Feature - Supercomputing promises super-insight into human evolution

Visualization by John L. Moreland.

Humans and chimpanzees are closely related – even closer than mice are to rats. That’s why the slight differences between the two species could provide valuable insight into the origin and evolution of humans.

But it isn’t always easy for researchers to get access to the data they need to see those differences. Researchers at the Center for Academic Research and Training in Anthropogeny are using San Diego Supercomputer Center resources to change that. They are in the process of digitizing an extensive collection of skeletons and medical records from more than two dozen chimpanzees; eventually, the results will be made available to researchers for study.

The specimens and records were donated to CARTA by the Primate Foundation of Arizona, which cares for retired zoo primates and primates whose owners can no longer care for them. Jo Fritz, PFA’s director, took special care to maintain the samples, which were collected during routine medical care or from chimpanzees that had died from natural causes. It was Fritz’s idea to donate the collection to researchers who could really put it to good use.

Screen capture of a movie demonstrating the program researchers will use to study the primate bones. Movie by John L. Moreland. Click on the image to download the Quicktime video

“In trying to understand human origins, we ask how we evolved from a common ancestor with the chimpanzee,” said CARTA co-director Ajit Varki. “So you want to compare everything you can between humans and chimpanzees, searching for clues as to what is uniquely human. Functional chimpanzee care records and skeletal specimens are a good place to search.”

With the help of SDSC, CARTA plans to produce computed axial tomography scans of the skeletal specimens, also known as C.T. scans. The CT device is capable of producing three-dimensional representations of the bones with sub-millimeter resolution, so researchers can zoom in and rotate the virtual bones to take extremely precise measurements, said John Moreland of SDSC. Scientists can download CARTA CT data and then use desktop computer applications to virtually cut open the bones and hide parts above or below a certain density threshold. This will allow them to study the bones in ways that are not practical with the actual specimens.

For example, “one way chimpanzees differ from humans is in their gait,” said Margaret Schoeninger, CARTA co-director. “By digitizing the skeletal specimens, researchers anywhere can study the structure of the bones chimpanzees use to walk to compare their locomotive patterns to that of humans.”

Researchers across the world will be able to browse, search and download the data and derived images and movies through CARTA’s website and can examine the bones without ever having to touch the actual specimens, Varki said.

Screen capture of a movie showing a digitized skull as it rotates. Movie by John L. Moreland. Click on the image to download the Quicktime video

SDSC will provide storage space for CARTA’s data, set up databases to query and display the information, and help make the data available on CARTA’s website. CARTA and SDSC have completed the first test scan and will continue to scan portions of the skeletons throughout the summer in preparation for producing high-resolution scans of the entire collection.

“The idea is to take a physical collection that is traditionally stored on dusty shelves in the back of anthropological storehouses and labs and move it into the digital realm where it can be accessed by a wide array of scientists,” Moreland said.

CARTA is a joint research unit of the University of California, San Diego, and the Salk Institute for Biological Studies.

—Amelia Williamson, for iSGTW