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Understanding Evolution and Understanding Science February updates

The UCMP's Understanding Evolution and Understanding Science websites have been updated for February with the following features:

Bay Area Field Guide: Tilden Park

I think it took us all by surprise to learn that Tilden Park contains several fossil localities and has a rich history with the UCMP. Don Savage, a former professor of paleontology and past chair of the Department of Paleontology at Cal, found a gomphothere jaw by Inspiration Point off Nimitz Way in 1961 and John C. Merriam collected the type specimen of Eucastor lecontei from deposits near Vomer Peak.

Underlying the beautiful rolling hills of the park are terrestrial deposits of the Miocene. The oldest of these deposits are the Claremont Formation containing chert and siliceous shale layers deposited 14 to 16 million years ago in a deep marine basin. Overlying this formation are the alluvial-fluvial mudstone, sandstone and conglomerate deposits of the Orinda Formation that originated from a higher, mountainous region west of the East Bay. You can see clear views of the Orinda Formation just east of the Caldecott Tunnel on Highway 24. The Moraga Formation overlies the Orinda Formation. This basaltic flow erupted from a volcano at Round Top in the Robert Sibley Volcanic Regional Preserve, just south of the Caldecott Tunnel, about 9-10 million years ago.

There are a number of lava flows visible from Highway 24, east of the Caldecott Tunnel, that are several feet thick. Many of them have a red zone or baked contact at their base where the hot lava contacted with the wet and cool alluvial deposits of the Orinda Formation, oxidizing the sediments. These volcanic deposits are resistant and now form the ridges of the Berkeley Hills and San Pablo Ridge. Some of the lava flows dammed rivers causing the formation of lakes. Deposits from these lakes formed the Siesta Formation composed of fine-grained light gray sediments. These soft rocks are easily eroded and have resulted in several landslides. Capping these deposits is another lava flow called the Bald Peak Basalt (9 million years old), visible at Vomer Peak in Tilden Park. All of these rock layers were folded due to tectonic activity. This created a large north to south plunging syncline that encompasses Tilden Park.

Photos courtesy of Nick Matzke, Tony Huynh, and Lucy Chang.

Please note that a collecting permit and official permission is required to collect, or even pick up, any vertebrate fossil or fossil fragment in any of California's State and National Parks. Other public lands, including city parks and open spaces, may have similar regulations. Best to check in with the appropriate land use office wherever your adventures take you to inquire where the best spots are to see fossils in the field and what is and is not permitted while hiking and exploring our fossil heritage in these natural preserves.

The eternal value of Natural History and the dazzling molecular promise

nescent imageThe advent of highly efficient and low cost sequencing techniques along with increased computing power have been important catalysts for the massive generation of genomic data (Davey et al., 2011). In parallel have come studies of gene expression and regulation, each of which has earned its own field such as "trancriptomics," "proteomics," "metabolomics," etc. (Zhou et al., 2011). In addition, the combination of these disciplines with ideas associated with graph theory has produced a new area of study called Systems Biology (Saito and Matsuda, 2010). Certainly in the last 30 years we have learned more than we ever imagined and unexpected avenues of research have opened. Every day the dream of deciphering the genetic identity of every living organism becomes more and more possible.

However, in the middle of the Post-Genomic Era it has become clear that we have forgotten something. That "something" is what has been fundamental to biology since its inception: Natural History. The great technical complexity, versatility and explanatory power of molecular studies have produced a shadow on the more “traditional” approaches. Some argue that the age of exploration to remote areas and the discovery of new species and detailed monographs with morphological descriptions are part of a distant and romantic past. However, we have described about 1.8 million species and there are calculations that estimate a total of 10 million without considering those present in the fossil record. Is the exercise of the natural history really an anachronistic activity?

The lack of knowledge of the species with which we share our planet is only the tip of the iceberg, because in many cases the knowledge of the biology of those already described is even more precarious. Walking through the shelves of various libraries I have found that most new books address issues associated with genetics and molecular biology, while most of those which are about anatomy or taxonomy are written in brown paper and illustrated in ink. At some point I thought the latter would look good in a museum, but now I have another opinion. Who is capable of replicating that knowledge today? How many students are being instructed in these areas today? To my relief a few names do come to mind, but it’s is a very small number.

