Day after day, over the course of nearly three years, the massive tunnel borer worked its way through the sedimentary rock layers of the Berkeley Hills during the construction of the fourth bore of the Caldecott Tunnel, grinding up the rocks in the process into fist-size pieces that were later deposited outside the entrance of the tunnel. At the end of each work day, paleontologists sifted through these piles, referred to as the day’s "spoils." They were not only on the lookout for fossils of plants and animals; each day they also collected samples of the rocks for later testing for microfossils.

These samples eventually made their way into one of the prep labs of the UC Museum of Paleontology, a room that has become my second home during the spring semester of 2013. One of my jobs as a graduate student researcher on the CalTrans project is to break down and process these rock samples to look for evidence of ancient microscopic life.

Here I am in the UCMP prep lab. In the foreground are some of the microfossil samples to be processed. Photo by Pat Holroyd.

Looking at forams
Microfossils are by definition too small to be studied with the naked eye. A group of microfossils that we are particularly interested in are the Foraminifera, commonly referred to as “forams.” These single-celled amoeboid-like organisms, which are usually about the size of a sand grain, have shells, known as “tests,” often consisting of multiple chambers, arranged in a myriad of configurations. Living specimens extend strands of protoplasm from their tests in order to “communicate” with their ambient environment. This enables benthic (bottom-dwelling) forms to crawl and the planktonic (floating) forms to remain in suspension, while providing both with a means of obtaining food. Forams are common in marine environments all over the world, and their tests are often a major component of marine sediments.

Left: Drawing of the living foram Polystomella strigillata, from John H. Finley ed. Nelson's Perpetual Loose-Leaf Encyclopaedia (vol. 5) (New York, NY: Thomas Nelson and Sons, 1917); Right: © Creative Commons, Mihai Dragos

Foram tests are important fossils because they are paleoenvironmental indicators. As the tiny fossils accumulate in marine sediments they leave records that are often continuous for long geological stretches of time. By comparing the fossils to modern species, we can infer a great deal about the temperature, ocean depth, and depositional conditions that existed at the time that the organisms were living millions of years ago.

Processing the samples
In order to separate the microfossils from the shale and mudstone matrix, we first gently disaggregate the rocks by soaking them in water and adding Calgon water softener to prevent the finer sediments from clumping. If the rocks don’t readily start to disaggregate, heat and hydrogen peroxide are added. Because the shells of forams and other creatures often contain calcium carbonate we do not use acids to break down the rocks or we will dissolve the fossils at the same time!

Left: First stages of the process; Right: Some of the rocks in this sample are already starting to break down.

Once the rocks have completely broken down, the sediment is rinsed through a sieve with 63 micron (1 micron =0.001 mm) openings to remove silt and clay. After the residue is filtered and dried, it is ready to examine for forams under the stereomicroscope.

Left: Sieving to remove the smaller silt and clay particles; Right: Filtered samples drying in the oven.

So far the process sounds pretty straightforward, but the reality of doing science doesn’t always live up to our expectations. The first batch of samples were from the Orinda Formation; these broke down readily but revealed only a few charcoal fragments. The absence of forams was not surprising, as this unit was deposited in freshwater! I am hoping the Orinda will yield some ostracodes (another kind of microfossil), but none have been observed in the material processed thus far.

I next turned my attention to the samples collected from the definitely marine Sobrante Formation. While a few forams were noted on the surface of some partially broken-down rocks, most of the rocks did not break down at all. While experimenting with some alternative treatments on these samples, including soaking them in kerosene, I have begun to process the tunnel samples of the Claremont Formation, which is stratigraphically between the younger Orinda and older Sobrante formation, and represents the final sequence of marine deposition before emergence of the sea floor.

The first batch broke down readily with our gentle treatments and, when the results were viewed under the microscope, the sediment sample contained not only tiny pieces of coalified plants but a fair number of foraminifera shells.

Left: Examining the dried residue under the stereomicroscope; Right: The view through the eyepiece. Each square in the grid is about 4 mm wide.

UCMP’s foram expert Ken Finger identified the three most common taxa as Martinotiella communis, Pyramidulina acuminata, and Lenticulina sp. Today this benthic association occurs on the continental slope, no shallower than 500 meters. Try to identify the three genera in the close up of the microscope photo on the left, below, based on the reference drawings on the right.

