Ornate Fruit-Dove (Photo: Bruce Beehler)

The genomes of modern birds tell a story of how they emerged and evolved after the mass extinction that wiped out dinosaurs 66 million years ago. But the family tree of modern birds has confused biologists for centuries and the molecular details of how they arrived at more than 10,000 species is barely known.

Now that story is coming to light, thanks to an ambitious international collaboration underway for four years that has sequenced, assembled and compared full genomes of 48 bird species. The first findings of the Avian Phylogenomics Consortium are being reported nearly simultaneously in 23 papers — eight papers today, Dec. 12, in a special issue of Science and 15 more in Genome Biology, GigaScience and other journals. The full set of papers in Science and other journals can be accessed by clicking this link www.sciencemag.org/content/346/6215/1308.full

Led by Guojie Zhang of the National Genebank at BGI in China and the University of Copenhagen, Erich D. Jarvis of Duke University and the Howard Hughes Medical Institute and M. Thomas P. Gilbert of the Natural History Museum of Denmark, the consortium focused on species representing all major branches of modern birds including the crow, duck, falcon, parakeet, crane, ibis, woodpecker and eagle.

Red bellied woodpecker (Photo by Ken Thomas)

The Avian Phylogenomics Consortium has so far involved more than 200 scientists from 80 institutions in 20 countries, including the BGI in China, the University of Copenhagen, Duke University, the University of Texas at Austin, the Smithsonian Institution, the Chinese Academy of Sciences, Louisiana State University and many others.

This first round of analyses suggests some remarkable new ideas about bird evolution. The first flagship paper published in Science presents a well-resolved new family tree for birds, based on whole-genome data. The second flagship paper describes the big picture of genome evolution in birds.

Six other papers in the special issue of Science describe how vocal learning may have independently evolved in a few bird groups and in the human brain’s speech regions; how the sex chromosomes of birds came to be; how birds lost their teeth; how crocodile genomes evolved; ways in which singing behavior regulates genes in the brain; and a new method for phylogenic analysis with large-scale genomic data.

The new family tree resolves the early branches of Neoaves (new birds) and supports conclusions about some relationships that have been long-debated. For example, the findings support three independent origins of waterbirds. They also indicate that the common ancestor of core landbirds, which include songbirds, parrots, woodpeckers, owls, eagles and falcons, was an apex predator, which also gave rise to the giant terror birds that once roamed the Americas.

The whole-genome analysis dates the evolutionary expansion of Neoaves to the time of the mass extinction event 66 million years ago that killed off all dinosaurs except some birds. This contradicts the idea that Neoaves blossomed 10 to 80 million years earlier, as some recent studies suggested.

Based on this new genomic data, only a few bird lineages survived the mass extinction. They gave rise to the more than 10,000 Neoaves species that comprise 95 percent of all bird species living with us today. The freed-up ecological niches caused by the extinction event likely allowed rapid species radiation of birds in less than 15 million years, which explains much of modern bird biodiversity.

(Visit Science to learn more.)

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How 3D technology is used at the Smithsonian to create world class exhibits!

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3-D–printed bust of President Obama created by the Smithsonian using 3-D scanning technology (Photo courtesy of Digital Program Office / Smithsonian Institution)

The first presidential portraits created from 3-D scan data are now on display in the Smithsonian Castle. The portraits of President Barack Obama were created based on data collected by a Smithsonian-led team of 3-D digital imaging specialists and include a digital and 3-D printed bust and life mask. A new video released today by the White House details the behind-the-scenes process of scanning, creating and printing the historic portraits. The portraits will be on view in the Commons gallery of the Castle starting today, Dec. 2, through Dec. 31. The portraits were previously displayed at the White House Maker Faire June 18.

The Smithsonian-led team scanned the President earlier this year using two distinct 3-D documentation processes. Experts from the University of Southern California’s Institute for Creative Technologies used their Light Stage face scanner to document the President’s face from ear to ear in high resolution. Next, a Smithsonian team used handheld 3-D scanners and traditional single-lens reflex cameras to record peripheral 3-D data to create an accurate bust.

The data captured was post-processed by 3-D graphics experts at the software company Autodesk to create final high-resolution models. The life mask and bust were then printed using 3D Systems’ Selective Laser Sintering printers.

3-D–printed bust of President Obama created by the Smithsonian using 3-D scanning technology (Photo courtesy of Digital Program Office / Smithsonian Institution)

The data and the printed models are part of the collection of the Smithsonian’s National Portrait Gallery. The Portrait Gallery’s collection has multiple images of every U.S. president, and these portraits will support the current and future collection of works the museum has to represent Obama.

The life-mask scan of Obama joins only three other presidential life masks in the Portrait Gallery’s collection: one of George Washington created by Jean-Antoine Houdon and two of Abraham Lincoln created by Leonard Wells Volk (1860) and Clark Mills (1865). The Washington and Lincoln life masks were created using traditional plaster-casting methods. The Lincoln life masks are currently available to explore and download on the Smithsonian’s X 3D website.

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myVolcano is a crowd-sourcing app that enables you to share your photographs and descriptions of volcanic hazards, as well as collecting samples and measurements of volcanic ash fall, helping scientists to gather vital new information about volcanic eruptions. myVolcano has been made possible through collaboration with the British Geological Survey and the Smithsonian Institution’s Global Volcanism Program. Click here to learn more.

