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Collections and Research Annual Reports
“Innovation” might not be the first word that springs to mind when people think of research at a natural history museum. With subjects like 60 million-year-old fossils and Bronze Age artifacts, and scientific disciplines traceable back through Darwin to Aristotle, our research might strike some as heavily weighted toward the “history” in natural history. Yet as I look back over a quarter century immersed in the science being conducted at The Field Museum I am struck by a feeling of having witnessed a surge in innovation in our research that is increasing the pace of scientific discovery by leaps and bounds. Much of this innovation has been the result of rapidly changing technologies, but we also see innovation in the application of new methods to approach enduring research questions.
Not surprisingly, an area that has seen some of the most dramatic advances is molecular systematics. The Field Museum has had a DNA lab since the 1970s, but the difference between today’s techniques and those of even a decade ago are mind-boggling. Twenty years ago, sequencing involved radioactive dyes and x-ray photography to identify the nucleotides, resulting in a “gel” image used to analyze the sequence. It would take a skilled tech several days to generate between 12 and 24 samples and 350 to 400 base pairs per sample. Today, with automated sequencing a researcher in our Pritzker Lab can produce almost 10 times as many samples in about 10 hours. “Next-generation” sequencing technology is leading to a revolution in molecular studies by vastly increasing the amount of DNA information that can be generated—and with vastly reduced turnaround time and costs. Here at the Field, Associate Curator Rick Ree (Botany) and Assistant Curator Corrie Moreau (Zoology/Insects) are both exploiting this massive computational power. Rick is applying next-generation DNA sequencing technology to the study of plants. He just kicked off a $400,000 National Science Foundation project aimed at unraveling the evolutionary history of Pedicularis, one of the largest genera of flowering plants, with 770 species found in mountain ranges across the Northern Hemisphere. Since the mountain ranges where these plants occur are biodiversity hotspots, the documentation of the plants’ evolutionary dynamics is critical to conservation planning.
Moving from plants to ants, Corrie is using “next gen” sequencing to explore the complex multitude of bacteria and other microbes that live inside ants (“microbiomes”). Corrie and her team have found that, like humans, ants have a diverse gut microbiome, and that these bacteria help the ants exploit low-nutrient food sources such as plant sap and honeydew from sap-feeding insects, and live in virtual “food deserts.” Corrie and her students are also using next-generation sequencing to sequence seven genomes of plant-ants to investigate the evolution of mutualisms in ants. By looking across the genomes of mutualists (ants that live in symbiosis with particular plants and/or other insects), and generalists (those that can live in varied habitats and exploit a variety of resources), Corrie and her team hope to uncover the genes responsible for this complex behavior.
DNA barcoding is another rapidly developing trend in molecular systematics. Identification of organisms, especially in groups with subtle physical characteristics, requires highly skilled specialists, and the number of species in mega-diverse groups is so high that no single specialist can know all species in detail. The solution is “DNA barcodes,” short fragments of a gene located in a standard position in the genome that facilitate rapid identification of species. With DNA barcoding, researchers sequence a large number of species to create a DNA barcode library, which can then be used to identify organisms. There is a global push to develop DNA barcodes for a wide variety of biological groups, and Thorsten Lumbsch (Associate Curator and Chair, Botany) is on the forefront of “DNA barcoding” for lichens (composite organisms composed of a fungus and an algae or cyanobacteria). In 2011, with support from the Negaunee Foundation, Thorsten and a colleague from the Complutense University of Madrid developed a lichen barcode that was approved by the International Consortium for Barcode of Life, with results soon to be published in the Proceedings of the National Academy of Sciences.
Just as emerging tools and techniques unlock ever more mysteries at the molecular level, the new technologies are changing the way we analyze specimens at a more macro-level. For example, the use of Computed Tomography (CT) X-ray technology has revolutionized anatomical studies of living and extinct organisms, as well as facilitated unprecedented analysis of cultural objects. A CT scan takes a stack of X-ray “slices” through the thickness of the object under study, yielding very accurate three-dimensional images.
This past July, an Anthropology team led by Regenstein Conservator JP Brown and A. Watson Armour III Curator Bob Martin coordinated the scanning of several Egyptian and Peruvian mummies and other large objects. Thanks to Genesis Medical Imaging, a mobile medical CT scanner mounted in a specially adapted truck was brought to the Museum, and used for a pilot study to generate scans of specimens. In all, seven Egyptian mummies, three major Pacific pieces (including a seven foot, 220 lb. temple drum from the Marquesas Islands), and three Peruvian mummies were scanned as well as nine smaller, but nonetheless important, pieces from the Pacific, the Middle East, and Asia. The scans were imaged using two state-of-the-art 3-D rendering computers in the Anthropology Department’s Regenstein Laboratory. This detailed look inside these objects was impressive, and the story received wide press coverage (especially the mummy scans, of course); but the scientific potential of the technique for Anthropology goes well beyond a virtual “opening” of a mummy. Using this non-invasive means of studying internal structure, anthropologists can determine age, sex, dental condition, disease, trauma and perhaps the cause of death. The 3-D images obtained will also facilitate appropriate conservation of objects, and provide a means of ensuring that any future collection of small tissue samples for investigation of genetics, bone chemistry is minimally invasive.
