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Lupé's story, part 2: Prototyping the mammoth exhibit

LupeSkullUCMP graduate student Kaitlin Maguire is working with the Children’s Discovery Museum in San Jose to develop a new exhibit about the life of Lupé, a mammoth fossil that was found in the nearby Guadalupe River.  This is the second in a series of blogs about Lupé and the new exhibit. Read Kaitlin’s first Lupé blog here.

Development of the Lupé Story Exhibition is moving along quickly as exhibit ideas come to life in prototyping labs, in which the development team at the Children’s Discovery Museum (CDM) sets up preliminary exhibits and opens them up to the public for feedback. Prototyping labs are an important aspect of developing an exhibition; the prototyping labs show how children interact with the exhibits and if the exhibits are successful in teaching the children something about Lupé, paleontology, and the process of science. Maureen Callanan, a professor at UC Santa Cruz, is also interested in the prototyping labs because it gives her and her graduate students a chance to study how children learn and interact with their parents and caregivers.  Maureen and her students then provide additional feedback to the CDM team from a cognitive psychology perspective. Preliminary exhibits in the first prototyping lab included bone puzzles, play dioramas of the Pleistocene, and sifting for fossils. The most popular exhibit in the first prototyping lab was the dig site where some children spent hours using wooden tools to dig out fossils of Pleistocene mammals.

In December, we all got the chance to meet Roger Castillo, the San Jose citizen who found the Lupé fossils as he was walking his puppy along the Guadalupe River. Hearing Roger tell his story about the discovery was inspirational. As a citizen scientist, he is invested in the health of the Guadalupe River and all it has to offer, including fossils. Growing up in San Jose, he has monitored the river his entire life. Specifically, he has looked at salmon populations in the river, changes in the level of the river, and erosion caused by the river.

Upon hearing Roger enthusiastically describe how he discovered the fossils, the CDM team decided to focus on recreating the “discovery moment” for children to experience at the museum. The next prototyping lab will contain exhibits designed to create an experience of discovery, excitement, and curiosity. Children will discover fossils on a riverbank, uncover them, and ask questions about the fossils much in the way Roger did. This prototyping lab will be open through the spring. A third prototyping lab will open in the fall and final production of the exhibition will start afterward leading up to the grand opening in the spring of 2011.

DigPit BonePuzzle Sifter

Collaborating, with the help of the collections

Triassic research group A few weeks ago, we blogged about the discovery of a new species of dinosaur, Tawa hallae. Two UCMP alums, Sterling Nesbitt and Randy Irmis, described this new dino in the journal Science. A few weeks ago, Sterling, Randy, and two of their Tawa co-authors, Nate Smith and Alan Turner, visited the UCMP. They've come from Texas, Utah, Illinois, and New York, to work together and delve into the UCMP's collections. Along with UCMP Faculty Curator Kevin Padian and graduate student Sarah Werning, they are looking at the fossils in old collections — dinosaurs and crocodile relatives that lived around the same time as Tawa, in what is now Arizona and New Mexico.

"We're looking at the old fossils in the context of new ones," says Randy. Many of the fossils were collected by Charles Camp in the 1930s — others were collected even before that. Quite a few were never identified and have not yet been entered in the UCMP’s database. For those specimens that were identified, says Sarah, "we're potentially re-identifying them." There are many new species that were not known when the fossils were last studied. In looking through these old collections, the team could find additional specimens of Tawa, or specimens that represent species that have not yet been described.

Their work in the collections will likely influence their field work plans this summer.  They're returning to the Hayden Quarry, in New Mexico, for their 5th full season. They'll also visit nearby areas where fossils from the old collections were found, years ago. "Some of the big discoveries in paleontology have happened when you re-identify fossils that have already been collected, and then you go back to a particular area to look for more," says Nate.  For example, Tiktaalik, an important fossil that represents an intermediate form between fish and amphibians, was found when paleontologists re-visited a field site in Nunavut, Canada.

The scientific community will reap some benefits as a result of this week's work. As experts in the field of Triassic dinosaurs, "we play a mini-curatorial role," says Nate. They straighten out the identities of the fossils, and they add the specimens to the database, so other researchers can access this information.