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Today the Smithsonian launches its Transcription Center website to the public. The website is designed to leverage the power of crowds to help the Smithsonian unlock the content inside thousands of digitized images of documents, such as handwritten Civil War journals, personal letters from famous artists, 100-year-old botany specimen labels and examples of early American currency.

A tray of bumble bees from the National Museum of Natural History’s bee collection awaits digitization. The museum is digitizing all 45,000 specimens in its collection and using virtual volunteers to help transcribe important data found on each specimen’s tag. This data will help scientists studying declining bee populations in North America

The Smithsonian has already produced digital images for millions of objects, specimens and documents in its collection. Many of the digitized documents are handwritten or have text that computers cannot easily decipher. Transcription by humans is the only way to make the text of these items searchable, which will open them up for endless opportunities for research and discovery.

“We are thrilled to invite the public to be our partners in the creation of knowledge to help open our resources for professional and casual researchers to make new discoveries,” said Smithsonian Secretary Wayne Clough. “For years, the vast resources of the Smithsonian were powered by the pen; they can now be powered by the pixel.”

The Smithsonian’s collection is so vast that transcribing its content using its own staff could take decades. By harnessing the power of online volunteers that goal can become a reality. During the past year of beta testing with nearly 1,000 volunteers, the Transcription Center completed more than 13,000 pages of transcription. In one instance—transcribing the personal correspondence of members of the Monuments Men held in the Smithsonian’s Archives of American Art collection—49 volunteers finished the 200-page project in just one week. By some estimates, the volunteers are completing in a couple of days what it would take the Smithsonian months to complete without their help. Once a document is done, the work is reviewed by another volunteer before it is certified for accuracy by a Smithsonian expert.

Projects selected for transcription during the beta-test phase were chosen due to high demand from scientists, researchers and enthusiasts for certain items that presented accessibility challenges. For example, the Smithsonian’s National Museum of Natural History has one of the world’s largest bumble bee collections—nearly 45,000 specimens. Information about each bee, such as where it was collected and when it was collected, is extremely valuable to scientists studying the rapid decline of bee populations during the past few decades. The only way to obtain this information before digitization and transcription would be for a scientist to come to the museum and read each tiny, handwritten label (often as small as 3 millimeters by 7 millimeters) and record the information. Now, with the information digitized and transcribed, scientists anywhere in the world can understand more about the population history of the bumble bee and its recent population decline. The bumble bee transcription project is currently one of the highlighted projects on the site.

Curators at the Archives Center at the Smithsonian’s National Museum of American History chose to contribute the diary of Earl Shaffer, the first man to hike the entire length of the Appalachian Trail. Hiking enthusiasts, naturalists and other researchers frequently consult this now fragile document. Once the diary was digitized and uploaded to the Transcription Center, members of the online Reddit community devoted to the trail promoted the project. As a result, all 121 pages were transcribed in two weeks. The diary is now available for download, allowing the public to read, study and search for key words or landmarks and reducing the need for researchers to handle the delicate artifact.

How to Volunteer

Volunteers can register online today to help the Smithsonian transcribe a variety of projects relating to art, history, culture and science, including:

For art lovers: Handwritten personal letters of artists from the Archives of American Art
Read and transcribe personal letters from artists such as Mary Cassatt, Grandma Moses and Claes Oldenburg. Transcriptions of these letters will be part of the Archives forthcoming book The Art of Handwriting. In an age of emails, texts and tweets, when handwritten letters have ceased to be a primary mode of person-to-person communication, this book will explore what can be learned from the handwriting of artists.

For armchair archeologists: Field reports from Langdon Warner
Langdon Warner was an American archeologist and art historian who specialized in East Asian art. He was also one of the Monuments Men who worked to protect monuments and cultural treasures in Japan during World War II. A professor at Harvard and Curator of Oriental Art at Harvard’s Fogg Museum, he is reputed to be one of the models for Steven Spielberg’s Indiana Jones.

For bird lovers: Observation notebooks of James Eike
James Eike was a Virginia bird watcher who kept impeccably detailed field observations of birds and the weather nearly every day from 1960 to 1983 near his home in Northern Virginia. In addition to being an important resource for ecologists, it also includes tidbits of cultural events from that time, including the 1969 moon landing.

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Eight conservation biologists from various organizations and institutions have found that shale-gas extraction in the United States has vastly outpaced scientists’ understanding of the industry’s environmental impact. Each gas well can act as a source of air, water, noise and light pollution that—individually and collectively—can interfere with wild animal health, habitats and reproduction. Of particular concern is the fluid and wastewater associated with hydraulic fracturing, a technique that releases natural gas from shale by breaking the rock up with a high-pressure blend of water, sand and other chemicals. Image of Wyoming’s Jonah Field, a major site of shale development. (Photo courtesy of Ecoflight.)

In the United States, natural-gas production from shale rock has increased by more than 700 percent since 2007. Yet scientists still do not fully understand the industry’s effects on nature and wildlife, according to a report in the journal Frontiers in Ecology and the Environment.