CT scanning also provides for “virtual dissection” of biological specimens. Not long after the mummies were scanned, Associate Curator Peter Makovicky (Geology) and colleagues published a study in the journal PLoS Onethat applied CT technology and computer modeling to “weigh” five T. rex specimens, including Field Museum Geology specimen PR 2081 (also known as “Sue”). The study used precise laser scans of museum-mounted skeletons as templates for fleshed-out digital models whose masses could then be computed. (Sue’s skeleton was scanned by detectives of the Chicago Police Dept. using a forensic device, supplemented with CT scans of individual bones produced at Loyola University Medical Center and Ford Motor Co.). The laser scans are accurate to less then half an inch—fantastic resolution for skeletons that are 40 feet long. T. rex appears to have been significantly heavier than previously believed, with Sue estimated to weigh over nine tons. The new mass estimates alter previous understanding of T. rex biology. The higher masses found for the larger specimens and a lower one for the smallest individual indicate even faster growth than was proposed in a study five years ago—an estimated gain of 3,950 pounds a year during their teens. The rapid growth to gargantuan size came at the cost of speed and agility, because the torso became longer and heavier, while limbs grew relatively shorter and lighter, shifting the center of balance forward. Between these new tools and the world’s largest and most complete T. rexskeleton, we have learned more about the terror of the Cretaceous in the past five years than in the 100 years since it was first described.
Nothing conjures up the image of high-tech tools like lasers, and Curator of Zoology Mark Westneat and colleagues Luisa Marcelino and Vadim Backman from Northwestern University are using biophotonics techniques to study how corals handle sunlight. An array of photon detectors is being used to measure the back-scattering of light to determine the susceptibility of corals to coral bleaching, which occurs when a coral loses the ability to make energy from the sun, and often dies. The team analyzed coral skeletons in the Field’s collections, including some displayed at the World’s Colombian Exposition of 1893, and are also conducting light-scattering experiments on living corals in collaboration with the Shedd Aquarium. Early results of the research show that coral bleaching can be predicted from the way that the coral skeleton scatters light. Deeper understanding of this process will aid in reef conservation efforts.
So far we have seen research calling on cutting-edge technology to investigate organisms and objects from an “up close”—or even inside—view. For his part, Bill Parkinson (Associate Curator of Eurasian Anthropology) is approaching his Körös archaeological project in Hungary from a more distant perspective—the sky. This past year Bill received a grant from the European Facility for Airborne Research (EUFAR) to conduct aerial fly-overs to use LIDAR and hyperspectral remote sensing technology to collect data that will help him and his team model how early villages evolved on the Great Hungarian Plain nearly seven thousand years ago. LIDAR (Light Detection and Ranging) is akin to radar, but uses reflected light pulses to precisely determine the location and elevation of features on the earth’s surface. Hyperspectral remote sensing uses spectrometric instruments to identify materials on and beneath the ground, from rock types, minerals, vegetation, man-made features, even plant species. In March, 2012, EUFAR will send an airplane equipped with several sensors over the project study area in the Körös Region to collect data that will permit Bill and his team to link the archaeological remains of ancient villages to remote sensing anomalies at several scales—from satellites to aerial flyovers to ground-based techniques. This technology allows very subtle buried features, such as ancient walls and ditches, to be detected from satellites. Bill’s pioneering use of multiple levels of geophysical data—from ground-level to satellite—will allow him to reconstruct large-scale maps of ancient European villages.
But for innovative projects at The Field Museum, the sky is not the limit. Philipp Heck (Robert A. Pritzker Assistant Curator of Meteoritics and Polar Studies) is looking at the very edges of the cosmos through his NASA-funded project involving atom probe tomography of nanodiamonds from meteorites. Since 2009 Phil and his collaborators have been developing atom probe tomography, a novel analytical technique, to analyze nanodiamonds atom by atom to answer the two-decade-old question of whether these nanodiamonds have a presolar origin or originate from our solar system. Phil is also involved in analyzing the interstellar dust gathered by NASA’s Stardust space mission, using the Field Museum’s scanning electron microscope. Nearly every element that makes life possible, including carbon and oxygen, was formed by stars, and analyzing contemporary stardust will provide a unique opportunity to learn how such materials have evolved over geologic time, and ultimately understanding how life on earth, and the earth itself, came to be.
