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X-ray analysis of fossil whale baleen

Modern baleen XRD map

Elemental map of a cross-sectional view of the modern minke whale baleen. Image: Mark Goodwin.

Two years ago I approached UCMP Assistant Director Mark Goodwin and asked if he had any room for some student help in his research. I had no previous experience in paleontology, just a passion for learning about dinosaurs and biology. Now, as a third-year graduate student in the Department of Materials Science and Engineering, I work on a variety of projects with Mark and the UCMP. For my own research, I study the micro- and nano-scale features in fossil bone with electron microscopy. I have always enjoyed interdisciplinary work, and the opportunity to use cutting edge X-ray and electron microscopy techniques to uncover new knowledge about the preservation of fossilized structures is very exciting to me.

The Lawrence Berkeley National Laboratory, which sits overlooking the UC Berkeley campus from atop the Berkeley hills, offers many amazing opportunities to conduct state-of-the-art science. In particular, the Advanced Light Source (ALS) offers a variety of techniques for analyzing material properties, for studying the structure of biological specimens or molecules, or for investigating chemical reactions in real time. All of these techniques use X-ray light, which is a higher-energy form of light than the visible light that our eyes can see.

UCMP Assistant Director Mark Goodwin has been using several techniques at the ALS to study a variety of fossil and modern samples. Most recently, Mark investigated the elemental composition and physical structures of a sample of 5.8 million-year-old fossil whale baleen and then compared it to a sample of modern minke whale baleen.

Baleen whales don’t use teeth to catch and chew their food; instead they use hair-like baleen to strain microscopic organisms from the water. The hair-like structures of baleen are actually small tubules composed of concentric, alternating layers of keratin and hydroxyapatite. Keratin is the same tough protein found in fingernails, and hydroxyapatite is the same mineral that makes bones strong. Just as fossilized bones are altered from their original state, in fossil baleen the keratin and hydroxyapatite can be replaced by other minerals.

That’s where the X-ray absorption techniques at the ALS come in. Because whale baleen has such a large protein component, like muscle or skin, it usually is not preserved during fossilization. The fossil whale baleen that Mark analyzed, with the help of ALS scientists Sirine Fakra and Matthew Marcus, is an incredibly rare sample. Two techniques were used to study the preservation of this remarkable fossil whale baleen, including (1) elemental analysis to spatially map where a variety of different elements are in the baleen and (2) X-ray Absorption Near Edge Structure (XANES) to discern the chemical structure of the elements present. In both cases, the data must be compared to the modern minke whale baleen, or the standard, to assess what has actually changed during fossilization.

An example elemental map of a cross-sectional view of the modern minke baleen can be seen in the figure. The colors each represent a different element present in the baleen and they highlight the concentric circular structure of the baleen tubules. The maps show us that the keratin protein rings in the fossil baleen have largely been replaced by mineral. The original hydroxyapatite rings are still there, too, although some elemental substitutions have occurred in the mineral structure.

From this data we now know the secret behind the preservation of this amazing, rare fossil baleen discovery! The keratin was replaced by mineral, which preserved the three-dimensional structure of the original whale baleen – the mineral prevented the tubules from flattening under pressure in the rocky fossil bed. Measuring the characteristics of the three-dimensional structure, like tubule diameter and thickness, Mark was able to determine that this fossil whale is evolutionarily related to the modern minke whale. This one piece of fossil baleen, therefore, has taught us two lessons: (1) how baleen fossilizes to preserve its original structure and (2) that this extinct whale is related to the modern minke whale.

CT scan of fossil baleen, courtesy of Mark Goodwin.