As gas extraction continues to vastly outpace scientific examination, a team of eight conservation biologists from various organizations and institutions, including Princeton University and the Smithsonian Conservation Biology Institute, concluded that determining the environmental impact of gas-drilling sites—such as chemical contamination from spills, well-casing failures and other accidents—must be a top research priority.

With shale-gas production projected to surge during the next 30 years, the authors call on scientists, industry representatives and policymakers to cooperate on determining—and minimizing—the damage inflicted on the natural world by gas operations such as hydraulic fracturing, or “fracking.” A major environmental concern, hydraulic fracturing releases natural gas from shale by breaking the rock up with a high-pressure blend of water, sand and other chemicals, which can include carcinogens and radioactive substances.

“We can’t let shale development outpace our understanding of its environmental impacts,” said co-author Morgan Tingley, a postdoctoral research associate in the Program in Science, Technology and Environmental Policy in Princeton’s Woodrow Wilson School of Public and International Affairs.

“The past has taught us that environmental impacts of large-scale development and resource extraction, whether coal plants, large dams or biofuel monocultures, are more than the sum of their parts,” Tingley said.

The researchers found that there are significant “knowledge gaps” when it comes to direct and quantifiable evidence of how the natural world responds to shale-gas operations. A major impediment to research has been the lack of accessible and reliable information on spills, wastewater disposal and the composition of fracturing fluids. Of the 24 American states with active shale-gas reservoirs, only five — Pennsylvania, Colorado, New Mexico, Wyoming and Texas — maintain public records of spills and accidents, the researchers report.

“The Pennsylvania Department of Environmental Protection’s website is one of the best sources of publicly available information on shale-gas spills and accidents in the nation. Even so, gas companies failed to report more than one-third of spills in the last year,” said first author Sara Souther, a postdoctoral research associate at the University of Wisconsin-Madison.

“How many more unreported spills occurred, but were not detected during well inspections?” Souther asked. “We need accurate data on the release of fracturing chemicals into the environment before we can understand impacts to plants and animals.”

One of the greatest threats to animal and plant life identified in the study is the impact of rapid and widespread shale development, which has disproportionately affected rural and natural areas. A single gas well results in the clearance of 3.7 to 7.6 acres (1.5 to 3.1 hectares) of vegetation, and each well contributes to a collective mass of air, water, noise and light pollution that has or can interfere with wild animal health, habitats and reproduction, the researchers report.

“If you look down on a heavily ‘fracked’ landscape, you see a web of well pads, access roads and pipelines that create islands out of what was, in some cases, contiguous habitat,” Souther said. “What are the combined effects of numerous wells and their supporting infrastructure on wide-ranging or sensitive species, like the pronghorn antelope or the hellbender salamander?”

The chemical makeup of fracturing fluid and wastewater is often unknown. The authors reviewed chemical-disclosure statements for 150 wells in three of the top gas-producing states and found that an average of two out of every three wells were fractured with at least one undisclosed chemical. The exact effect of fracturing fluid on natural water systems as well as drinking water supplies remains unclear even though improper wastewater disposal and pollution-prevention measures are among the top state-recorded violations at drilling sites, the researchers found.

“Some of the wells in the chemical disclosure registry were fractured with fluid containing 20 or more undisclosed chemicals,” said senior author Kimberly Terrell, a researcher at the Smithsonian Conservation Biology Institute. “This is an arbitrary and inconsistent standard of chemical disclosure.”

The paper’s co-authors also include researchers from the University of Bucharest in Romania, Colorado State University, the University of Washington, and the Society for Conservation Biology.

The work was supported by the David H. Smith Fellowship program administered by the Society for Conservation Biology and funded by the Cedar Tree Foundation; and by a Policy Fellowship from the Wilburforce Foundation to the Society for Conservation Biology.

–from Princeton Journal Watch, by Morgan Kelly

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Ten years ago, eight antennas on the summit of Mauna Kea, Hawai’i, united to form a telescope unlike any other. Since then the Submillimeter Array (SMA) has examined the universe in unprecedented detail and provided new insights into subjects as diverse as planetary formation and distant galaxies. Its achievements were celebrated earlier this month at a conference in Cambridge, Mass.

A joint project of the Smithsonian Astrophysical Observatory (SAO) and the Academia Sinica Institute of Astronomy and Astrophysics (ASIAA), the SMA opened a new window onto the cosmos by observing radiation from some of the coldest, dustiest, and most distant objects in the universe. It explores the universe by detecting light at wavelengths (or colors) that are not visible to the human eye.

Timelapse photo of the Submillimeter Array on Mauna Kea (Photo by Nimesh Patel)

The SMA receives millimeter and submillimeter radiation, so named because the wavelength ranges from 0.3 to 1.7 millimeters, or 0.01 to 0.07 inches. It combines signals from eight 6-meter-diameter movable antennas to achieve very high resolution, comparable to the best ground-based optical telescopes.

The SMA was built because of the vision of then-SAO director Irwin Shapiro, who felt that the time was ripe to explore the universe at submillimeter wavelengths at high resolution.

Former SMA director Jim Moran notes, “I’m amazed to realize that the most notable accomplishments of the SMA were not envisioned by its proponents. For example, in 1983 we hadn’t seen any exoplanets or protoplanetary disks. Yet the SMA has had a major impact on studying gaps in protoplanetary disks, which are thought to be cleared by planets.”

