Pulled from an unlikely source, ancient microbial DNA represents a new frontier in the study of the
past—and modern health
By SAMIR S. PATEL
Monday, September 26, 2016
The largest ancient DNA laboratory in the United States sits behind a heavy steel door in a plain service hallway at the University of Oklahoma. Inside, researchers find, extract, isolate, and amplify DNA molecules and proteins, producing voluminous mounds of data that can address grand, complex questions about migration, diet, and human health—in the deep past and today. They’re probing the limits of new methodologies. They’re encountering the advantages and pitfalls of interdisciplinary science. And they’re writing the first drafts of a new chapter in archaeological research. But before they can do any of this, they have to ensure that the lab is scrupulously clean.
Next to the door, a red button, when pressed, produces a satisfying thump and turns off powerful UV lights inside. A series of pressure gauges climbs next to it. The lab’s six rooms are kept under positive pressure, double-sealed, and have their own air supply, filtered free of anything larger than 1,000 daltons—the mass of just 1,000 hydrogen atoms. People who enter must take off their shoes, change into scrubs, and, by the time they reach the two innermost rooms, don Tyvek suits, surgical masks, hairnets, and face shields. Those chambers are free of anything extraneous: Only sample vials and scientific equipment are visible. The DNA and proteins that the researchers work with there come from ancient microbes, and keeping the lab free of contamination is a tall order in a world that is positively swimming with their modern counterparts.
“Usually, ancient DNA work is performed in dungeon-like labs located in windowless basements,” says Christina Warinner, anthropologist and codirector of the Laboratories of Molecular Anthropology and Microbiome Research (LMAMR). This lab, however, is fitted with picture windows that face the atrium of the university’s Stephenson Research and Technology Center, so visitors can watch the scientists and students inside process microscopic genetic samples that can be centuries or even millennia old.
The microbes that are the focus of the LMAMR—from both ancient and modern sources, with separate lab facilities for each—come from what is known as the human microbiome, the myriad communities of bacteria (as well as eukaryotes, viruses, and archaea) that reside in and on our bodies. In only the last few years researchers have begun to understand that studying how the microbiome has shifted over thousands of years, particularly at moments of great change in human history, has the potential to reveal some of the ways in which how we eat, live, and move around the world have affected human biology. Any number of questions—medical, archaeological, demographic, evolutionary—that were unframeable just five years ago can now be asked and ultimately answered on scales ranging from molecular to continental.
There are, according to the latest estimates, something like 30 trillion human cells in your body. Alongside them, throughout your gut, in your mouth, on your skin, there are even more—40 trillion, give or take—individual bacteria. Together they make up 2 percent of your body weight, roughly equivalent to the weight of your brain, and carry some 3.3 million genes, to your paltry 22,000. Like every other multicellular organism, we coevolved with them, we incorporated them into our cells, we’re built from them. We may think ourselves individuals, but we’re each a multitude.
The term “microbiome” isn’t yet two decades old but it is already clear that these communities have a profound impact on human health. In addition to critical roles in oral and digestive health, the microbiome has been associated in some way with everything from mood disorders to cardiovascular disease, from autism to rheumatoid arthritis, not to mention countless infectious diseases. The old idea of sickness being caused by individual bugs is now giving way to a much more complex microbial ecosystem model. “On balance it is very clear that the microbiome plays a fundamental biological role,” says Warinner.
The microbiome is a key point of contact between humans and the world around them. It is affected by—and therefore may reflect—changes in how we manipulate our environments and in what we consume. And we change with it. The Neolithic Revolution, for example, saw the rise of agriculture and settlement. The last 150 years have brought the Industrial Revolution, megacities, modern hygiene, processed foods, and antibiotics. They’ve also seen a rise in the incidence of chronic disease: cardiovascular ailments, autoimmune disorders such as asthma and allergies, and metabolic disease such as obesity and diabetes. Experts speculate that changes to the microbiome could be a significant link between lifestyle and health. But examining such connections means knowing how the microbiome has changed—and that means knowing what it was.