When they're not looking through the collections, the team clusters around their laptops in the Padian lab, drinking coffee and Diet Coke and bouncing ideas off each other. It's great to be all in one place, they say. Online communication is "good for getting things started and wrapping things up," says Alan, "but for the meaty part in the middle it's best to be in one place."

This research was made possible in part by the Welles Fund. To learn how you can support research at the UCMP, click here.

Conifer evolution workshop

ConiferIf there were a Guinness Book of World Records for conifers, California would be one of the top record holders: the Golden State has the tallest conifer, the most massive conifer, and the oldest conifer. Learn much more than just conifer trivia at an upcoming workshop, The Origin and Evolution of Conifers, co-hosted by the UCMP and The Jepson Herbarium. Through talks, discussions, and a hands-on lab, you'll learn all about the origin, evolution, and diversification of this unique plant group. Museum Scientist Diane Erwin, Faculty Curator Cindy Looy, and UCMP Post-doc Lenny Kouwenberg will lead the workshop. It will be held on Saturday, February 6, from 9am to 4pm. For more info on the workshop, including registration information, click here.

UCMP short course: Predicting the future of San Francisco Bay

predicting_web1How will sea level rise and climate change affect San Francisco Bay in the coming years? To predict the future, we need to look at the past — history shows us that San Francisco Bay has undergone some major changes throughout its history. Learn more about the Bay at this year's UCMP Short Course, Predicting the future of San Francisco Bay: Learning from history. This all-day course will be on Saturday, February 6, at UC Berkeley. It features talks by five renowned Bay Area scientists, as well as a panel discussion, giving you the chance to ask questions and delve deeper into the Bay's history — and its future.

The speakers include Doris Sloan, Adjunct Professor of Earth and Planetary Science at UC Berkeley and author of the book Geology of the San Francisco Bay Region; UCMP Faculty Curator Jere Lipps; San Francisco Estuary Institute scientist Robin Grossinger; Andrew Cohen, Director of the Center for Research on Aquatic Bioinvasions; and Will Travis, Executive Director of the San Francisco Bay Conservation and Development Commission. Learn more about the speakers and their talks here.

Registration information is available here. The cost is $30 for the general public, $25 for Friends of the UCMP and members of the co-sponsoring organizations, and $15 for students. Proceeds support graduate student research and outreach efforts at the museum. Teachers attending the course can receive a certification of professional development hours.

The UCMP hosts a short course for the general public every year; we've covered a variety of exciting topics over the past few years. Last year's UCMP short course, Darwin: the man, his science, and his legacy, was very popular, with over 300 attendees.

Join us for 2010's short course, Predicting the future of San Francisco Bay: Learning from history!

Thank you, Roy Caldwell!


UCMP Assistant Director Mark Goodwin gives Roy Caldwell a cast of a Smilodon skull as a thank you gift.

At the close of 2009, Roy Caldwell stepped down from his position as UCMP Director. Thankfully, Roy isn't going anywhere — he will continue to be a Faculty Curator at the museum and a professor in the Department of Integrative Biology. Roy became the interim director in 2005 and director in 2006. Says Roy, "Acutely aware of my lack of training and experience as a paleontologist, the most I could hope for was to be a facilitator — and hope that I didn't muck things up. Judging by the high quality research conducted in the UCMP, the excellent students who have been trained in UCMP and the success of our UCMP education and outreach programs, I think that goal was met." We at the museum agree!

To thank Roy for his years of great leadership, the UCMP held a party in his honor at the end of December. The museum gave Roy a cast of a Smilodon skull as a thank you gift.

Join us in giving Roy a round of applause!

Roy's party 5 Roy's party 4 Roy's party 3 Roy's party 6 Octopus Cake Roy's party 2 Roy is surprised Roy's party 1

Welcome Charles Marshall, new UCMP Director!

Charles Marshall

Charles Marshall on the Permian Wandrawandian Siltstone, Warden Head, Ulladulla, New South Wales, Australia. Photo: Swee Peck Quek.