From the start, the SMA made fundamental contributions to astronomy. In 2005, it monitored the Deep Impact mission, which sent a projectile to impact Comet Tempel 1. The impact produced more dust and less water vapor than expected.

Moving outward from our solar system, the SMA pierced the thick clouds where stars are born to learn more about the formation process. It revealed the key roles played by magnetic fields and turbulence in shaping star formation. It also unveiled how small cosmic seeds grow into big stars.

The SMA excels at exposing otherwise hidden galaxies in the distant, young universe. It peered across 12 billion light-years of space to uncover the brightest galaxies of their time, and a galaxy forming stars at a surprisingly furious rate. It has even teamed with other observatories to study a black hole and measure its “point of no return.” And, it served as a pathfinder for the Atacama Large Millimeter/submillimeter Array (ALMA), which is currently under construction in Chile.

The future of the SMA looks bright. In particular, it will act as a key element of the Event Horizon Telescope, a collection of telescopes that will operate as an array of unprecedented resolution. The Event Horizon Telescope is expected to produce images of the event horizon around the black hole at the center of our Galaxy.

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It was a first for the Federal Aviation Administration recently when it granted approval for the commercial operation of an unmanned aerial vehicle over United States’ soil. British Petroleum received a thumbs-up from the FAA on June 10 to use drones to fly aerial surveys over Alaska of BP oil equipment and pipelines. This decision is the latest development in the rapidly evolving realm of commercial and amateur demand for UAVs, an exploding technology that National Air and Space Museum curator Roger Connor likens to a Wild West situation. Here Connor answers a few questions about the FAA’s decision and the UAV revolution.

Q: What is the significance of the FAA’s decision?

Connor: The FAA is being very traditional, very methodical in its approach to UAV regulation. Comprehensive FAA rules for UAVs, its leaders have made clear, will probably not be in place until 2020 or 2021. Until then the FAA plans on certifying particular types of operations, ones where unmanned systems would operate over uncongested areas such as Alaska, and allowing companies to apply for individual exemptions.

An AeroVironment Puma UAV, the type approved by the FAA for use by BP, is launched in Alaska. (Image courtesy AeroVironment)

The problem is that right now the pace of civilian adoption of small-unmanned systems for commercial use has greatly outpaced the FAA’s ability to regulate them.

For example, real estate agents are using UAVs to take aerial photos of their listings; people are selling UAV-shot footage to TV stations of accident scenes; and people are posting “dronies” [self-portraits taken with a UAV camera in the sky] rather than “selfies” on social media. This is all being done for the most part, as the FAA would say, illegally. People are deliberately turning their backs on the FAA’s slow process and going ahead and using drones for all types of applications.

What I have seen in the last four to six weeks in particular are news stories of people who are blatantly violating the FAA’s position and are even reporting that to the media. The U.S. has essentially the best-regulated air space in the world, but one of the most cumbersome in terms of introducing new regulations especially for something as sweeping and revolutionary as UAVs are today.

Q. What will be the outcome?

Connor: I think the best analogy right now is the Wild West. It’s really a very turbulent time. There are people who are resisting drone use because of privacy and safety concerns, but others are pushing ahead and rapidly adopting the technology.

Exactly where things are going to fall in the end is not entirely clear. What is clear is that the current situation is probably untenable. There’s going to have to be a faster pace for regulation, otherwise someone is going to suck one of these drones into a jet turbine and there’s going to be a serious accident.

On the other hand, the fact that we haven’t had real serious incidents with the current profusion of drones is an indication that it is going to be a viable industry. These things can be operated relatively safely and with low risk.

Amature footage shot with a UAV quadcopter in California

Q: Will drones soon become a common part of our lives?

Connor: I think certainly anything to do with photography from an aerial perspective is going to continue to take off. We’re very accustomed now to a Google Earth perspective of things and we like that, we want more of it. Drones go a long way to fulfilling that. Google Earth is somewhat static in terms of not seeing things change for a long time. Drones offer the same perspective but in a much more dynamic way, a real-time way. There is a huge demand for that and I think we are going to see much more of it in the next five years, particularly if the technology becomes more capable, reliable and easier to use.

Heavy industry also has a pressing need for some of these things. For example, oil pipeline patrol has long been a high-risk activity. Helicopters and even light aircraft have been used for pipeline patrol but it’s a fairly hazardous activity because it means flying along at low altitude sometimes in not great weather. It is tedious and you are often operating in the vicinity of power lines. The ability to have something you can send out on a particular GPS track with a camera, you send it out and it just follows that power line is solving pilot risk and it is cheaper too.

Q. Should we fear drones are going to expand a surveillance state?

Connor: Obviously, they do have a potential to increase the persistence of surveillance. In terms of new capability they are not adding anything new. What they are adding is a persistence, you can keep a drone on the scene a lot longer and there is concern about that. While the FAA has been extremely reluctant to allow the general public to fly any type of commercial activity over populated areas—and that doesn’t seem to be likely to happen at all until the end of the decade— it has been allowing police departments to do that. A number of police departments have applied for exemptions with the FAA, which have been granted.

A Draganflyer X4 quadcopter carrying a camera.

Q: You are curator of the Air and Space Museum’s unmanned aircraft systems collection, what have you collected recently?