The gut is our most prolific microbial ecosystem, and evidence of ancestral microbiomes—these microbial communities vary by place, time, and culture—though rare, has been found in coprolites, or preserved feces, in particular by LMAMR codirector Cecil M. Lewis, who also studies the modern gut microbiome. But the gut is just one microbial hub in the human body. In your mouth, right now, there are hundreds of species of bacteria, living in nine major niches, including below the gums, on the cheek, and in the saliva. The mouth is the microbial equivalent of a rainforest, teeming with creatures, interspecies warfare, cataclysms. Some of these residents form a film on your teeth, colonies stuck together with DNA, proteins, and polysaccharides. Left unbrushed, this plaque, for reasons that aren’t really known, occasionally fossilizes in your mouth to form tartar, dental calculus. Calculus is tough and almost universally observed clinging to the teeth of adult skeletons discovered at archaeological sites. For many years this material was ignored, discarded, and otherwise overlooked, as were human bones prior to the introduction of modern archaeological practices. “We’ve always thrown stuff away—and that stuff becomes revolutionary,” says Greger Larson, director of the Palaeogenomics & Bio-Archaeology Research Network at the University of Oxford. “If you don’t understand that it exists, then you can’t understand its power.”
When Courtney Hofman, a researcher at the LMAMR who has since joined the full-time faculty there, begins the DNA extraction process, the first thing that registers is the sound. She takes a dental scaler to a 2,000-year-old tooth from Spain and produces the raspy scratching and resonant clinks familiar to anyone who’s had their teeth thoroughly cleaned. After a moment, the tip of the scaler finds purchase and a fragment of calculus pops loose. Hofman does the same with a few more teeth, wiping everything down between each step to limit the possibility of contamination. “We go through a lot of bleach here,” she says.
Each sample goes into a tiny vial to be decontaminated with UV light, and is then crushed, rinsed, and demineralized, leaving behind a gauzy pellet. After a spin in a centrifuge, DNA from 2,000 years ago floats invisibly in each vial. This is the most sensitive part of the process, as the protective calculus is gone. Next, the DNA must be purified and processed for sequencing and analysis.
As a source of ancient biomolecules, calculus differs from coprolites. They contain distinct microbial ecosystems, of course, and preserve very differently. Coprolites are open systems, subject to the elements, contamination, and domination by soil microbes. Calculus, on the other hand, fossilizes while you’re still alive. But it wasn’t clear until very recently—through Warinner’s work and parallel projects in labs in Chile, Australia, and Denmark—that calculus traps or preserves DNA at all. “Dental calculus is really an unlikely hero,” she says.
Warinner, who had excavated the earliest known epidemic mass graves in Mesoamerica early in her career, began to see the potential in calculus in 2007, when she worked at the Smithsonian. A colleague there was Amanda Henry, now at the Max Planck Institute in Leipzig, who searches calculus for trapped plant fragments, such as phytoliths and starch grains. By 2010, Warinner was a postdoctoral researcher studying ancient disease and diet at the Institute of Evolutionary Medicine at the University of Zurich. When she tried to replicate Henry’s methods there, she had trouble counting plant granules. “There were so many bacteria that were getting in the way,” she says, “but I had a kind of aha moment.” Other research groups were exploring the same idea, but at the time nothing had been published, other than a review article from the 1950s that stated that there was no DNA in calculus. She saw an opportunity to test her hypothesis that it could be a source of ancient microbial DNA, but it was a risky, expensive proposition for a postdoc. “People thought it was just a nuts, nuts idea,” Warinner says. “I was sort of doing microbiome research without knowing the word.”
“In German we say überflieger; that means someone who flies higher than the others. I could immediately see her potential,” says Frank Rühli, director of the Institute. But the calculus idea didn’t seem promising. “I was a bit reluctant at the very first moment.” Warinner’s first few attempts in 2010 failed. She then got a more sensitive fluorometer, and it still didn’t appear to be working. “I saw a message that I didn’t even know existed,” she says. “It said ‘Error, DNA too high.’” So she diluted the sample 50 to 100 times. “I started realizing, as I started quantifying, that I had just discovered the richest source of ancient DNA ever described in an archaeological sample.” There was more DNA in her sample than there is in fresh liver tissue.