Liz Boatman Fossil baleen locality Modern baleen XRD map Minke Whale

No backbones allowed

Erin in collections The UCMP Invertebrates Collection includes over 31,000 catalogued specimens! Corals, crabs, bivalves, snails, ammonites… both fossil and recent — if it doesn't have a backbone, it's in this collection. I am a UCMP and Integrative Biology graduate student and have been assisting with curation of the Invertebrate Collection. I catalogue and label specimens, process loan requests, manage the Invertebrates Collection database, curate private collections that are donated to the UCMP, and do numerous other small tasks. This might sound tedious, but I really enjoy the process of curation and am constantly exposed to exciting and unique inverts. Why am I interested in animals without backbones? Well, I was hooked after my first introduction to them during an Invertebrate Zoology course, while I was an undergraduate at Rutgers University. Since taking that class, I have traveled all around the world working on projects that focus on invertebrates, including crustaceans and mollusks in the kelp forests off of Alaska; gastropods, cephalopods, and corals in Bermuda; and bivalves in Thailand. My current research takes me to the islands in the Caribbean Sea and Western Atlantic. (Read more about my research on Caribbean inverts in my previous UCMP blog post!)

The UCMP Invertebrates Collection's 31,000 cataloged specimens may sound like a lot, but the collection contains far more than 31,000 individual invertebrates. The actual holdings are nearly impossible to accurately estimate because a single specimen number could be associated with 100 individuals.  Why do we keep so many individuals of the same species from a single locality? Well, having more than one individual is extremely useful to researchers, especially when they are investigating the morphological variation of a species, because the quality of the preservation can vary from specimen to specimen.

The collection consists of specimens that were collected by museum scientists, faculty curators, and graduate students in the course of their research, as well as specimens that were donated to the museum. Some of the major holdings within the UCMP Invertebrates collection include the USGS fossil invertebrate collection, the Crawfordsville crinoid collection, the Geological Survey of California fossil invertebrate collection, the Lambert modern coral collection. For more information about the special collections within the UCMP, please check out this article written by Jere Lipps, one of our Faculty Curators.

Working as Graduate Student Researcher in the UCMP has allowed me to experience what it is like to be a museum scientist, which is something that I may want to do after I finish my PhD. Also, working in the collections has exposed me to all sorts of amazing fossils that I never would have seen otherwise, including Tessarolax sp. (marine gastropods of the Cretaceous), the strange organisms of the Vendian, and rugose corals of the Permian, to name a few.

Check back to the UCMP blog later this fall and spring for more posts about my work with the Invertebrates Collection!

Tessarolax sp. Erin in collections

Flat Stanley visits the UCMP

Stanley and Mammoth SkullThe UCMP has hosted several Flat Stanleys this year, as part of the Year of Science 2009. Flat Stanley is a fictional character from a children’s book, written by Jeff Brown in 1964. In the original story, Stanley is a little boy who is flattened when a bulletin board above his bed falls on top of him. He finds that, in his new flattened state, he is able to have many great adventures by being mailed from place to place in an envelope. Inspired by this story, the Flat Stanley project began as a classroom exercise in an elementary school in Canada and has now grown into a communication network among primary school students around the world. In a variation of this idea, students in Piedmont, California made paper Flat Stanleys and sent them to Berkeley to learn about scientific research on campus. Three of these Stanleys came to visit the UCMP.

The first Stanley to visit in 2009 was hosted by Kaitlin Maguire, a member of the Barnosky lab. Kaitlin showed Stanley the skull of a Columbian mammoth from the Pleistocene of California, and took Stanley’s photo next to one of the mammoth’s teeth. You can check out Stanley’s full adventure with Kaitlin and the mammoth here.

The next Stanley was hosted by Jann Vendetti, a member of the Hickman Lab. Jann took Stanley with her to one of the classes taught in Integrative Biology, called Principles in Paleontology. Stanley got to see a lot of invertebrate fossils, and learned how paleontologists measure the size and shape of animals in the fossil record. See Stanley’s full adventure with Jann here .

The last Stanley to visit the UCMP was hosted by Susumu Tomiya, who is also a member of the Barnosky lab. Susumu introduced Stanley to Flat Darwin, whose real-life counterpart would have celebrated his 200th birthday this year! Flat Darwin took Stanley on a grand tour of the UCMP collections, with a special emphasis on the fossil mammals of South America. One of the highlights was the glyptodont, a giant, extinct relative of the armadillo. You can read about Stanley’s visit with Susumu, Flat Darwin, and the mammals of South America here.

This isn’t the first time Flat Stanley has visited the UCMP — to read about his previous adventures, click here.