Faced with this "molecularization" of biology, those old natural history books take a new value as the sole repository of a discipline that in many cases has not been practiced for years. So those faded pages are the only remnant we have of that knowledge. Not only are the data and descriptions in these books important, but the hypotheses and speculations have enormous value, because they are the products of an integration that emerged from someone who had an extensive knowledge of biodiversity. So despite the lack of molecular understanding these ideas have elements that only someone who has spent years in the field or amongst museum specimens is able to see.

The lack of support for the study of natural history is a critical problem that if left alone will likely reach a tipping point from which recovery would be difficult if not impossible. The lack of master-apprentice continuity in the study of a group of organisms can be fatal, because much of the taxonomic and technical knowledge is simply lost. What is the cause of this trend?

As was the case with positivism, when it was stressed that all of the sciences be quantifiable and models, today molecular biology shines with its own splendor. This glow was won by the large amount of data and the results that have been produced from it. However, it has also shaded the importance of non-molecular studies.

This can be seen not only in major research programs, but also in the training of future biologists. More than once I came to know a great deal of metabolic and genomic data for a particular organism, but had no idea how big it was. Similarly, on several occasions I have seen how the tree of life is reduced to a phylogeny of only "model organisms."

Although the molecular approach can reveal a lot of secrets, there are other secrets that molecular approaches simply cannot reveal. The over-emphasis of techniques, can reduce or even stop the investment of resources in non-molecular studies and close funding opportunities and job positions. In an extreme case, this could make taxonomists swell the lists of endangered species that only they are able to recognize.

The dazzling molecular promise is that by reducing everything to its scale, it would allow an understanding of most biological phenomena. This initially generated great enthusiasm, but it also prohibits considering the existence of unique properties at different levels of organization that are not possible to study from a simple decomposition of the whole into numerous small parts. Molecular tools have opened vast windows in understanding the phenomenon of life, but like all tools, are not able to open them all. It is important to overcome the excitement of a novelty itself and be able to assess the limitations of these powerful techniques.

The eternal value of natural history, on the other hand, relates to the fact that the questions like "What is this?," "Where does it come from?," "What does it eat?" never become outdated. The human capacity to identify and recognize the components of the natural world is the foundation of all our biological knowledge. For hundreds of years the tools of natural history have remained unchanged, and the data produced by these tools is critical for the future as well. Either deep in the forest or collecting along the coast line, whenever the naturalist finds a new organism he/she always returns to the same eternal questions ….

Darko Cotoras Ph.D.(c)
Department of Integrative Biology
University of California, Berkeley

This text will be presented in the blog contest sponsored by National Evolutionary Synthesis Center (NESCent). It is based on: “El eterno valor de la historia natural y la encandilante promesa molecular” uploaded by the author to on 08/04/2011.

Literature cited

Davey J.W., P.A. Hohenlohe, P.D. Etter, J.Q. Boone, J.M. Catchen, and M.L. Blaxter. 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics 12:499-510.

Saito K., and F. Matsuda. 2010. Metabolomics for functional genomics, systems biology, and biotechnology. Annual Review of Plant Biology 61:463–89.

Zhou Z., J. Gu, Y. Du, Y. Li, and Y. Wang. 2011. The -omics era — toward a systems-level understanding of Streptomyces. Current Genomics 12:404-416.

Cal Day 2011 Highlights!

Interested in learning more about fossils and what they can tell us about the history of life and how they inform our understanding of biodiversity and climate change?  Well you're in luck!  Just join us for Cal Day!  Every April the UCMP and the entire campus is open to the public to engage with UC Berkeley's ongoing research. Check out the events during the 2011 Cal Day in the video below and be inspired to join us next year, April 21, 2012!


A Walk Through California's National and State Parks

Wednesday, October 12, 2011, was this year's National Fossil Day and if you missed the festivities, you can still celebrate our Earth's natural history by visiting your local, national, or state parks. To learn more about fossils and the UCMP, check out the East Bay Science Cafe next Wednesday, November 2, when UCMP's Dave Lindberg will talk about "The History of Kelp Forests: Global and Local Surprises." You can also hear from UCMP graduate students, Jenna Judge and Rosemary Romero, at Discovery Days at AT&T Park on Sunday, November 6, one of the many events at this year's Bay Area Science Festival.

Who Ever Said Turtles Were Slow?

Turtles have been around for hundreds of millions of years, but it turns out most North American turtles we see today are new to the block.

Museum scientist Pat Holroyd and retired paleontologist Howard Hutchison have been exploring UCMP's vast collection of fossil turtles from Wyoming in hopes of tackling the little addressed question of how turtles and other aquatic reptiles respond to changing climates.  These fossils have managed to tell the story of several ancient takeovers back in the Eocene, about 55 million years ago.  The Eocene was when several abrupt global warming events took place - the first of which defines the start of the epoch, the Paleocene-Eocene Thermal Maximum (PETM) - and semi-tropical forests extended across the northern United States.

It turns out that with warming temperatures came a case of turtle wanderlust.  While most groups of North American animals are thought to disperse via high latitude dispersal routes (like along the Bering Land Bridge or through Greenland) to the continent they call home, some reptiles, especially turtles and lizards, also opted to disperse from the south as new corridors opened up during the PETM.  The eclectic mix of creatures in North America resulting from these long treks included pond turtles and tortoises from Asia and mud turtles and river turtles from Central America.

These foreign arrivals rapidly dominated their new environments, reminiscent of classic invasive species dynamics.  And this doesn't only happen in the PETM.  Another warming event later on in the Eocene has the same signature turnover, but with a new set of immigrants, including the ancient relatives of today's tortoises.  But while the composition of North American turtles during these times shifted dramatically in favor of the migrants, there is no sign that there were any extinctions of the locals.  They merely got shunted into relatively smaller abundances.

So it is critical to understand dispersal and dispersal routes in order to understand how the composition of a fauna changes in response to climate, stresses Pat.  It'll be interesting to see how the turtles respond to the modern age of global warming.

CAL:BLAST at Bodega Bay, June 28-29, 2011

Despite a fluke June rainstorm, grad students managed to keep spirits high during two days of field work at Bodega Bay. Just as the rain began to fall, each of the graduate students — Jenny Jacobs, Misha Leong, Joey Pakes, and Rosemary Romero — welcomed 37 elementary school teachers and took them in groups of ~10 on a preliminary tour of the Bodega Marine Reserve (BMR). This would serve as an initial orientation to the buildings and the different coastal habitats that would be their focus area for the next two days.

The name of the project is CAL:BLAST — a fun acronym for a complex title — Collaborative Approach to Learning: Bridging Language And Science Teaching — and an extraordinary project focusing on professional development for 3rd, 4th, and 5th grade teachers from Oakland Unified School District (OUSD). Our goals were to increase teachers' science content knowledge as well as their interest and confidence in science, so that in turn they would increase the amount of time spent on science in their classrooms! So when we saw the predictions for rain during our stay at Bodega, we were somewhat concerned that field science might become a "tough sell," but we soon realized that this was an amazing group of teachers, and it would take more than rain to dampen their spirits!

The teachers were presented with an overarching question: what lives in the many habitats of the Bodega reserve and how do these organisms interact with one another and their environments? — clearly a question beyond the scope of a two-day field investigation, so the focus was to have the teachers become familiar with the variety of habitats and then find smaller questions that actually could be answered within that time frame and that would help to inform the larger question.

Teachers were assigned by school and geographic region to one of four "research groups" led by a graduate student and joined by at least one additional CAL:BLAST project partner from either the Lawrence Hall of Science, the Bay Area Writing Project, OUSD, or the Berkeley Natural History Museums. Each group participated in roughly the same activities, but in different habitats of the BMR.

1. Site assessments – observing habitats at different levels
Teachers used words and/or sketches to record initial habitat observations in their field notebooks. Each team then headed in a different direction, taking note of any changes that they noticed as they moved across the landscape. Once in their new location, they discussed changes noticed and then began to observe the new habitat, often making comparisons to the first.

2. Field Research: Learning field techniques – Exploring, discovering, asking questions
Depending upon the environment, teachers learned how to use a variety of tools (bug nets, beating sticks, quadrats, etc.) with which to make collections and to learn about the biodiversity of that habitat. Returning to the lab facility, teachers were asked to reflect on all that they had explored and discovered and to list a minimum of 19 questions in their notebooks that related to their field experiences. The next challenge was to determine which of these questions were testable and which they might actually be able to investigate the next morning, given the constraints of both time and resources. By the end of the afternoon, each group had identified ~ the top 10 questions of interest to them, which they presented to the whole group.

3. Evening activities
Once checked into their rooms and with dinner consumed, there was time for whole group reflection and then meetings with grad students. Teachers identified which questions would be the focus of their explorations in the morning and with whom they would be working. For those who still had some energy left, there was a night hike or time for sketching and quiet conversation, before lights out.

A summary of Day Two
Despite the early hour for a low tide, about dozen CalBlasters enjoyed some early morning tide-pooling. Then, following breakfast, it was off to the lab and a team meeting to prepare for the investigations — strategies for gathering and recording data, equipment needed, identifying study areas, etc. With rain still falling, the teachers headed to their field sites and began their investigations. Each grad student assisted their teacher teams. All data was recorded in their notebooks, and as each team completed data collection, they headed back inside for data analysis. With a short lunch break, the final task was to prepare for the upcoming symposium in which they would be sharing their findings with their colleagues.

The 2011 CAL:BLAST Bodega Biodiversity Symposium
Each research team presented their findings to the whole group, taking ~ 5-10 minutes to share their original question/hypothesis/prediction, challenges and modifications, procedures, findings, and new questions generated. They also responded to questions from their colleagues. See a PDF summary of the poster presentations.

After a celebration of watermelon and chocolate, teachers reflected on the different parts of their scientific journeys and identified strategies for incorporating the same kinds of experiences into their classrooms. A final circle of sharing took place just as the sun came out and then teachers headed back home.

Overall summary
The CAL:BLAST project team (which included the graduate students) was more than impressed by the positive energies and the depth of science that took place. Basically within less than twelve "working" hours, the teachers (novices to biological field research) arrived, became familiar with multiple habitats, learned collecting techniques, identified a testable question of interest, prepared for the investigation, gathered and analyzed their data, and presented their findings to their peers. Not bad, not bad at all!!

All images courtesy of Caleb Cheung and Jenny Jacobs

KQED Quest features Kaitlin Maguire and Lupe the mammoth!

Considering a visit to the new mammoth exhibition at the Children’s Discovery Museum of San Jose?  UCMP graduate student Kaitlin Maguire provides a sneak preview of the exhibits in this Science on the SPOT video produced by KQED. Listen in as she discusses the 2005 mammoth discovery in San Jose and what the fossils can tell us.

UCMP's Spring Break in the Bay Area

It's a spring break tradition here at UCMP to organize a trip exploring the geology and paleontology of a particular region. In the past, students and faculty have traveled to places like Oregon and Baja. But why run off when there's so much to see in our own backyards?

In a series of trips to nearby parks, Integrative Biology graduates, undergraduates, faculty, and affiliates literally got their feet wet trekking across the product of the Bay Area's complex geologic history. From UC Berkeley's next door neighbor, Tilden Regional Park, to Mount Diablo State Park and Point Reyes National Seashore, we took an up-close and personal look at the physical processes that have shaped the local landscape and the rich paleontological record we are surrounded by everyday.

Stay tuned for future posts about the trips and the geology and fossils found in the Bay Area and enjoy some teaser photos below.

UCMP celebrates National Fossil Day!

On October 13, come celebrate the first ever National Fossil Day with UCMP!

National Fossil Day is a nation-wide event organized by the National Park Service in partnership with American Geological Institute to promote public awareness and stewardship of fossils, as well as to foster a greater appreciation of their scientific and educational values. It falls during Earth Science Week and we here at Cal have been busily preparing for the festivities!

To highlight the museum’s history of contribution to the world of fossils, we will be launching a special online exhibit: Fossils in our parklands: Examples of UCMP service and stewardship. The website will highlight fossil contributions from national and state parks to the UCMP collections and tell the story of UCMP’s pivotal role in the formation and preservation of some of these parks.

Also, October 13 will mark the release of the 2011 UCMP Fossil Treasures Calendar. Each month will feature a unique specimen from our collections, compiled by our resident scientists and complete with photographs and first-hand accounts. Proceeds will benefit the museum and, in particular, support the future of paleontological research through graduate student funding.

To learn more about National Fossil Day, including a list of participating events at locations across the country, visit the official website.