In the few years before these first experiments, several scientific currents were converging. In 2008, Lewis, who didn’t yet know Warinner, published some of the first reports of the ancient microbiome from coprolites. The same year, the Human Microbiome Project (HMP), a multi-institution effort to catalogue the biota, was established with funding from the National Institutes of Health. This placed the term and its connection to human health in wide view. Microbes had long been seen only as biological villains to be exterminated, but with the launch of the HMP came the recognition that bacteria could be helpful and even essential to multicellular life and its processes. This was a seismic change.
Perhaps most importantly, genetic research itself was undergoing a revolution. Gone were the days of laboriously generating one DNA sequence at a time. The new wave of technology, called next-generation sequencing (NGS), was becoming widely available, and is able to create hundreds of millions of sequences at once. It opened the door for “shotgun metagenomics,” or amplifying and sequencing all the DNA from all the genes from all the organisms in a sample. NGS has made it possible, in a single pass, to describe entire microbial communities or reconstruct the full genome of a microbial species. It increased exponentially the amount of data researchers could gather. According to Warinner, “We were just racing as fast as we could to keep up with all of this.”
NGS, however, was expensive—the necessary reagents alone cost $13,000 for the experiment that Warinner planned to conduct. She was terrified, and thought at the time, “It’s a moon shot. If it works, it’s awesome. If it doesn’t, I’m hosed.”
Dalheim is a small town near Lichtenau, Germany, where in 1989 and 1990 the Westphalian Museum of Archaeology excavated the site of a medieval monastery, parish church, and convent. Remains from the 151 burials they uncovered were stored at the University of Mainz until the school needed the space and planned to incinerate and bury them. Rühli offered to bring the skeletal material to Zurich for research in 2010. “A big challenge when you’re trying to develop a new method is just having material to practice on,” says Warinner. While she was conducting her work on the Dalheim samples, several other groups were operating with the same idea. In 2012, researchers from the University of Chile were the first to publish the basic identification of DNA in archaeological dental calculus. A group led by Alan Cooper of the University of Adelaide was the first to apply NGS to it in 2013. Following these reports, the Dalheim burials offered Warinner an opportunity to produce the first shotgun metagenomic analysis and characterize complete ancient oral microbial communities. The Dalheim study stands now as the most forceful declaration of the possibilities of dental calculus, with orders of magnitude more data than had been reported before. The experiment resulted, Warinner says, in hundreds of millions of sequences. It took three years to analyze it all.
Warinner and her coauthors—32 in total from a broad range of disciplines—catalogued, from the mouths of four medieval individuals, 40 opportunistic pathogens, including species associated with cardiovascular disease, meningitis, and pneumonia, as well as what might be the oral ancestor of modern gonorrhea. They sequenced the entire genome of Tannarella forsythia, a cause of periodontal disease. They saw dietary DNA from pigs, cruciferous vegetables, and bread wheat. They looked for proteins as well, and found ones associated with pathogen virulence, others produced by the human immune system, and beta-lactoglobulin, a durable dairy protein. Among the genes identified, oddly, are ones associated with microbial antibiotic resistance—hundreds of years before the advent of antibiotic drugs. The expert on the subject for the study, Lars Hansen of Aarhus University in Denmark, says that the cellular machinery that creates antibiotic resistance can serve other purposes in cells. The modern phenomenon, he explains, comes from increased availability and expression of these existing mechanisms. “It is the first time [antibiotic resistance sequences] have been found in an ancient human-associated context,” says Hansen. “It shows that these building blocks are basically everywhere.”
The study has spun off in dozens of directions. For example, the LMAMR is using the presence of the milk protein to study the origins of dairying practices all over the world. Another of their studies announced the reconstruction of a full human mitochondrial genome from calculus alone. This affirms calculus as a possible alternative source of human DNA in cases, such as with Native American remains, where it is not permissible to sample bone. Archaeologist Mark Aldenderfer from the University of California, Merced, along with Warinner and her team, is studying the genetic adaptations that allow people to live and thrive at high altitudes in Nepal and Peru. The LMAMR is also collaborating with archaeologists who work in the Caribbean to see how well calculus preserves DNA in climates generally unfriendly to ancient biomolecules, and to study migration and colonialism alongside archaeological and linguistic evidence. And in the study that Hofman is working on, some 20,000 years’ worth of samples from a site in Spain are being examined to look for changes in pathogens, proteins, and microbial community structure over time in a single place. The origins and evolution of specific diseases can be examined as well—typhoid, tuberculosis, plague, syphilis. “We don’t know what the limits are yet,” says Warinner.
