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Archive for February 2013

The Looy Lab paleo detectives

Solving the mysteries of the past and present one rock at a time

East of the Berkeley campus, we see the beautiful, green Berkeley Hills, the golden letter "C" and a somewhat classy-looking, dome-shaped building on the Lawrence Berkeley National Laboratory campus. This houses the ALS, or Advanced Light Source. Personally, I find the name a bit silly because it doesn't seem to capture the awesomeness of this giant machine. It's like calling the Space Shuttle a Progressive Flying Tool.

synchotron at LBL

Photo from

The ALS is a synchrotron, a particular type of particle accelerator. The particles are sped up by a shifting magnetic field within a closed circuit. The shape of this circuit is an almost circular polygon and since the building was specifically designed for the synchrotron, the building is round. But what happens inside?

Each time when the particle beam is bent at each of the polygon's corners, light is produced — primarily ultraviolet and x-rays. The x-rays are not your ordinary dental office x-rays, but much "harder" x-rays. Unlike the relatively harmless photo at the tooth doctor, this beam would kill you before you could say "¿qué?"

But what can paleontologists and paleobotanists do with this advanced light? Hard x-rays allow us to see fossils while they are still inside the rock. This means that you don't have to crack open the rocks, clear away rock matrix and run the risk of damaging precious fossils. In some cases, the material is simply too fragile to be prepared; it would not hold up. Scanning the rock allows us to make 3D reconstructions of fossils hidden inside the rock without damaging them.

We've been scanning all kinds of really old fossils: horsetails from the Carboniferous (~300 million years ago, or Ma), kelp holdfasts from the Oligocene (~30 Ma), tiny (3 mm or ~1/8 inch) and not so tiny (7 cm or ~2¾ inch) pine cones, early land plants from the Devonian (~390 Ma), and pollen cones of extinct redwoods from the Cretaceous (~70 Ma). The size of the fossils is limited by the size of the protective shielding enclosure that keeps the scientists safe while using these lethal x-rays.

Because the cyclotron basically runs 24/7, the scanning time slots are generally 24 hours long and scanning rocks can take a while. Here's the general process that we go through for each scan:

Cindy and Ivo

Left: First, we select a fossil. Right: Then we mount it on a stand (improvising a la MacGyver). These and the rest of the photos are by Cindy Looy and Dori Lynne Contreras.

Orienting a fossil on the stand

Next we orient the fossil on the stand just right to get the best quality scan of the target specimen (which surprisingly takes a bit of work and "expert guess-timation").

The hutch

Once ready, the mount and fossil are placed in a "hutch" made of radiation shielding. Left: This is the hutch, a big container that protects everyone around from the harmful x-rays. Right: Inside the hutch there is a normal optical camera (at ~9 o'clock), the stand on which the fossil is mounted, and the x-ray detector (the big black box at the right).

The hutch doors and camera

To start the scanning process a number of safety procedures have to be followed, otherwise the beamline will not open. Left: The doors of the hutch have to be closed, and while an ominous alarm sounds, you have to press certain buttons to actually allow the x-ray to come into the hutch. Once it does, a red rotating emergency light comes on and the doors cannot be opened. Right: Once the sample is in the hutch we use the normal camera to focus in on the sample.

Adjusting the settings and set to go

Left: As each fossil sample is different, adjustments to the settings are needed. For instance, thicker rocks generally need a higher dose of x-rays than thin ones. Right: And we are good to go! It's scanning time!

Waiting for the scan to finish

And then, we wait …

Data analysis and celebration

Left: Actually, there is not a whole lot of sitting about going on, because the data that the x-ray collector gathers has to be analyzed. This takes up quite a bit of time (note the ridiculous amount of caffeine) and a LOT of computing power. Luckily, the computers at Lawrence Berkeley National Lab are up to the task! Right: Then we celebrate our success!

Darwin Day Roadshow

Lisa's presentation

Lisa White makes her presentation to Mrs. Ball's 7th grade class at the Urban Promise Academy in Oakland. Photo by Alison Ball.

It is not unusual to see evolutionary biologists around the world involved in celebration activities on February 12th — the reason? Charles Darwin's birthday! UCMP and the National Evolutionary Synthesis Center (NESCent) are no exception and this year the activities overlapped. Two years ago, NESCent initiated the Darwin Day Roadshow in order to bring evolutionary science to schools and museums around the country. This year, Lisa White was asked by NESCent to bring the Roadshow to Urban Promise Academy, a small Oakland Unified School District middle school serving students in the Fruitvale neighborhood of Oakland, CA. Presenting to Ms. Alison Ball's 7th grade classroom on February 15, 2013, Lisa highlighted research at the UCMP, profiling examples of evolution from the Understanding Evolution website, while conveying why the science of evolution is important and relevant.

To the enjoyment of the students, Lisa brought in an array of fossils for the students to touch and see the tangible evidence for evolution up close. Lisa also spoke about her own education and training, what it is like to be a paleontologist, and how she came to work at the UCMP. Lisa said "the students were such an inspiration and their enthusiasm and eagerness to learn more about paleontology suggests the next generation of potential scientists are alive and well in classrooms like Urban Promise Academy."

Caldwell's rare octopus research makes headlines

Roy Caldwell has been working with Richard Ross of the California Academy of Sciences to study a rare, beautiful, and so far unnamed species of octopus. Their work, along with some of Roy's photos, is the subject of a feature article in the San Francisco Chronicle.