The foregoing examples represent just a few of the current innovative projects and techniques being utilized by the scientists in Collections & Research. In addition to innovative tools, we are seeing innovative applications, including several projects that have intriguing implications for human health. For example, the Emerging Pathogens Project, spearheaded at the Field by Shannon Hackett, Richard and Jill Chaifetz Associate Curator of Birds, is a unique research program focused on the evolution of species-switching parasites or pathogens that result in diseases such as bird flu, malaria, and AIDS; the project is merging the Field’s robust research on biodiversity studies and evolution with the University of Chicago’s systems biology and genomics programs. Then there’s the groundbreaking work by Assistant Curator Leo Smith of Zoology/Fishes, whose studies on the evolution of venomous fishes has vastly increased the estimates of their diversity—from around 200 to more than 2,000 fish species—making fishes the most diverse group of venomous vertebrates on the planet; since animal venoms are a key source of bioactive compounds used in pharmaceuticals, the medicinal potential for this work is promising. Finally, Thorsten Lumbsch of Botany is in the planning stages of a project aimed at understanding the evolution of functional genes that are involved in the biosynthesis of aromatic molecules (PKS genes). While natural products from fungi are routinely scanned for pharmaceutical use, secondary metabolites from lichen-forming fungi (almost 1,000 of which are known), have not been studied in detail because lichens are slow growing and extremely difficult to cultivate. Thorsten’s project aims at eventually developing to a culture-independent strategy for pharmaceutical exploitation of lichen products. While all of these projects are still in their early days, their potential applications for human health are promising.
Overall, the range of projects being pursued by this generation of Field Museum scientists is nothing less than amazing. And it is worth stressing the ways we are taking advantage of new avenues for communicating this important work to the public. Thanks to support from the Negaunee Foundation, last year C&R launched a video series called “The Field Revealed” that takes on-line visitors on an intimate journey behind the scenes of The Field Museum, showcasing the fantastic objects and stories in the collections and highlighting the work of our scientists. The series consists of weekly videos of maximum two minutes, accessible on the homepage of The Field Museum’s website (http://fieldmuseum.org/explore/the-field-revealed) as well as on other science media platforms, e.g. NSF’s Science360, Vimeo, and social networks. The series is produced by Federico Pardo, Science Media Producer for Collections & Research, who is charged with developing media initiatives that rely on new media technologies to expand the scientific outreach of the Museum’s scientists. In addition to working closely with the scientists and collections staff, Federico collaborates with media producers outside the Field with an eye to expanding the visibility of the Museum, its research, and its collections. All of this is in addition to our ongoing “virtual field trips” site, expeditions@fieldmuseum, which is now a decade old and still going strong. It continues to rank as one of the Museum’s most visited science microsites, and captures the largest visitorship on The Field Museum’s YouTube channel. Expeditionsis undergoing a facelift, to be unveiled in spring 2012; it will include a new landing page that allows users to select expeditions by topic, or browse videos, interactives, photo galleries, and Google Earth maps, as well as new main pages for each scientist allow users to more easily access and explore new content and design their own pathways of discovery.
The Museum’s digital media team also worked closely with C&R scientists to develop a mobile app called “Specimania,” a game in which players collect “cards” featuring notable specimens and artifacts (and associated “fun facts”) from the Museum’s collections. Players compete against themselves or other players, and there is also an easier “concentration”-style memory game for younger children. The media team and the curators worked for months to make sure the game was both fun and scientifically meaningful.
“The Field Revealed” and “Specimania” are the latest tools in our never-ending quest to bring the science behind the scenes to the public. Our 24-million-objects-strong collections, and the multitude of projects underway around every corner, are fascinating subjects for media and outreach, as are the many innovative methods and novel tech-based approaches recounted in the preceding pages. All of these studies are yielding dramatic new insights across the gamut of our scientific fields. Still, next-generation DNA sequencing and Hyperspectral remote sensing notwithstanding, many of the research questions would be familiar to our first curators, and even Darwin (and probably even Aristotle)—questions of origins, change, and causes. How are organisms related to each other on the tree of life? How did the people in a given society live, and interact? The answers to these questions not only satisfy our innate curiosity about our world and ourselves, they provide insights that are relevant to our existence, and the survival of our planet—baseline data for conserving biodiversity, evidence for the impact of climate change, compounds with medicinal potential, the dynamics of political change, the deep history of ethnic strife. Some of the tools have changed and allow us to arrive at increasingly precise answers, and often at a much faster rate—although let’s be clear: we still use rock hammers, nets, plant presses, microscopes, pipettes, and Jeeps too. Old or new, all of these tools and techniques are in service to the same basic goal: exploring—and documenting, and understanding—the earth and its people.
Senior Vice President and Head of Collections and Research
Past Collections and Research Annual Reports:
