November 13, 2013
Over the past few years, Adam Metallo, Vince Rossi and other members of the Smithsonian Digitization Program Office have used 3D scanning to solve a century-old murder mystery, preserve a millennia-old fossil whale site threatened by highway construction in Chile and digitally capture every nook and cranny of Abraham Lincoln’s face, as represented in a plaster mask made just before his death, among other feats.
Now, they’re bringing together dozens of the world’s leading experts on 3D scanning and printing at the Smithsonian X 3D Conference. The event, held today and tomorrow at the Freer-Sackler Meyer Auditorium and simulcast above, is a celebration of the digitization work that’s occurred so far and a discussion of how such technology will transform the Smithsonian Institution—as well as the state of science, museums and education as a whole—going forward.
One of the event’s biggest announcements is the beta release of the Smithsonian X 3D Explorer—a web-based interface that allows users to explore, share and print 3D models of dozens of the Smithsonian’s most remarkable artifacts, with more to follow over the coming years. This technology will allow for all sorts of new uses of historical artifacts and scientific specimens: Researchers can share items with colleagues for analysis, teachers can use virtual objects in classroom lessons and members of the public can get unprecedented access to Smithsonian items, many of which aren’t on display due to space limitations.
The 3D data for the items shown in the Explorer will also be downloadable in full resolution, allowing anyone with a 3D printer to create replicas of these objects at any scale. As a demonstration, the Digitization Office will be creating a full-scale, 26-foot long 3D print of one of the fossil whales from Chile.
“I think 3D printing technology is a huge game changer, because you can actually replicate the three dimensional physicality of an artifact,” says Paul Debevec, a computer graphics pioneer who will be delivering a keynote at the event. “When you’re working on proposed reconstructions of what an ancient artifact might have looked like, for instance, you don’t have to actually mess with the original artifact—you can scan it without touching it, print out what you’ve got, and three different historians can come up with three different ideas how of the item may have once looked.”
The Digitization office is also pursuing plans to construct a state-of-the-art 3D scanning and printing lab at the Smithsonian Arts and Industries Building on the Mall, currently under renovation. “We’re basically going to bring our lab to the public,” Vince Rossi says. “Like the fishbowl at the Natural History Museum—where staff work on fossils—we’re going to bring our 3D scanning efforts out into the public eye, so people can see what we’re working on.” Additionally, in the new space, they’ll make their high-end 3D scanning and printing equipment available for public use.
The conference will feature panels and keynote addresses from dozens of leaders in 3D technology, including Saul Griffith, the inventor and founder of Otherlab, and Ping Fu, the Chief Strategy Officer of 3D Systems. Together with Rossi, Metallo and other Smithsonian staff, they’ll examine how digitization will shape the future of the Smithsonian and grapple with the challenges of effectively digitizing and making publicly available millions of artifacts and specimens.
“For a museum curator, there are scary aspects to letting collections roam digitally on the internet,” Debevec says, “but it seems that Smithsonian curators understand the potential of all this, and I think they’re going to be on the forefront of making it happen.”
Watch the livestream above for coverage of the two-day conference.
The Wright Flyer, the legendary aircraft built by the Wright Brothers and sent skyward over Kitty Hawk in 1903, was acquired by the Smithsonian in 1948. Since then, it’s been on public display nearly continuously.
Of course, visitors aren’t allowed to touch the plane, and educators teaching lessons on the Flyer have had to use models to give students the chance to handle it and see it from different positions. Engineers and historians have faced similar limitations, unable to climb inside to examine its inner machinery or take out a tape measure to assess its specs.
Now, though, anyone with an internet connection can handle a virtual 3D version of the Flyer and print a replica at any scale. The 3D model viewer above, along with 20 other 3D models released today as part of the Digitization Program Office‘s Smithsonian X 3D Conference, is the result of years of labor by Vince Rossi, Adam Metallo and other staff in the Digitization Office. As they continue their work of digitally scanning as many of the Smithsonian’s 137 million artifacts as possible, the Smithsonian X 3D Explorer is the means by which they’ll take this valuable 3D data public.
“For a while, we were able to create these incredible, high-resolution 3D models, but in terms of public access to the data, we were really limited,” says Rossi. “In developing these tools, we’re able to share our work with the world.”
Each model is a simplified version of the “point cloud“—the thousands of points that make up the contours of an item’s surface—that they collect using 3D scanning tools. Because the actual point cloud is far too large in size to make available in a web browser, some digital compression is necessary.
“If you play any video game, you’re looking at a polygonal model, and that’s also what you’re looking at in the viewer,” Rossi says. In essence, the 3D contours of an object are flattened, forming thousands of polygons (mostly triangles) that represent the surface of the object. As polygons, these triangles can be represented in two dimensions—at which point colors, shading and textures are added to the object’s surface—then contorted back into a 3D shape that captures most of the visual detail of the original but has a file size small enough to load in a web browser.
The viewer allows users to explore these models in detail—rotating the items, isolating different components of them, measuring them with built-in tools and creating specific views that can be shared over social media or embedded on a website or blog post just like a video. It also makes it possible to take a virtual guided tour of the object (by clicking on the globe icon), with text, images and video that accompany a specific set of views and let users learn historical and scientific background. “The 3D explorer allows you to tell a story,” Rossi says. “Essentially, you can use the 3D model as a scaffolding to tell the history of an object.”
The Digitization Office staff see dozens of potential uses for these models: Teachers can use them as education tools, researchers can use them to analyze their own artifacts and share them with colleagues, and most of all, they’ll allow the public to more easily appreciate millions of Smithsonian objects, both on display and hidden away in archives. Once, plaster masks—such as the mask of Abraham Lincoln made shortly after his death, above—were the height of technology used to preserve the three-dimensional shape of a specimen or artifact. Now, digital capture of an item’s contours in three-dimensions can be done with lasers and computer software.
In addition to the compressed versions of these artifacts available in the viewers, the Digitization Office has also made the full-size 3D datasets available for downloading, which will let users use 3D printers to recreate the objects in full detail at any scale. Although 3D printing at home is still in its nascency, they’re becoming increasingly economical, with base models now available for a few hundred dollars. “We think the implications of this are pretty big,” Rossi says.
So far, the Digitization Office has scanned hundreds of objects. For the first batch of viewable items, they chose a sampling that represents all of the fields of inquiry the Smithsonian is involved in—art, history and science, conveyed with priceless artifacts, ancient specimens and, in the case of an orchid, actual living organisms.
This whale fossil, for instance, was scanned when dozens of seven million-year-old whale remains were discovered in Chile, in the path of imminent Pan-American Highway construction. To preserve the specimens in their geological context, Metallo, Rossi and others scanned them in 3D. “[Paeleontologist] Nick Pyenson is already planning on using these viewers to share information with researchers in Chile,” Rossi says. “So this site no longer exists in Chile, but anyone is still able to take measurements of it and use that data.”
Scanning has also been put to use as part of internal Smithsonian projects, such as the comprehensive scanning of Dinosaur Hall to document the position of all of the hall’s specimens before it closes next year for a ground-up renovation. As part of the project, the team scanned the wooly mammoth represented above.
“This was challenging not only because of the size, but also its complexity,” Rossi says. To capture the contours of every rib bone and tusk, he and Metallo had to position their scanners in more than 60 different vantage points, then carefully knit together the data sets to yield a complete animal.
They’ve gone small, too, with specimens such as the bee above, taken from the Smithsonian’s entomology collection. In order to capture details as small as the hairs on its abdomen, Metallo and Rossi used a micro CT scanner, which is similar to a medical CT scanner, but able to capture smaller objects at high resolution.
With their scanning technique practiced and a new means of sharing their data with the public, Rossi and Metallo’s plan going forward is to increase the scale of their operation. “The next step is going big—scanning hundreds or thousands of objects per year, instead of a few dozen,” Rossi says. It might not be possible to digitally capture all 137 million of the Smithsonian’s items, but they want to scan as many as they possibly can.
For the rest of the first batch of models—including digital versions of Amelia Earhart’s flight suit, a 550 A.D. intricately carved “Cosmic Buddha” sculpture and the remnants of a distant supernova—head over to the Smithsonian X 3D site. The conference is sold out, but is being simulcast online, and an associated showcase of 3D technology is open to the public.
November 4, 2013
Until 1982, anyone who used insulin to manage their diabetes got it from what we’d now think of as an unusual source: the pancreases of cows and pigs, harvested from slaughterhouses and shipped en masse to pharmaceutical processing plants. But there were problems with getting all our insulin this way—fluctuations in the meat market affected the price of the drug, and projected increases in the number of diabetic people made scientists worry that shortfalls in insulin supply could strike within the next few decades.
That all changed with the introduction of Humulin, the first synthetic human insulin. But the drug was a milestone for another reason, too: It was the first commercial product to come out of genetic engineering, synthesized by bacteria that had been altered to include the gene for producing human insulin.
Last year, the American History Museum acquired a handful of key items used to create Humulin from Genentech, the San Francisco company responsible for its development, and put them on view last week in a display titled “The Birth of Biotech,” giving visitors a look into the dawn of the era of genetic engineering.
Genentech’s work began with a discovery made in the 1970s by a pair of Bay Area scientists, Herbert Boyer of UC San Francisco and Stanley Cohen of Stanford: Genes from multi-cellular organisms, including humans, could be implanted into bacteria and still function normally. Soon afterward, they teamed with venture capitalist Robert Swanson to form the company, with the hope of using genetic engineering to create a commercially viable product.
Early on, they decided insulin was a logical choice. “It was convenient. It was an easy protein to handle, and it was obviously something that a lot of people needed,” says Diane Wendt, a Smithsonian curator who worked on the display.
One of their first achievements was synthetically building the human insulin gene in the lab, a single genetic base pair at a time. In order to check the accuracy of their sequence, they used a technique called gel electrophoresis, in which electricity forces the DNA through a gel. Because larger pieces of DNA migrate more slowly than smaller pieces, the process effectively filters the genetic material by size, allowing researchers to pick out the pieces they want, one of the key steps in early genetic sequencing methods.
Electrophoresis is still widely used, but the equipment donated by Genentech is decidedly more improvised than the standard setups seen in labs today. “You can see it’s sort of made by hand,” says Mallory Warner, who also worked on the display. “They used glass plates and binder clips, because they were working really quickly all the time and they wanted something they could take apart and clean easily.”
In order to manipulate DNA and other microscopic molecules, the researchers used a variety of tiny glass instruments. They made many of these tools themselves with a device called a microforge—essentially, a tool shop in extreme miniature, equipped with its own microscope so the makers could see what they were doing.
After synthesizing a gene for insulin, the scientists needed to assimilate it into a bacterium’s DNA so that the organism would produce insulin on its own. They used a variety of enzymes to do so, including Eco R1, a chemical that cuts DNA in a precise location, based on the surrounding base pairs. Researchers extracted small DNA molecules called plasmids from the bacterium, severed them with these enzymes, then used other enzymes to stitch the synthetic insulin gene in place. The new hybrid plasmid could then be inserted into live bacteria.
After the Genentech scientists successfully created bacteria with copies of the insulin gene, they confirmed that the microbes could produce human insulin in sufficient quantities in a fermentation tank like this one. Then the genetically modified bacteria were passed off to researchers at Eli Lilly, who began producing it in commercial quantities for sale. Voila: synthetic human insulin.
Of course, the state of biotechnology continued to evolve in the years after Humulin debuted, and the museum has collected notable items from that time as well. One is a prototype of a gene gun, developed by scientists at Cornell University in the mid-1980s.
The device makes it easier for scientists to introduce foreign genes into plant cells, by coating tiny metal particles in DNA and firing them at plant cells, forcing a small percentage of the genetic materials to penetrate into the cells’ nuclei and enter their genomes. The original gene gun prototype used a modified air pistol as a firing mechanism, and the technique proved successful when it modified onion cells, chosen for their relatively large size.
Another subsequent innovation ushered in the age of biotechnology in earnest: polymerase chain reaction, or PCR, a chemical reaction developed in 1983 by biochemist Kary Mullis that allowed scientists to automatically multiply a DNA sample into greater quantities with significantly less manual work. The first prototype PCR machine, or thermal cycler, was based on researchers’ knowledge of how enzymes like DNA polymerase (which synthesizes DNA from smaller building blocks) functioned at various temperatures. It relied on cycles of heating and cooling to rapidly generate large amounts of DNA from a small sample.
“The Birth of Biotech” is on display on the ground floor of the American History Museum through April 2014.
October 9, 2013
As we reach day nine of the federal shutdown, it’s widely known that all 19 of the Smithsonian Institution’s museums are closed to the public due to the furloughs of all non-essential federal employees.
What’s less often discussed, though, is the fact that the Smithsonian is also an international research organization that employs hundreds of scientists—and consequently, the shutdown has impacted dozens of scientific projects across the U.S. and in far-flung locations around the world. Interrupting this work for even a short-term period, scientists say, can have lasting effects down the road, as in many cases, projects may have to be started anew due to gaps in data.
Because of the furloughs, many researchers and other personnel are unreachable (some may even face penalties for merely checking their e-mail), so collecting information is difficult. But here’s a partial list of Smithsonian research projects interrupted by the ongoing shutdown:
Nick Pyenson of the Natural History Museum has conducted fieldwork on every continent except Antarctica, excavating ancient fossils to understand the evolution of modern marine mammals. As part of his team’s current project, in Chile, they’re 3D scanning a particularly rich site that includes whale, penguin and seal fossils so scientists worldwide can study the digital data.
But last week, that work was abruptly halted. “The Smithsonian is closed, due to a federal government #shutdown. All Pyenson Lab social media, including coverage of the ongoing joint UChile expedition, will be suspended starting 12 pm EST (noon) today (1 Oct),” Pyenson wrote on Facebook. “Also, all federally funded Smithsonian employees are forbidden, under penalty of a $5,000.00 fine and up to 2 years in a federal prison, from logging into their SI email accounts. I will be out of contact until the federal government reopens.”
In 2011, Pyenson’s crew discovered a set of ancient whale fossils in the path of the Pan-American Highway and excavated them just in time. There might not be any looming highway projects currently, but leaving these precious fossils exposed to the elements still poses an enormous risk to their scientific value.
The Smithsonian Astrophysical Observatory, which partners with Harvard to operate and analyze data from dozens of astronomical telescopes, located both on the ground and in space, has managed to keep most of its facilities operating thus far. “You have to shutter federal buildings, but some of these aren’t technically federal buildings,” says David Aguilar, an SAO spokesman, noting that many telescopes, such as those at the Fred Lawrence Whipple Observatory in Arizona, are shared with local universities and are still staffed by skeleton crews comprised mostly of non-federal employees.
Many SAO researchers, though, depend on data that comes from a range of non-Smithsonian telescopes that have already been shut down. This group includes radio astronomer Mark Reid, who conducts research with the Very Long Baseline Array, a group of telescopes operated by the National Radio Astronomy Observatory that stretches all the way from Hawaii to New England and was closed last week. “This is really bad,” he told Science. “If they don’t operate the telescopes, it could mean a year’s worth of data becomes useless.”
At the National Zoo, the Smithsonian Conservation Biology Institute in Front Royal, Virginia, and various research sites around the world, staff has been stripped down to the minimum level necessary to care for animals—and that means all of the research into how these animals behave and how their bodies function has been shut down.
“All of the scientists, with very few exceptions, have been furloughed,” says Steve Monfort, director of the SCBI. “So everything is shut down. All of our labs are closed, and dozens of projects have been put on hold.” This includes the Zoo’s endocrinology lab (which provides crucial services to dozens of zoos across the country to help them breed elephants and other animals) and the genetics lab (which analyzes biodiversity to sustain severely endangered species on the brink of extinction). “We’re pretty much dead in the water, as far as ongoing science work,” he says.
Additionally, some of these projects are conducted in some 35 different countries annually, so travel arrangements and international collaborations—such as a trip to China to study pandas and a Zoo team’s research into emerging infectious animal diseases in Uganda—have been delayed or cancelled.
“What the public sees when we put on displays is only the tip of the iceberg,” says David Ward, a curator at the National Portrait Gallery, which opened the (briefly) acclaimed exhibition “Dancing the Dream” the day before the shutdown. “There’s a tremendous amount of day-to-day work and research necessary to keep everything going, and we can’t do it right now. It’s very frustrating.”
Apart from designing exhibitions—a whole host of which will likely be delayed in opening, including the Sackler Museum’s exhibit on yoga in historic Asian art, the Hirshhorn’s “Damage Control,” a much-anticipated exhibition on the theme of destruction in contemporary at, and the American Art Museum’s “Our America” exhibition on Latino art—curators conduct research to expand knowledge in their fields. This work, too, has been interrupted by the shutdown.
Kristopher Helgen, the Natural History Museum curator and biologist who announced the discovery of the olinguito species to great fanfare in August, announced on Twitter today that he “had to turn away mammalogists from Oz, NZ, S Africa, Brazil, etc. Long way to come to find the collections closed.”
Because the majority of Smithsonian researchers and curators are furloughed and out of contact, what we currently know about interrupted science is only a small measure of the total effects of the shutdown. “I don’t have much information because, scientists are largely furloughed and silent,” says Kirk Johnson, director of the Natural History Museum. “The real impact of this will emerge once the lights are back on.”
October 4, 2013
In June, the Natural History Museum announced one of its most significant acquisitions in some time: one of the most complete Tyrannosaurus rex specimens in existence, a fossil known as “Wankel’s Rex,” on a 50-year loan from the Museum of the Rockies in Bozeman, Montana. The 38-foot-long, 7-ton skeleton was set to be shipped from Bozeman on October 11 and complete its cross-country trip on October 16, arriving amidst celebrations for National Fossil Day on the National Mall.
Today, after much speculation, the museum officially announced that the T. rex‘s journey will be postponed due to the shutdown of the federal government. New plans call for the specimen to arrive sometime during April. “It’s a major specimen, so we’re being very prudent about how we handle it,” said Kirk Johnson, the museum’s director. ”There’s a lot of uncertainty with the shutdown, and uncertain availability of federal workers to do the work that we need to do.”
The decision to push back the highly anticipated shipment all the way until spring was also influenced by weather concerns. “There’s an early winter storm that’s in the Rockies right now. We’d been hoping to get the thing moved before winter came, so now we’ll have to wait until winter has passed,” Johnson said. “There aren’t too many T. rex skeletons around, so you want to take care of the ones that you have.”
When the specimen was discovered in 1988 by an amateur fossil hunter named Kathy Wankel on the Fort Peck Reservoir in Montana, it was the most complete T. rex in existence—roughly 85 percent intact, in total—and included the first ever T. rex forearm bones ever found. Plans call for the fossil to serve as the centerpiece of the of the museum’s new Dinosaur Hall when it opens in 2019, with a series of temporary exhibits that feature parts of the skeleton and digital renderings on display in the meantime.
Smithsonian researchers will also continue study on the specimen. Staff from the 3D Lab in the Smithsonian’s Digitization Program Office—who’ve already pioneered the digitization of many scientific specimens, from fossilized whales excavated in Chile to many of the skeletons that currently fill the museum’s Dinosaur Hall—plan to create digital renderings of the T. rex‘s bones, so that researchers can print replicas of the fossil at any scale and study them in a virtual environment.
In due time, Wankel’s Rex will still fuel these research and educational roles—but for now, the shutdown means all plans are on hold. The arrival festivities timed to coincide with National Fossil Day, a celebration organized by the National Park Service, however, will be permanently cancelled, as the event will have to go on without the T. rex. “It would have been nice to deputize those 600 kids on the Mall as junior paleontologists,” Johnson said.
The postponement comes four days into the federal shutdown, which has closed the Natural History Museum, along with all Smithsonian facilities. “As the most visited museum in the U.S., we’re eager to open our doors as soon as possible for all visitors,” said Ryan Lavery, a spokesman for the museum.
Typically, the museum is visited by roughly 7.6 million people per year, or 20,000 per day, free of charge. “The majority of our staff is furloughed right now, so all the work that we do is being postponed as we wait for the government to open,” said Johnson. “We have tens of thousands of visitors every day who want to come to the museum, and right now they aren’t able to access it.”