Let’s give a great, big UCMP welcome to Charles Marshall — the new Director of the UCMP!  Charles recently joined the faculty of the Integrative Biology department after being on the faculty at Harvard as well as being the curator of invertebrate paleontology at Harvard’s Museum of Comparative Zoology.

"Greetings to all members and friends of UCMP," says Charles. "I am very excited to be part of UCMP and look forward to meeting you all, and in joining you as we work to make UCMP an even stronger center for paleontological research, teaching and outreach."

"I am interested in how paleontology informs our understanding of the history of life, especially the processes that control it." Charles has broad research interests, including integrating both paleontological and molecular phylogenetic data to look at speciation and extinction rates at different times in the past. A confessed math-lover, he also develops quantitative methods to compensate for the incompleteness of the fossil record; his work looks at the rapidity and timing of mass extinctions, diversification, and the calibration of molecular clocks. His research also has a strong empirical component — he has published papers on the functional morphology of diverse taxa, including fossil plants, marine invertebrates, and the fish-amphibian transition. His current research examines the synergy of tectonic processes, climate change, and changes in diversity on geologic timescales, as well as the import of new genomic data on our understanding of the Cambrian explosion.

More Charles Marshall facts:

  • Charles did his undergraduate work at the Australian National University and his Masters and Ph.D. are from the University of Chicago.
  • Charles enjoys teaching students of all levels.
  • Favorite pastime: playing soccer.
  • Charles' wife, Swee Peck Quek, is also a biologist, and is a Berkeley alum, with a B.A. in Integrative Biology. She also holds a Ph.D. in Biology from Harvard and a M.Sc. in Epidemiology from the Harvard School of Public Health. Charles and Swee Peck are expecting their first child in February.

So join us in greeting Charles, and stay tuned for continuing coverage of his work at the UCMP.

Genetics and Evolution of the Skeleton Research Initiative conference

gesriThe Genetics and Evolution of the Skeleton Research Initiative recently had its semiannual meeting in San Francisco. Organized by UCMP Faculty Curator Leslea Hlusko, the focus for this year’s meeting was Development, Diseases, and Evolution of Mineralized Tissues. Two graduate students from the Hlusko lab, Theresa Grieco and Sarah Amugongo, give us these snapshots from the conference:

Highlights from the conference, by Theresa Grieco:

The GESRI meeting draws bone biologists from all over the Bay Area — UC Berkeley, UC San Francisco, UC Davis, Stanford, and Lawrence Livermore National Lab. The speakers and attendees work in a variety of contexts, including biomed, EvoDevo, paleontology research, and veterinary/clinical research. It is great that this meeting is able to draw together a diverse group that is willing to talk across field boundaries and present their findings to the broader scientific community. We heard talks about fracture repair, bone mineralization and its changes during fossilization, osteoarthritis, tooth bioengineering, and how bones and teeth can be used to infer life history traits.

For me personally, it is a great way to meet and keep in touch with local mentors and colleagues and get fresh ideas. It’s really the best way to find out about potential resources and collaborations for research projects. It was also great to see a presentation by a biochemist or embryologist drawing questions from practicing MDs or bioengineers, and to see such different people getting excited about each other's work. One thing that I thought was interesting was that sometimes questions would be misunderstood, usually because people trained in different fields catch on to very different aspects of your research than the ones you’ve been trained to look at. Talking about these kinds of questions in a little more detail can reveal significant implications of your research in other arenas, or where the methods or data collected from another field could make your research better.

A highlight of the day was one of our plenary speakers, Dr. David Kingsley, who gave a talk about why he developed the stickleback fish as a model system for EvoDevo and a case study about pelvic reduction and hindlimb loss in these fish. Through genetic mapping, his lab identified a set of chromosome deletions in the regulatory region of a gene called Pitx1. These deletions have been selected for in many different stickleback populations around the world. These deletions only affect the molecular switch for Pitx1 expression in the hindlimb, allowing the rest of the gene’s vital functions to be preserved. He then showed us how similar phenotypes can be seen evolutionarily, with hindlimb loss and pelvic reduction in snakes, manatees, and in mice missing the Pitx1 gene. Dr. Kingsley then brought us into the clinic with case studies of club foot in humans. Wow!