Stanley and Mammoth Tooth Stanley and Shells Stanley and Invertebrates Stanley and Darwin Stanley, Darwin, Glyptodont and Armadillo Stanley and Mammoth Skull

T. rex gets a manicure

Gluing on the clawA few months ago, the UCMP’s Tyrannosaurus rex broke a nail. The right claw mysteriously went missing. We needed to replace it, but obviously the standard-issue drugstore press-on nail just wouldn’t do. We had to re-construct a new right claw by making a copy of the intact left claw.

Danny Anduza, a UCMP volunteer, carried out the claw restoration. First, he mixed up a rubbery substance and painted it over the T. rex’s left claw, to make a mold. Once the rubber hardened, he carefully sliced it and removed it from the claw. Next, Danny used the mold to make a new claw. He mixed up some resin and poured it into the rubber mold. Once the resin had set, Danny painted the new claw with brown paint — the same paint that was used to paint the rest of the T. rex in 1995. Danny attached the new claw to the finger bone using a special kind of hot glue, formulated to bond plastic to plastic.

Now that its claw has been repaired, the T. rex can resume hunting prey after we’ve all gone home for the night. Or sneaking into the classrooms and scratching the chalkboards.

Casting the left claw Left claw New right claw T. rex gets a manicure Gluing close up T. rex claw repair Finishing touches New right claw Gluing on the claw

Lupé's story: A mammoth's journey from the ground to a museum

Lupe DigIn 2005, Roger Castillo found the fossilized bones of a juvenile mammoth in the Guadalupe River near San Jose. Roger was walking his dog along the river, which he did frequently as a volunteer for the Guadalupe-Coyote Resource Conservation District, when he saw the tusks of the mammoth's skull poking out of the soil along the riverbank. At the time he wasn't exactly sure what he was looking at but recognized their importance and contacted the UCMP. The fossilized mammoth has been named Lupé, after the Guadalupe River. The San Jose Children's Discovery Museum (CDM) will open a new exhibit in 2011 about Lupé's discovery. The exhibit will focus on how Lupé lived in the past and how scientists have pieced together evidence to understand her life.

I am a graduate student in the Department of Integrative Biology at UC Berkeley, and I have been working with the UCMP and CDM on the mammoth exhibit since February. At Berkeley, I study mammals from the past, their evolution, how they lived and their relationship with the environment. I got involved in this project because of my research interests. I mostly help the CDM team answer questions about mammoths and other Pleistocene mammals, as well as show them how paleontologists figure out the past from fossils and rocks. The CDM team visited the UCMP twice this spring to look at the collections and get a feel for what a typical day is like as a paleontologist. We also went on a field trip to the coast to look at fossils and learn about the local geology. I really enjoy sharing my experiences with the CDM team and love how excited everyone is to learn more about mammoths and paleontology.

But it's not just me teaching the CDM team! I have been learning quite a bit about how a children's museum designs exhibits for all ages. I attend CDM's brainstorming meetings and have been astonished by how creative a process it is. How do you design an exhibit that holds the attention of a 4 year old and her 12 year old sibling!? It's not easy, but with a lot of brainstorming and testing, the team comes up with fantastic exhibits.

Luckily, the project team also includes a group of researchers from UC Santa Cruz, led by Maureen Callanan. They focus on understanding how children learn science. One question the team has had during development of the exhibit is when do children understand the concept of time? Do they know that dinosaurs lived before mammoths? The UC Santa Cruz team is currently running experiments at the CDM to better understand what children will be able to learn from the exhibit. Their research has really helped guide the exhibit development.

I am very excited to be part of such a dynamic team of researchers and professionals. As we all learn from each other, great ideas unfold and the exhibit design moves forward. Over the next few months, I'll be updating you on our progress as we design and construct the mammoth exhibit. And I'll let you know when the exhibit opens in 2011!

UPDATE: Read Part 2 of Lupé's story!

Lupe Dig Lupe Lupe Map Lupe Locality

Cal Day at the UCMP

The UCMP is open to the public just one day a year — Cal Day. Watch this video to see the UCMP's exhibits from Cal Day 2009.