Connor: We just recently collected a Draganflyer X4, which is a quadcopter [helicopter with four rotors]. The particular one we are getting received international attention in May because it was used by the Canadian Mounties in what was claimed to be the first use of a police drone to save a human life. This one actually had a FLIR (forward looking infrared) on it so they sent it out at night at 20-below zero and found a guy who had hit his head and wandered away from an accident scene. They found the guy fairly easily using this UAV and did it at a lower cost and more rapidly than they could have gotten a helicopter to look for the guy.

We’re also looking at a Boeing Scan Eagle, one from the first commercial operation approved by the FAA last summer for use over water in Alaska by BP.

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The largest fully preserved great ape collection in the world is about to make its online debut. Scientists from the Smithsonian’s National Museum of Natural History have been working during the last few weeks to CT scan all 38 specimens in the museum’s “wet” great ape collection, including chimpanzees, orangutans and even a full-grown western lowland gorilla. Once completed, the thousands of high-resolution scans of the animal’s insides will be made publicly available on the Internet, giving scientists from around the world access to a once largely inaccessible collection.

Our collection is more than just bones
Beyond just the bones contained in the Natural History Museum’s dry collections, with which the public is most familiar, the museum’s “fluid” collection preserves the entire animal in an alcohol solution.

“Our fluid specimens are an invaluable resource as the entire animal is preserved intact,” says Darrin Lunde, Mammals Collection Manager for the museum. “We have the muscles, we have the internal organs, we have blood vessels – nothing is lost. These specimens are invaluable for researchers wishing to study tissues and internal organs that the dry collections cannot provide”.

Scientists from around the world  seeking to answer questions in biomedical, environmental and evolutionary fields have vied for access to this fluid collection for years but have been restricted by the difficulties in handling the preserved great apes.

Bruno Frohlich and Sabrina Sholts guide a great ape specimen, wrapped in plastic for protection, through a CT scanner at the National Museum of Natural History. (Photos by Micaela Jemison)

“Wet specimens are difficult to work with,” Lunde says. “These new high-definition scans will enable researchers to non-invasively study tissues, organs and bone structure from our specimens from the comfort of their computer screens anywhere in the world.”

Speed, care & alcohol fumes
While the  final product will mean endless possibilities for research, getting the apes scanned is a mammoth undertaking. Preserved in alcohol tanks the size of small compact cars, fishing out the apes is no small feat. Transporting the animals also must be done with the utmost speed and care due to their fragile condition.

An orangutan, part of the the great ape wet collection maintained by the National Museum of Natural History’s Division of Mammals.

Well aware of the medical insights the great apes could provide, Smithsonian Biological Anthropologist Bruno Frohlich, along with other museum staff, has spent weeks scanning the specimens in often smelly and certainly challenging conditions. A round-the-clock cycle “ape shuttle” has transported the great apes from their tanks at the Smithsonian Museum Support Center in Suitland, Md. to the Natural History Museum in Washington, D.C. for scanning.

Placing the great apes in the CT scanner comes with its own risks, not only to the specimens but to the scientists themselves.

“To ensure the specimens remain in pristine condition, they must be kept moist in their alcohol solution” Frohlich says. “The alcohol fumes, however, are highly flammable and an explosive hazard should any electrical sparks from the equipment come in contact with them. To protect both us, the apes and the scanner, we place the apes in specialized bags that keep them wet and the fumes inside.”

Bruno Frohlich and Sabrina Sholts retrieve a specimen from its storage container at the Smithsonian Museum Support Center in Suitland, Md.

Will the king of jungle fit through the scanner?
The scanning of the great ape collection is nearly complete but the final hurdle is proving to be quite the challenge. All that remains is to scan the centerpiece of the collection, a full-grown male western lowland gorilla known as “Hercules.”  Weighing in at roughly 400 pounds, his gigantic size may prove to be too much for the museum’s CT scanner to handle.

If scanning the gorilla can be achieved, it and the other 37 specimens will provide research insights for scientists all over the world. “To my knowledge this is the first time a large collection of great ape anatomical specimens is being made available online,” Lunde says. “Having these scans not only means we can try to answer many of the research questions we have now, but also the many more to come in the future.”

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For scientists who study non-insect invertebrates, the sheer diversity of these odd and fascinating creatures is both intoxicating and daunting. Occupying niches in habitats the world over are a stunning array of mollusks, worms, jellyfish, sponges, crustaceans, corals and other spineless animals representing more than 500 million years of evolution. But where does science begin to organize the vast biodiversity revealed in the morphology of these animals and unlock their genetic secrets, information that could help us understand our own genetic evolution?

The alciopid polychaete worm or segmented marine worm is related to earthworms. They have very large eyes and presumably use them to find prey and avoid predators in the top few hundred meters of the open ocean. Segmented worms in this family range from a few inches, such as this individual, to more than a meter. They swim in fantastic coiling spirals. (Photo by Karen Osborn)

An important step toward this goal was made recently with the founding of the Global Invertebrate Genomics Alliance, an organization created to bring together the world’s top researchers to sequence the genomes of non-insect invertebrates. GIGA originated at the Nova Southeastern University Oceanographic Center in Florida, spearheaded by Professor Jose Lopez. To find out more about this new alliance, Smithsonian Science turned to Karen Osborn and Allen Collins, zoologists in the Department of Invertebrate Zoology at the Natural History Museum, who are founding members of GIGA.

Q: First of all, what is a genome?

Osborn: A genome is the sum total of the entire genetic code of an organism, all of the genetic information that it contains. DNA is the material that makes up the genome. But a strand of DNA is only one piece of the entire and much larger genome.

When sequencing a genome you can generate tons of raw information but it doesn’t mean anything until you figure out how it all goes together. Once researchers have assembled a genome, essentially mapped out where individual genes and pieces of DNA that regulate the activity of genes fit together, it is typically published in a scientific journal such as Nature or Science.

Glass sponges (Porifera, Hexactinellidae) from the Philippines are largely restricted to cold waters. In the geological past, they were common reef-building species and in some places still form cold water reefs. They create structure in deep water habitats often accompanied by a great variety of species. A pair of symbiotic shrimp live their entire lives housed within the delicate lattice-like sponge skeleton. (Photo courtesy Allen Collins)

Q: What is the aim of the Global Invertebrate Genomics Alliance?

Collins: Many, scientists are interested in sequencing the genomes of different invertebrates. The idea behind GIGA is that we all work together to increase the efficiency by which we can get these genomes done. Work for this project is going to be carried out all over the world in multiple labs. GIGA’s objective is to coordinate the efforts of everyone so we are not duplicating work and so that we are focusing on some of the most important and useful invertebrates from the start.

Osborn: Yes. GIGA’s objectives include building a community to get people collaborating on genome projects, and during a workshop of GIGA members at NSU in Florida we hashed out such things as which specific genomes to prioritize for sequencing, standards for collections, sample preparations, and data analysis.

One of the biggest hurdles in working with genomes is dealing with the massive amount of data that is generated. Developing the software tools that everybody can use to analyze and manage all that data is a priority.

A juvenile squid, “Planctoteuthis oligobessa.” This individual, which is about 5 inches long, changed instantly from nearly transparent to this red/orange when startled by the camera flash. (Photo by Karen Osborn)

While just one genome on its own is interesting, the real power in genomic information is comparing different genomes. With GIGA we may eventually grow its website (GIGA.nova.edu) into a database where scientists can go, pull things up, and compare one animal’s genome to another.

Q: What is the Smithsonian’s role in GIGA?

Collins: One special role the National Museum of Natural History will play is in housing both the archival DNA and RNA used to determine a species’ genome, as well as the actual voucher specimen from which the genetic material was extracted. The genetic material will be stored in the museum’s Biorepository, a cryo-collection of millions of specimens stored at negative 80 degrees Celsius in the Museum Support Center in Suitland, Md. The rest of the animal will be deposited in the NMNH’s more traditional collections. Very few institutions are equipped to do this.

GIGA also dovetails well with another Smithsonian-led project, the Global Genome Initiative, a program to collect, voucher, and genetically characterize all major branches of the Tree of Life. We want to collect genome quality DNA samples from species around the world.  This collection would make it possible to ask questions now and in the future such as: What species live where? How has a species changed?  How did nervous systems evolved in different animals? How did multicellular animals evolve? And really any other questions you can imagine about animals.

 “Cystisoma pellucida,” a hyperiid amphipod (crustacean related to sand hoppers) is similar to a cellophane bag with big eyes. They are completely transparent and their entire head is taken up by their gigantic upward looking eyes. (Photo by Karen Osborn)

Q: What will be the payoff of GIGA?

Collins: It is a natural extension of doing cutting edge biology with more and more types of organisms. As we have learned more and more about the genomes of different invertebrates—which are sort of the non-standard model organisms that we don’t really think of—they have really helped in interpreting how genomes have evolved in the animals that people are generally more interested in, such as humans. So we expect that by sampling whole genomes from across this huge diversity of animals we should get a much better picture of not only genome evolution but also how the genomes are related to creating all these different body plans.

Osborn: There are a host of different biological questions that can be addressed with the genome data and one of the most important ones is how does an individual species react to a changing environment or climate. Some species will actually be targeted by GIGA because we know that the boundaries of their habitat are shifting, for instance warming oceans or changing ocean acidity. Genomes can provide information about how an organism is able to deal with or not able to deal with a changing environment.

“Copula sivickisi” from Moorea, French Polynesia is a box jellyfish (Cnidaria, Cubozoa). Like other box jellyfish, it has complex eyes capable of vision. This species is also notable because males are easily distinguished from females (sexually dimorphic) and they pair up and mate in sort of an elaborate (for jellyfish) manner. (Photo courtesy Allen Collins)

Researchers might look at an animal’s genome now and then 10 years later look at the genome of that same species again. If its environment has changed dramatically and the animal has adapted to it, researchers may be able to look at particular genes and see how they have changed or shifted how they work over time. If we wait 10 years to collect those animals then we wouldn’t be able to see that. There are many interesting questions you can ask when you have genome-wide information. –John Barrat

A new paper on this alliance “The Global Invertebrate Geonomics Alliance: Developing Community Resources to Study Diverse Invertebrate Genmes,” published in the Journal of Heredity, can be found by clicking this link.