A sampling of GESRI talks, by Sarah Amugongo:

Though only in its infant stages, GESRI has already become very popular among bone biologists in the Bay Area and beyond. I was astounded by the turnout, especially from the un-registered members. The range of topics covered was quite impressive: from basic bone biology, to clinical application, to evolutionary history of bone mineralization.

Here are a few of the talks that were given at the conference:

  • One talk focused on the repair of fractures. A high oxygen level was demonstrated to be very important for the healing of fractures. Interestingly, the process of fracture repair is different from the process of normal bone development in several ways. The source of bone cells is different, and the processes that regulate cell fate are different too.
  • The inverse relationship between osteoarthritis and osteoporosis was also notably interesting. With the loss of cartilage, there is an up-regulation of bone growth as demonstrated by research on osteoarthritis of the hip.
  • The growth hormones TGF-beta and IGF-1 have different signaling pathways, but both have been demonstrated to be important to the skeleton as they regulate osteoblast differentiation and proliferation. Osteoblasts are cells that are responsible for bone formation.
  • In addition to studying the extant organisms, learning that soft tissue is also preserved in the fossil record through the study of dinosaur fossils was really amazing. It made me wonder what else we’ve been missing by just focusing on bones. This might open a whole new area of research in paleo!

View the full meeting program here.

Fossils provide baseline for mammal diversity


Skull of a short-faced bear from northern California, an example of a species that went extinct after humans arrived in North America. Photo: Tony Barnosky

As more and more species go extinct, biologists wonder whether we are on the verge of the earth's sixth mass extinction.  A new study, by Marc Carrasco and Tony Barnosky of the UCMP and Russell Graham of Pennsylvania State University, uses the fossil record to examine mammal biodiversity in North America over the past 30 million years. Carrasco and his collaborators used data from two fossil databases, MioMap and Faunmap, to determine the baseline of mammal diversity before humans arrived in North America. Their results, published in the journal PLoS ONE, show that the arrival of humans 13 thousand years ago coincided with a 15 to 42% decline in mammal diversity. These data show that humans had a negative impact on mammals long before we factor in the effects of current industrialization and global climate change. Now that a pre-human baseline of North American mammal diversity has been established, we can compare current diversity to the continent's "normal" diversity level — an important comparison as we plan and evaluate conservation efforts in the future.

To learn more about Marc and Tony's study, read the paper on the journal PLoS ONE, the UC Berkeley News press release, and this article in the San Francisco Chronicle.

New dino described by UCMP alums

Field crew 2006

The field crew that excavated Tawa hallae in 2006: Kevin Padian, Sterling Nesbitt, Alan Turner, Nate Smith, Randy Irmis, Amy Balanoff, and Gabe Bever. Photo: Nathan Smith, Field Museum of Natural History

Last week, two University of California Museum of Paleontology alums, Sterling Nesbitt and Randall Irmis, described a new species of dinosaur in the journal Science. The new species, Tawa hallae, sheds light on early dinosaur evolution — and the importance of the UCMP's collections.

Tawa's bones were first found by hikers in Ghost Ranch, New Mexico, in 2004. Around that time, Sterling and Randy were doing fieldwork at the nearby Petrified Forest National Park in northern Arizona, excavating fossils from rock layers from the Late Triassic — the same rock formation where the new fossils were found. That fall, park paleontologist Alex Downs approached Sterling and Randy at a scientific meeting and asked them if they'd be interested in excavating and describing what appeared to be a novel species. At that time, Randy was a graduate student at Berkeley, and Sterling had finished his undergrad at Berkeley and begun graduate school at Columbia. They decided to collaborate with Alex to describe the specimens and made plans to start fieldwork during the summer of 2006.

"Three weeks before our first major expedition," says Sterling, "the provost at the American Museum of Natural History called and asked if I'd like to be accompanied by an NSF-funded IMAX movie crew."  They wanted to film the excavation of the fossils for a movie, Dinosaurs Alive!. Sterling was a little worried that the filming would interfere with his fieldwork, but he agreed. The film crew followed Sterling, Randy, and the rest of the team for a week and a half. Sterling needn't have worried about having enough time to do his research — there was plenty of down time. "IMAX film is expensive," he says, and the film crew spent a lot of time setting up each shot. During some of this down time, Sterling was excavating the area where the hikers had found the fossils. "That's when I hit the ankle bone of the articulated leg of what became the holotype."