Another step in this research concerns the study of proteins, or proteomics. Proteins, which are also found in calculus, may persist much longer than DNA and reflect the actual expression of genes. According to Lewis, “That’s going to change everything.” One thing that proteomics may be able to show is direct interaction between microbes and the human immune system. Matthew Collins, an LMAMR collaborator and specialist in ancient proteins with the Universities of York and Copenhagen, compares proteins in calculus to the port of an ancient city destroyed suddenly and preserved in situ. The calculus holds evidence, in proteins, of ongoing battles between “migrant workers” and the “local police force.” “The body fights against infection and you can see the bugs fighting back,” he explains. “You’ve got this whole dynamic system preserved there.” The work will require innovation and refinement in extraction and analysis, but the potential is vast.
Research is going forward, but it remains in its early stages, and will have notable pitfalls and hurdles to overcome. The LMAMR, working with Kirsten Ziesemer of Leiden University in the Netherlands, has already identified one of these problems. Apparently a gene segment called 16s, commonly used to identify species from their DNA, can’t be relied on for conventional genetic analysis of ancient microbes because of the way it breaks down over time. The array of processes and methods is complicated and has yet to be standardized. “One of the problems has been, in microbiome research in general, that different methods of extraction produce different results, different computational pipelines produce different results, different sequencing platforms produce different results, different primer sets produce different results,” says Camilla Speller, another LMAMR collaborator from the University of York. There’s a lot of troubleshooting before innovation can become practice. “This is a problem,” Lewis says, “of being on the frontier.”
At the LMAMR, after the calculus has been demineralized, the scale of the work goes from tiny to microscopic to molecular. The DNA floating in the solution has been broken down by time into fragments, from just a few base pairs up to maybe 100 in length. Conveniently, next-generation sequencers are designed to work on DNA fragments of about that length, around 50 to 100 base pairs. The samples are treated with a series of enzymes, buffers, and primers, and attached to segments of synthetic DNA. These manmade genetic fragments, which can later be excised from the data, are used to fill in gaps, tag each sample with a unique genetic barcode, and make the samples machine-readable. This process is called “building a library.” The library is then “read” at a genomics facility, such as the Yale Center for Genome Analysis, and what comes back is a stream—a tsunami, really—of data.
The quantity is intimidating. “I wouldn’t say it’s a wall, but I’d say it’s a very steep mountain,” says Warinner. According to LMAMR codirector Krithi Sankaranarayanan, who is a microbial ecologist adept at data analysis and interpretation, the next steps also include confirming, on the basis of damage patterns, that the DNA is indeed old. The reads are then assembled and modeled and interpreted to create longer and longer sequences: partial genes, full genes, and even complete genomes. Then the researchers must try to manage and corral these massive data sets to make them comprehensible. They pool them, build frequency tables, parse species into different bacterial groups. They look for questions and structures and layers that bring order. Modern computing power is staggering, but analysis still takes days or weeks.
If the whole thing sounds Borgesian, that’s because it is. Jorge Luis Borges imagined the universe, in his 1941 short story “The Library of Babel,” as an infinite library containing every possible combination of the alphabet—an expanse of gibberish concealing magical insights. The librarians there are wandering mendicants driven to superstition, madness, and worse. In today’s research, even a single sample of calculus creates tomes upon tomes, composed of patterns of four letters representing the nucleobases that make up DNA: A, G, C, and T. There is a seemingly limitless, global, paralyzing abundance of potential samples in museums, archaeological collections, and unexcavated sites. Complicating matters, the databases against which these DNA patterns are checked are imperfect, skewed toward specific species that have been studied because of their potential impact on human health or agriculture. There’s also DNA “dark matter,” or sequences that don’t match up with anything that has been described or characterized—undiscovered biology. Interpretation requires knowledge of these flaws, computational mastery, a global perspective, and savage, callous skepticism.