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Santa Claus and his sleigh full of gifts has been upstaged early this holiday season by news of autonomous drones possibly delivering packages to your patio in the future. Amazon.com founder Jeff Bezos recently announced his company’s new project Amazon Prime Air. Its aim is to have a package delivered from an Amazon fulfillment center to your house just 30 minutes after you have ordered it online, carried by “unmanned aerial vehicles.”

“Putting Prime Air into commercial use will take some number of years,” according to the company, but its research and development lab is hard at work today to make it a reality. Smithsonian Science turned to Roger Connor, an expert on instruments and vertical flight at the Smithsonian’s National Air and Space Museum to ask him a few questions about autonomous drones and home package delivery.

An Amazon Prime Air drone prototype delivering a package. (Photo courtesy Amazon.com)

Q: What is your take on the idea of drones being used to make home deliveries of goods ordered on the Internet? 

Connor: Well, the idea certainly has a Jetsons aspect to it. It’s got a “this is the future we were always promised but never got” feel.

For me it brings to mind the helicopter in the late 1940s when they first came on the market. Everybody was kind of pushing this notion that you would be able to commute from the suburbs in a personal helicopter that wouldn’t cost any more than the family car. We were going to have flying helicopter busses. At the time the government put a lot of money into supporting these ideas.

We do use helicopters commercially today but not for anything like the uses that were first proposed.

Q: So what are some of the challenges of developing drones that can deliver books and packages?

Connor: First, Bezos proposes using fully autonomous drones—aircraft that fly and navigate by themselves with some sort of artificial intelligence and GPS coordinates. These are not aircraft rigged up with radio control and flown remotely by a pilot on the ground.

One of the biggest hurdles for any such autonomous system is to make certain its drones are not going to get in the way of an airliner or other aircraft. To do this, a drone would first have to have what the industry calls a “sense and avoid” capability, allowing it to avoid other aircraft.

There are technologies that are now coming into play in the air traffic system that allow this but they are expensive and too large and heavy to put into any aircraft like we have seen proposed by Amazon. It would be a pretty significant technological advance alone to just make this aspect of the proposal viable.

U.S. Army, Navy, and Marine units began using the RQ-2A drone, shown here, in the late 1980s to provide field commanders with real-time reconnaissance, surveillance, target acquisition, and battle damage information. Unlike an autonomous drone this drone was piloted by controllers on the ground with radio waves. This one in the National Air and Space Museum collection operated from the battleship Wisconsin during the 1991 Gulf War. (Photo by Eric Long)

Q: What else?

Connor: Second, what’s really pie-in-the-sky about the Amazon idea is they are proposing to navigate autonomous drones in extremely challenging environments. So far the military has developed autonomous drones for combat use only in a prototype form. There’s one that the navy is using now that is designed to take off and land on aircraft carriers. But taking off and landing on a pitching carrier deck is really nothing compared with the idea of trying to navigate in a suburban environment with trees, and power lines and kites and geese and chimneys and all those other things that are going to cause problems.

Nobody has ever tried anything even approaching this in terms of the complexity of it. It is one thing to have Google Earth imagery and know that there is a house in a certain area and quite another thing to know exactly how tall a chimney is and if there’s a TV antenna sticking up or whatever.

To be able to do this you’d have to have something like a LIDAR [a remote sensing technology that measures distance by illuminating a target with a laser and analyzing the reflected light] system that would actually be able to see using some fairly sophisticated sensors. Those do exist but again they are expensive and pretty heavy.

So by the time you have added these two components you’re talking somewhere in the low hundreds of thousands of dollars worth of sophisticated equipment and you’ve upped it to a fairly significant weight level.

Even if you are trying to stay below some arbitrary threshold that the Federal Aviation Administration has set, let’s say 55 pounds or so, you also are going to need some sort of recovery system for liability reasons, some sort of little ballistic parachute, and of course that is more weight.

So there’s this really vicious spiral that you get into of weight and cost that makes it extremely difficult to carry out something like this.

People who are aware of drone technology at the moment look at this and really kind of scratch their heads. Practically speaking in the next five years there’s virtually no hope of doing anything along the lines of what Bezos is proposing here.

Not only is the legality of it going to be kind of far off in terms of trying to define the kinds of operations but also technically there is really just no hope for it at the moment. All the pieces necessary for it do exist in some form but putting those pieces together in a package that is small enough to do the task and do it affordably…that is what’s really the challenge here. It’s hard to see that existing in five years, it is hard to see it existing in 20 years.

Q: How are autonomous drones being used commercially today?

Connor: The Federal Aviation Administration has recently approved type certification for the first two unmanned aerial vehicles to operate commercially in the national airspace system. They are being used commercially by oil companies on the north shore of Alaska to spot wildlife, because these companies have an obligation in environmentally sensitive zones to locate what wildlife is moving through the area. Manned aircraft can also do this but they are expensive, noisy and are going to frighten the wildlife, so if you can do this with an unmanned system that’s a good way of doing that.

There’s also a pretty good market for autonomous drones in fighting forest fires by using thermal imagery to find hot spots and in agriculture to survey and do mapping for precision agriculture –putting down seed and fertilizer with GPS coordinates. Police applications are also a big one.

When you get beyond that trying to determine where this type of technology is going to pay off is really a much more open question.