Other early dinosaur fossils are not as complete or as well preserved as those of Tawa hallae. Sterling, Randy, and the team found two nearly complete skeletons, as well as bones from several other individuals. Some of the bones are so well preserved that you can see very fine details, like the places where the muscles once attached. The neck vertebrae and the bones of the braincase have small depressions with raised rims — suggesting that there were air sacs adjacent to these bones. The air sacs filled up the depressions. Modern birds have air sacs attached to their bones, which they use for respiration. As Sterling and Randy write in their paper (co-authored by Nate Smith, Alan Turner, Alex Downs, and Mark Norell), we can't know if Tawa's air sacs served a similar function. However, we do know that Tawa is the earliest dinosaur with a pneumatic skeleton.

Tawa is particularly important because it fills a gap between early carnivorous dinosaurs, found in South America (where dinosaurs are thought to have originated), and later carnivorous dinosaurs found throughout the world. Randy, Sterling, Nate, and Alan figured out where Tawa fit by comparing it to other specimens, many of which were in the UCMP's collection. "The UCMP collection was instrumental in helping us understand what was at Ghost Ranch," says Randy. Sterling also points out the importance of the museum's collections, both in this study and in his paleontological education. "I came to Berkeley for the paleo," he says. As an undergrad, "I was in the collections a couple times a week, learning anatomy, learning what the fossil record is really like."

"This project really had its genesis when we were all graduate students," says Randy. "This study speaks to what a fantastic program we have at Berkeley, that we can have such fantastic research coming out of a graduate student-led project."

Randy is now an Assistant Professor at the University of Utah, and Sterling is a post-doc at the University of Texas Austin. Both intend to continue working at Ghost Ranch — "I plan to go back for many years to come," says Randy. "It's an amazing site." And, they plan to continue working in the UCMP collections – they'll be back in January. Check the UCMP blog for an update!

Sterling and Randy are currently collaborating with UCMP graduate student Sarah Werning, Kevin Padian, Nate Smith, and Alan Turner, to examine the growth and bone histology of early dinosaurs (including Tawa) and their relatives from Ghost Ranch. Stay tuned for an upcoming blog about dinosaur bone histology in the New Year.

Sterling and Randy's work was funded by a National Geographic grant to UCMP Faculty Curator Kevin Padian and by grants from Integrative Biology, UCMP’s Welles Fund, and the UCMP Graduate Student Research Award. Learn how you can support graduate student research at the UCMP.

There has been some great news coverage about Tawa hallae. To learn more, check the National Science Foundation's Special Report: Tawa hallae – it includes an audio slide show, a press conference, and lots of photos. There is an interview with Sterling in this Science magazine podcast, and an interview with Randy in this blog from the Utah Museum of Natural History. Also check out this article from the San Francisco Chronicle.

Nesbitt and Irmis, excavating at the Hayden Quarry Ghost Ranch Carrying Tawa Stocker and Nesbitt, excavating at the Hayden Quarry Ghost Ranch research Smith and Nesbitt Field crew 2006 Field Crew 2008 Tawa jaws Tawa lower jaw Tawa hand Tawa fibulae Tawa reconstruction Tawa skeleton

Ardi is Breakthrough of the Year

Credit: Jay Matternes © 2005

Credit: Jay Matternes © 2005

Ardipithecus ramidus has been named Science magazine's Breakthrough of the Year. At 4.4 million years old, Ardi is the oldest hominid skeleton. This fall, a series of 11 papers about Ardi and her paleoenvironment were published in Science. UCMP Faculty Curator and Human Evolution Research Center (HERC) director Tim White was one of the lead scientists on the project, which involved an international team of researchers, including UCMP Faculty Curator Leslea Hlusko. To learn more about Ardi, Breakthrough of the Year, read this article in today's issue of Science, watch this video, also on Science's website, and read this article on BBC news. For more links and more info on the discovery of Ardi, visit the UCMP's previous blog post.