Taking data sets so large that they can only be contemplated through summary statistics or pure abstraction and working them into the discipline of archaeology is a challenge. But this new methodology certainly isn’t the first time that archaeologists have had to come to grips with scientific innovation. Radiocarbon dating, isotopic signatures, and remote sensing have all become regular analytical tools. Similarly, geneticists have to begin to acknowledge and understand the language and questions of archaeologists.
“There have been revolutions in archaeology before, and archaeologists have been able to adapt to them,” says Hannes Schroeder, who studies ancient DNA and the Caribbean at the Natural History Museum of Denmark, and is also working with LMAMR. “But none of these other fields are as demanding in analytics, techniques, and working with the data as what is happening now with ancient DNA.” For York’s Speller, it means that archaeology is growing in a new direction, one that includes computer science and medical bioscience.
Warinner and Lewis at the LMAMR, and a number of other researchers looking at the ancestral microbiome, have backgrounds and experience in archaeology and anthropology. “The goal is to find common questions we’re really interested and invested in,” says Warinner. “The challenge of a scientist is to chart a path through these questions so you don’t get totally overwhelmed by them. It is such enormous territory.”
At the moment, the areas most suited to examination through the lens of ancestral microbiomes are big ones—the peopling of continents, agriculture, migration, exploration, colonialism, industry, globalism. Researchers want to know what these transitions mean for the shape of the modern world—specifically, who we were and who we are, physically, genetically, microbially. We can now investigate patterns, identify specific bacteria or entire microbial communities that have been lost, and attempt to understand what they did for us after tens of thousands of years of coevolution. We might also ask whether we can get them back, or if we even want to. “Now that we know so much about the microbiome, it’s very hard to think of ourselves solely from the perspective of our genome,” says Warinner, “because if you just have genomic information you’re missing such a huge part of the biology that it’s almost irresponsible not to consider it.”
In the late seventeenth century, Dutch draper and scientist Antonie van Leeuwenhoek looked through one of his pioneering microscopes at a sample from inside his own mouth. He found it crawling with what he called “animalcules.” Science perhaps still has moments of revelation, but more progress comes from patience, technological refinement, some new algorithm or process, and ways to think around dead ends and blind alleys. Innovations developed this way build upon one another to a point at which we can see a gene associated with antibiotic resistance in the mouth of a medieval German nun, and this helps us understand something about cellular machinery—machinery that happens to be at the root of a modern healthcare crisis. “I feel,” says Warinner, “like we’re standing at the beginning of a new branch of archaeology.”
Once we reach the spot, you won’t believe your eyes,” says archaeologist Luciana Jacobelli of the University of Molise as she opens a small door to the crypt of the church of Santa Maria Assunta in the center of town. It’s very dim inside, and she has to use a flashlight as we make our way. We slowly climb down a series of ladders through a forest of iron scaffolding toward what seems to be the only well-lit area, nearly 30 feet under the church. Jacobelli then leads me into a room and, as promised, frescoes in dazzling green, yellow, red, and blue seem to illuminate the space on their own. We have arrived at the extraordinarily well-preserved remains of a lavish villa marittima, or seaside villa, once a luxurious retreat for the rich of ancient Rome to escape the summer heat and the hustle and bustle of city life in the first centuries B.C. and A.D.
Swiss architect and engineer Karl Weber, the first scholar to supervise excavations of the areas destroyed by the eruption of Mount Vesuvius in A.D. 79, appears to have seen the villa on April 16, 1758, during his explorations. In his field report he writes that he had begun to dig near the “church with bell tower, not far from the beach that is at the base of Mount Santa Maria a Castelli and Mount Sant’Angelo; at a depth of 30 spans we found a famous ancient building whose first mosaic is made of white and fine marble.”
It was only during restoration work on the crypt in 2003 that archaeologists had a chance to enter the villa’s stunning triclinium, or dining room, for the first time. But after only three years of digging, they were forced to stop when funding ran out, and it wasn’t until the summer of 2015 that excavations resumed. For the rest of the year, before funding for the project ran out again, Jacobelli led a rescue excavation under the supervision of the local archaeological superintendent, Adele Campanelli, and archaeological supervisor Maria Antonietta Iannelli. A team of archaeologists and conservators worked to remove mud and lapilli (small stones ejected by a volcanic eruption) and to expose and clean the stunning wall paintings emerging from the debris.
Slideshow:
Roman Holiday
Thanks to an ancient system of artificial terraces cut into the hillside on which Positano sits, the villa may have sprawled across more than 2.25 acres. Some scholars think that it might even have been as large as the town of Positano. Mantha Zarmakoupi of the University of Birmingham, an expert on the ancient Roman luxury villas of the Bay of Naples, disagrees. “I can imagine that the villa was perched on a terraced platform with ramps leading to other terraces below, and may have stretched over two or more levels in the hillside, as houses do today, but I don’t think that it would have occupied the entire village,” she says.What isn’t in doubt, however, is the excellence of the frescoes covering the villa’s walls. “The quality of the wall paintings is very high, and the triclinium’s decorative program seems unique,” says Zarmakoupi. “The combination of frescoes with stucco is rare and remarkable. The rendering of details in stucco, for example in the figures both holding and decorating the drapery, accentuates the feeling that the cloth is actually pliable.”
In addition to the magnificent paintings, in a hole opened in the layer of volcanic debris under the triclinium’s northern wall, archaeologists unearthed a pile of oxidized jars, cups, and dishes that formed a set of silver intended for a symposium—just the type of conversational gathering that would have taken place between the villa’s owner and his important guests.
Local administrators hope to open the property to the public and are planning a transparent footbridge over the site. This will allow visitors to get a small taste of the luxe life as it was almost 2,000 years ago.
Marco Merola is ARCHAEOLOGY’s Naples correspondent.
Taking an innovative approach to
one of ancient architecture’s most intriguing questions
By JARRETT A. LOBELL
Monday, August 15, 2016
For a variety of field projects over the last decade, archaeologist Phil Sapirstein has lugged more than 20 pounds of high-tech laser imaging equipment around the Mediterranean gathering data to create 3-D models of ancient monuments. “I have been working on architectural history for quite a while,” says Sapirstein, who teaches at University of Nebraska-Lincoln, “and one of my main focuses has been the general problem of the origin of architectural styles, especially the Doric style, in the Archaic period [ca. 700–480 B.C.].”
More often than not, little remains of Archaic buildings. The mid-seventh-century B.C. Old Temple at Corinth, dedicated to the god Apollo, burned down and was replaced, obliterating most evidence of the original building. Other structures from the period were flawed due to the lack of experience with engineering and construction techniques needed for monumental stone architecture. The early temple of Hera on the island of Samos, for instance, which Sapirstein characterizes as an “experimental building,” didn’t survive because it subsided into the marshy land on which it was built. Further complicating the effort to identify these early buildings, the stone was often reused, obscuring its original context.
What does frequently survive, however, are the temples’ ceramic roof tiles. Sapirstein realized that these tiles, which are relatively abundant, were an underutilized source of information, especially when examined using 3-D imagery. “I started working with 3-D modeling software early on because you often have to reconstruct the roofing system from very tiny fragments,” explains Sapirstein. “With this software, I could see what the roofs actually would have looked like and how they functioned. It worked great.” But Sapirstein knew the technology was impractical, if not impossible, for most archaeologists to use. “You have to acquire a scanner, which takes some doing, and it’s really expensive,” he says. “You then have to know how to use it and how to process the models. It’s a huge investment.” Sapirstein wanted to find an alternative method—and for this he returned to one of the temples that started it all.
The temple of Hera at Olympia, or the Heraion, dates to around 600 B.C. and is one of the oldest surviving Greek stone Doric temples. In his Description of Greece, the second-century A.D. traveler Pausanias describes legendary events that, along with actual stylistic attributes of the Heraion, led Wilhelm Dörpfeld—a German archaeologist working in the late nineteenth and early twentieth centuries, and the scholar most closely associated with the structure—to date the original building to 1096 B.C. However, while there is evidence of ritual activity at Olympia dating back to the eleventh century B.C., there were no permanent large structures at this early date. And even when the Olympics first took place, probably well after the traditional date of 776 B.C., there were likely no sizeable buildings at the site.
Located in the north part of the Altis, Olympia’s sacred precinct, the Heraion is probably the site’s first monumental stone building. Dörpfeld dug trenches under the temple and found two structures he interpreted as predecessors. But scholars today no longer believe there were in fact any previous buildings on this spot, and that what Dörpfeld had actually uncovered was the Heraion’s foundation. “The Heraion is actually very well preserved,” says Sapirstein, “and doesn’t appear to have been significantly altered or renovated after its construction, despite its thousand-year history of use. It’s one of the very few of these early buildings we can date from stratigraphic and not just stylistic evidence.” The temple is also the first well-preserved peripteral Doric temple—that is, having columns completely surrounding it. “This is an important moment in Greek architecture,” says Sapirstein. “The fact that the Heraion’s columns are made of stone, which is expensive and labor intensive, signifies a major expansion of the investment the Greeks put into building a monumental structure.”
Slideshow:
Olympia Slideshow
What is equally as significant as the existence of the stone columns is the long-accepted narrative about them. “The big story about the Heraion is that its columns were originally made of wood and gradually replaced with stone,” explains Sapirstein. “This fits with the time-honored idea that the Doric order was first developed in wood.” The concept of the wooden columns is mostly drawn not from archaeological evidence, but from Dörpfeld. Dörpfeld was a stalwart supporter of what is termed tectonic theory, an idea developed in the mid-nineteenth century that in ancient architecture form follows function. For Dörpfeld this meant that the Heraion would not have evolved in stone the way it did if it had not been conceived of and made from wood—that is, the function of the original elements determined how they would appear in wood, and thus how the same elements would appear in stone.
Architectural historians of the time could draw on the works of the Roman architect Vitruvius and his De Architectura, 10 books on architectural history written at the end of the first century B.C. Vitruvius believed that certain architectural elements of the entablature—the lintel of a classical building that is supported by the columns or walls—of Doric stone buildings had evolved from wooden prototypes, as had decorative elements, such as mutules, guttae, and triglyphs. The theory of the wooden origins of the Doric order became the prevailing one.
Because the sizes of the Heraion’s columns vary—some are composed of distinct drums (the individual sections that make up the shaft of a column) stacked atop one another, while others are monolithic—and because many of its capitals are of different styles and belong to different time periods, Dörpfeld theorized that as the original wooden columns decayed, they were replaced with stone ones. Nineteenth-century archaeologists conjectured that little would be found of early Greek monumental architecture because it all would have disappeared and been replaced by stone—a useful explanation for why none of these wooden architectural elements did, in fact, survive. “The temple of Hera at Olympia provided the best example of an older wooden Doric architecture in the midst of the hypothesized conversion to stone,” says Sapirstein.
Inspired by a long-standing interest in the Heraion, which had not been comprehensively reexamined since Dörpfeld’s publication of his work on the temple nearly a century ago, and with the success of his 3-D models in mind, Sapirstein decided it was time to take another look. “Early on in my research I saw some evidence that the Heraion’s stone columns were mostly original to the building and that the model of the wood-turned-stone columns was actually pretty dubious,” Sapirstein says. “But I didn’t have the time or the technology to support this new idea, and because it’s one that’s been ensconced for 120 years, if you want to undermine it, you better have your ducks in a row.” Sapirstein knew that he didn’t want to take the traditional approach and spend the next two decades recording, measuring, and drawing each of the temple’s extant stone fragments. He also knew that laser scanning was probably out of the question. “I liked the idea of looking at the Heraion again, but laser-scanning the whole monument, while feasible, wouldn’t give me the kind of data I needed for the restudy,” he says. “In the meantime, the technology of photogrammetry had become a powerful alternative, so I thought I would give it a shot, even though the technique hadn’t yet been attempted at such a large site at the level of detail I needed.”
Slideshow:
Olympia Slideshow
Photogrammetry, the science of using photographs to make measurements, has its roots in the nineteenth century. At the time, balloon-mounted cameras were used, for example, to survey the city of Paris, and a Prussian architect named Albrecht Meydenbauer built special cameras that allowed him to shoot from the ground and use the measurements to survey inaccessible features such as church spires in Germany that had never been drawn accurately before. Digital photogrammetry takes the same basic approach. Thanks to the power of inexpensive modern computers, with their large memory and storage capacity, it’s now possible to use this computationally intensive approach—for the Heraion, Sapirstein used 4,350 unique images taken from different vantage points—to create 3-D models of specific features or entire buildings. “All of a sudden you don’t need a 3-D scanner,” says Sapirstein, “just a decent digital camera, some software, and a little time.” Over the course of five days, Sapirstein recorded the entire Heraion—a building measuring 165 feet long by 62 feet wide—at one millimeter resolution with plus or minus one millimeter of accuracy, providing a tremendous level of detail and precision. “It takes a bit to learn how to take the photos, use the software, and control for error, but once you’ve figured it out, photogrammetry is highly effective, cheap, and visually appealing,” Sapirstein says.
The 3-D models produced by photogrammetry make possible virtual reconstructions of buildings that can never be rebuilt either because they are too fragile or because too many pieces are missing. There are more than 100 stone fragments and fallen column drums belonging to the Heraion, none of which would likely ever be rejoined to the building. Sapirstein explains, “There are drums missing, which would mean that some would have to ‘float.’ With these models, we can place them, virtually, in their correct locations. I even have a few columns that I can digitally reconstruct based on fragments lying on the ground. I can completely restore something that isn’t even there.” Anastylosis—reconstructing a building using its original elements as much as possible—is an inestimably valuable tool, and this digital version no less so. The technology allows scholars to test hypothetical placements of fragments, and to correct them if they seem wrong. “This would be extremely difficult to do with a block of stone that weighs several tons,” says Sapirstein. But while photogrammetry was invaluable in creating these 3-D digital models, would they advance Sapirstein’s theory that the Heraion’s original columns had, in fact, not been made of wood, but rather had always been stone?
One of the main pieces of evidence cited to support the idea that the Doric order evolved from wooden origins is the crescent-shaped cuttings in the stylobate, the platform on which the columns sit. These cuttings were believed to have been used to facilitate the raising of wooden, rather than stone, columns. This theory, which has gone largely unquestioned for more than 80 years, has rested on century-old drawings of the Heraion’s early excavations. While cleaning the area of the stylobate where six of the columns are missing, Sapirstein realized that the cuttings actually didn’t have to have anything to do with moving wooden columns at all. “I had a eureka moment,” he says, “and it occurred to me that these crescent-shaped slots might actually be associated with lifting monolithic stone column shafts and not necessarily wooden ones. This would mean that none of the peristyle would ever have been wood. The 3-D recording was essential for revealing how all of this would have worked.”
Timing and technology always have and always will influence interpretation. When he visited Olympia more than 700 years after the temple was built, Pausanias saw what he describes as a “pillar of oak.” Scholars have long wondered what he actually saw, and what it might mean about the building’s history: Was it an original column located in the interior and thus not exposed to rot as the exterior peristyle columns would have been? Was he describing a repair made during the Roman period? Or was the wooden column one of the treasured remnants of the sacred site’s even-more-ancient past stored in the temple for safekeeping? Pausanias doesn’t tell his readers more.
At the time Dörpfeld was working on the Heraion, there was little scholarly interest in or understanding of early Greek architecture. Few buildings had been excavated or even identified as being “early.” In fact, there was no consensus about how to even date monuments, whether through stratigraphy, pottery sequences, or any other system, explains Sapirstein. “Dörpfeld was right there when the temple of Hera was excavated, and he suspected that it was very early, but the methodology of how to establish this just wasn’t around yet. With the Heraion being the only one of its kind, he didn’t have anything to compare it to,” he says, “so he came up with a theory that, at the time and for more than a century, explained a great deal.”
For Sapirstein, technology that wasn’t available even 10 years ago has allowed him to suggest a fresh interpretation of the Heraion in particular, and, indeed, of Greek architecture in general. “This raises the question of the validity of the tectonic theory,” says Sapirstein. “I believe it demands that we rethink in a fundamental way how the Doric order developed. In the past, the remains have been interpreted to fit the theory, rather than vice-versa. I’d like to start again with the evidence.”
Jarrett A. Lobell is executive editor at ARCHAEOLOGY.