito territory that seemed to swallow the traditional lands of other indigenous Indian communities, such as the Pech and Tawahka, who are believed to be the actual descendants of the ancient people of Mosquitia. The issue of indigenous rights in Honduras is not simple; Honduras is a robust mestizo society in which most citizens, rich and poor, have a large proportion of Indian ancestry. The Miskito people are themselves of mixed Indian, African, Spanish, and English ancestry with roots not in the interior mountains
where T1 is located, but along the coast.

  When I asked Virgilio about the letter, he said the government was well aware of it, had long been expecting it, and would handle it. (As far as I could ascertain, the government handled it by ignoring it.)

  John Hoopes organized a talk at his university on what he called “lost city hucksterism” entitled “The Lost City That Isn’t.” When I asked him what the talk would cover, he explained to me the discussion would be mostly aimed at helping students “think about how ‘hot’ issues such as those of colonialism, white supremacy, hypermasculinity, fantasy and imagination, [and] indigenous rights… intersect with the narratives that have been and are being spun about the White City.”

  In mid-January I flew to Tegucigalpa to reenter the jungle and report on the excavation for National Geographic. I was curious to see how the president, his entourage, and the press were going to manage the snake- and disease-infested jungle. I also found myself stewing over the thought that the breathtaking perfection of the rainforest might have been ruined and the area degraded by human occupation, in which I had played a role.

  My return trip to T1 began the morning of January 11, 2016, when a driver met me before dawn in Tegucigalpa for the long, overland trip to the airstrip, where an 8:00 a.m. military flight would take me into the valley. Virgilio had warned me to pack everything required for an overnight stay in the valley, including food and water, because helicopter transportation was uncertain and I would probably have to spend at least one night out there, maybe more. I tossed my overstuffed backpack into the back of the old pickup truck with a cracked windshield and government logos emblazoned on the side. We took off at high speed, the truck zooming through the deserted, postapocalyptic streets of the capital. We were soon out of the city and roaring up and down dizzying mountain roads. An hour later, high in the mountains, we were enveloped in a dense fog. The yellow lights of the oncoming cars and trucks loomed ominously, flaring up like fireworks, and then thundered past, the taillights winking out in the inky dark. As the light of dawn crept up, tatters of fog clung to the hillsides and filled the lowlands with mist. The Honduran interior is spectacularly beautiful and rugged, one mountain chain after the other, separated by deep green valleys. As we went up and down, the enchanted names of the villages flashed past—El Mago, Guaimaca, Campamento, Lepaguare, Las Joyas. They were the same towns we had passed a year before, but this time, shrouded in early morning mist, they looked otherworldly and aroused in me a sense of the inscrutability and “cognitive dissonance” of Honduras today.