–John Barrat

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The scale of the universe can be difficult to comprehend. Pretend you are going to make a scale model with a basketball representing the Earth and a tennis ball as the Moon. How far would you hold the tennis ball “Moon” from the basketball “Earth?” Most people would hold them at arm’s length from each other, but the answer may surprise you: at that scale the balls would need to be held almost 30 feet apart.

A new study by Smithsonian researchers at the Harvard-Smithsonian Center for Astrophysics shows that students grasp the unimaginable emptiness of space more effectively when they use iPads to explore 3-D simulations of the universe, compared to traditional classroom instruction.

This study comes at a time when educators are increasingly questioning whether devices such as iPads should play a greater role in education. It suggests that iPads (and other tablets) can improve student understanding of challenging scientific concepts like astronomical scale.

“These devices offer students opportunities to do things that are otherwise impossible in traditional classroom environments,” says study leader Matthew H. Schneps. “These devices let students manipulate virtual objects using natural hand gestures, and this appears to stimulate experiences that lead to stronger learning.”

Schneps and his colleagues looked at gains in learning among 152 high-school students who used iPads to explore simulated space, and compared them to 1,184 students who used more traditional instructional approaches. The researchers focused on questions dominated by strong misconceptions that were especially difficult to correct via teaching. Many questions examined students’ understanding of the scale of space.

They found that while the traditional approaches produced no evident gain in understanding, the iPad classrooms showed strong gains. Students similarly struggle with concepts of scale when learning ideas in biology, chemistry, physics, and geology, which suggests that iPad-based simulations also may be beneficial for teaching concepts in many other scientific fields beyond astronomy.

Moreover, student understanding improved with as little as 20 minutes of iPad use. Guided instruction could produce even more dramatic and rapid gains in student comprehension.

“While it may seem obvious that hands-on use of computer simulations that accurately portray scale would lead to better understanding,” says Philip Sadler, a co-author of the study, “we don’t generally teach that way.” All too often, instruction makes use of models and drawings that distort the scale of the universe, “and this leads to misconceptions.”

Participants in the iPad study came from Bedford High School, in Bedford, Mass., one of a number of school systems around the country that made the decision to equip all students with iPad devices. “Since we began using iPads, we have seen substantial gains in learning, especially in subjects like math and science,” says Henry Turner, Principal.

“What is perhaps most remarkable is that we saw significant learning gains among students who used the simulations, in situations where little to no gains were observed in the traditional classrooms,” says Mary Dussault, a member of the research team. This study thereby provides experimental evidence supporting national trends promoting the use of new technologies in the classroom.

The study is published in the January 2014 issue of Computers and Education.

The research was spearheaded by the Laboratory for Visual Learning (lvl.si.edu) a member of the Science Education Department at the Harvard-Smithsonian Center for Astrophysics, as part of its mission to strengthen science, technology, engineering, and mathematics (STEM) education in the United States.

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Click photo to take a tour of the 1903 Wright Flyer with Smithsonian X 3D Explorer. The Smithsonian X 3D Collection features objects from the Smithsonian that highlight different applications of 3-D capture and printing, as well as digital delivery methods for 3-D data in research, education and conservation.

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What can you do to bring some of the Smithsonian’s 137 million objects to life? Put them in 3-D!

This is a full-time job for two of the Smithsonian’s very own “laser cowboys,” Vince Rossi and Adam Metallo, who work in the Smithsonian’s 3D Digitization Program Office. They work hard to document, in very high three-dimensional detail, many of the institution’s many priceless and important collections so that the objects are available for research, education and general interest.

Click here for Smithsonian 3-D Digitization on Facebook:

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Magnetic field measurement techniques have long enabled scientists to probe the internal structure of biological and material samples. For example, magnetic resonance imaging (MRI) provides information about the structure and function of tissue inside opaque biological specimens. A current limitation of such biologically-compatible magnetic imaging techniques is that their resolution is insufficient to resolve the internal structure of cells, which are instead typically studied using optical or electron microscopes.

In the current issue of the journal Nature, scientists from the Harvard-Smithsonian Center for Astrophysics David Le Sage, David Glenn, and Ron Walsworth, together with their collaborators, present a method for resolving the magnetic structure of living biological specimens at a sub-cellular level. In their study, they use a particular variety of bacteria that naturally produces an internal chain of magnetic nanoparticles. They place these live bacteria onto a diamond surface that has been modified to contain crystal defects that interact with magnetic fields and with light.

A typical electron microscope image of a bacterium; magnetic nanoparticles inside the bacterium appear as black spots. A new technique has been developed that is capable of studying living cells at comparable spatial resolutions by taking advantage of the presence of these magnetic particles.
Credit: Nature

By shining a laser beam onto the surface and measuring the pattern of the light emitted by the defects using an optical microscope, they are able to record images of the magnetic field pattern present at the diamond surface with a spatial resolution that is on the order of the wavelength of light. The technique is a spinoff from the group’s laser technology research on behalf of astronomical research, including exoplanet detection and radio interferometry.

These first results demonstrate the promise of the technique to probe magnetically the internal structure of living cells. This technique could be used to shed new light on the properties and life cycles of these magnetic bacteria, and it points the way toward more sophisticated probes of a wide range of other biologically interesting systems.

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