New bone histology book from UCMP and UC Press

The University of California Press has just published Bone Histology of Fossil Tetrapods: Advancing methods, analysis, and interpretation. The book represents the proceedings of an NSF-sponsored workshop and is the first comprehensive summary of the field of fossil bone histology. The twelve authors of the various chapters cover topics ranging from basic bone biology to calculating and analyzing the evolution of growth rates in bones, in addition to step-by-step instructions for setting up a hard tissue histology lab and processing specimens.

The microstructure of bone has a great deal to tell us about the biology of ancient vertebrates. The patterns of how bone tissue was deposited and the configuration of the blood canals in the bone provide a very good idea of how fast the animal was growing, and how its growth regime changed through life. Growth lines, deposited annually like tree rings, help us to calculate how old animals were when they died and even when they matured sexually. These data in turn give us information about life history strategies and metabolic regimes.

UCMP alum Andrew Lee and grad student Sarah Werning were two of the many contributors to the volume who have benefited from studying UCMP’s fossil collections. UCMP researchers have been in the forefront of fossil bone histology for decades, and our histology lab continues to be one of the most active research areas of the Museum. The book was edited by Kevin Padian of UCMP and Ellen-Thérèse Lamm of the Museum of the Rockies.

Cataloging the Archives: Three Fine Trikes

Another in a series of blog posts relating to the museum's "cataloging the archives" project

Ask children what their favorite dinosaurs are, and it's almost guaranteed that Triceratops (refer to them by their nickname, Trikes, and you'll earn tons of street cred) will be on the list. The three-horned, frilled wonder is one of the most recognizable creatures of the Cretaceous. Many a visitor has walked by the Triceratops display here in the Valley Life Sciences Building's Marian Koshland Bioscience and Natural Resources Library. Over time, the display has grown, not only to include more skulls, but to tell a bigger story. Now there are three skulls in the display, each with its own interesting history, but when taken together the tale reaches almost epic status (okay, "impressive" status).

Ruben at locality2


The largest of the skulls is UCMP specimen 113697, also known as "Ruben's Trike." While on a UCMP field expedition to Montana and neighboring states in July, 1970, paleontology graduate student John Ruben (now a professor in the Department of Zoology, Oregon State University) discovered the skull in the roughly 68-million-year-old rocks of the Hell Creek Formation of eastern Montana. The Hell Creek is one of the most fruitful formations for Trike discoveries, and if you've done field work in the Upper Cretaceous of Montana and haven't come across some part of a Triceratops, you're doing something wrong.

John Ruben (black hat) at his "Ruben's Trike" locality, V75046, where the skull, UCMP 113697, was found, McCone County, MT.


The medium-sized Triceratops skull, UCMP 136306, is also known as the "McGuire Creek Trike" since its discovery in badlands of the Hell Creek Formation exposed in the vicinity of this creek drainage in McCone County, Montana. Weathered fragments of bone or "float" from the skull were first sighted by paleontology undergraduate Wayne Thomas in the summer of 1984 on a UCMP field research trip. Further excavation by UCMP Assistant Director Mark Goodwin and crew that summer confirmed Wayne's discovery was a nearly complete juvenile Triceratops skull. The find was exciting in itself, but it also helped fill in some holes in the understanding of Triceratops growth from baby to adult (known as ontogeny) and generated new research by Goodwin, his colleague Jack Horner from the Museum of the Rockies, and their students. For more information on Trike ontogeny, stay tuned for a future blog entry centered on this exact topic.

The smallest of the Trike skulls, UCMP 154452, was found in the Hell Creek Formation (see a trend?) of Montana by long-time UCMP field associate and collector, Harley J. Garbani, in 1995.

When Harley came across the specimen, he first identified it as a possible pachycephalosaur because the tiny brow horn so closely resembled the horns and knobs seen ornamenting the back of the skulls of pachycephalosaurs, or "dome-headed" dinosaurs. Being a very young individual, likely less than a year old, the skull showed features not seen before on a Trike, was very delicate, and in many pieces. Trying to determine what some specimens are from many fragments can be a tedious and insanity-inducing ordeal (ask any fossil preparator).

After corresponding with, and providing pictures to, Mark Goodwin and Professor Bill Clemens, the specimen was correctly identified and also keyed Goodwin into finding a near identical isolated postorbital or "brow" horn from the skull of another baby Triceratops in the UCMP collections.

Baby trike collage 1

Left: HJG 1030, the Baby Trike Site. Photo by Bill Clemens. Top right: A portion of Harley Garbani's field notes. He crossed out "Dome-Head" (i.e., pachycephalosaur) after learning it was a baby Triceratops! Bottom right: An excerpt from a letter that Harley wrote to Bill Clemens. He knew he had something important, and very quickly corresponded with the right parties to learn why. Image courtesy of Bill Clemens.

Baby trike collage2

Top left: Photo of a table top covered with the bones of the baby Trike skull discovered by Harley Garbani. Bottom left: Reconstruction of baby Trike. Photo by Dave Smith. Right: Assistant UCMP Director and dinosaur paleontologist Mark Goodwin working on the baby Triceratops skull. It was prepared, molded, and cast so that an accurate reconstruction (on exhibit in the Biosciences Library) could be made available for research and display. Images of Mark Goodwin and skull bones courtesy of Bill Clemens.


Harley’s discovery was a game-changer since it was, and still is, the smallest Triceratops skull and by inference, the youngest yet known. Together, these three skulls tell a story about skull development and growth in a dinosaur that was named by O.C. Marsh of the Yale Peabody Museum over 120 years ago!

UCMP paleontologists are still discovering new things about this very popular dinosaur. Fossils are often known for whatever novel thing they can tell us, but sometimes a seemingly small and, at first, very fragmentary fossil becomes significant when studied in the context of other fossils and when you hear the story behind its discovery. These Triceratops skulls are interesting on both counts!