Read other blog posts about the Caldecott Tunnel fossils:

— Fossil neighbors, posted September 12, 2012
— The arrival of the fossils, posted October 1, 2012
— Prepping the fossils from the Caldecott Tunnel, posted May 16, 2013

All photos by Susan Tremblay except where indicated.

For the last semester I have been lucky enough to work as the GSR (graduate student researcher) for the spring semester at the UC Museum of Paleontology fossil preparation lab (prep lab) under the supervision of our new lab manager, Jason Carr.

It has been fun getting back into the preparation role, something that I did as a job after college. The material we have to work on varies a lot which keeps the work interesting. It requires a variety of techniques, so I get to do something different nearly every day.

When we started this project in the fall semester we stored dozens of boxes and stacked them high at the offsite Regatta storage facility. I have gone through enough material that now all of the boxes are in the prep lab. We are making good progress but there is so much we are still unpacking! But, it is okay because sometimes we find marvelous surprises like this nearly perfect marine snail shell (at left).

We are constantly amazed at the number of different materials that the collectors used to wrap and protect the fossils. One shark tooth was even cleverly protected in a cut-up Coke bottle! I guess you use whatever you can in the field. The majority of the fossils that I am preparing are fish bones and scales — several of the formations that the Caldecott Tunnel plunges through were marine, such as the Sobrante Formation where most of our material was found. We are also finding a variety of plants, charcoal, bones of mammals from both the ocean and the land (including tiny mammal teeth, which will be the subject of a later blog), turtles, whole oyster beds, and whole rock samples that we process for marine microfossils and shells of foraminifera. These are important fossils because they allow us to address questions of climate and stratigraphy and GSR Susan Tremblay will tell you more about the preparation of those materials in her blog.

I am using some quite different techniques than Susan since most of the fossils that I am preparing are visible with the naked eye. Most of what I am doing is surprisingly low tech! It does take a lot of practice though and a good supply of patience. Some fossils are solid enough that we can use special air-powered tools like this pneumatic air scribe.

Most of the marine mammal fossils are strong enough for this. The tools vibrate the rock though so more delicate fossils need to be stabilized with resins. I usually apply these with an eyedropper or gently brush them on like you can see here.

These techniques are simple but really important if the fossils are to last in the collections until someone wants to come examine them.

I am excited to spend this time working in the lab. I love opening a new box and getting to see firsthand some of the remains of the animals that roamed over the East Bay hills. To learn about a world that existed so long ago and was so different that it had camels and rhinos living in it and then to realize that it existed right here in the East Bay? Exhilarating! Hard to picture perhaps but every fossil we unwrap brings us a little closer to visualizing that world.

Read other blog posts about the Caldecott Tunnel fossils:

— Fossil neighbors, posted September 12, 2012
— The arrival of the fossils, posted October 1, 2012

Photos courtesy of Ashley Poust and Jason Carr

My visit to the Regatta Facility

The UCMP houses one of the largest fossil collections associated with a university in the world, so it is no wonder that some of the fossils need to be stored off-campus at the UC Regatta facility, located nearby in Richmond. This large warehouse is home to multiple campus-wide museum collections, including a variety of enormous whale skulls, huge ichthyosaur skeletons, and cyclopean bones of mammoths and dinosaurs from the Museum of Paleontology.

The Regatta facility is also the current location of the fossils that have been recovered from the 4^th bore Caldecott Tunnel project, and so I recently paid a visit. From the somewhat daunting pile of boxes, I selected several big, heavy ones labeled “vertebrates” and “invertebrates,” as well as some lighter, flat containers labeled “plants,” to take back to the UCMP in Berkeley. And the next day, I went to work.

Left: a newly-opened box of fossils from the Caldecott Tunnel 4th bore; Right: my workspace in the UCMP fossil preparation lab

Removing the lid of the first box revealed a pile of small bundles enveloped in toilet paper and neatly packed away in labeled plastic bags. After unwrapping a few of these small packages, I began to get an idea of the variety of fossils and rock samples that come from the Caldecott Tunnel. Most of the fossils I’ve seen so far are small, ranging in size from a tiny tooth several millimeters long, to some about as large as a fist. Many are broken or incomplete. But though they may not be visually impressive, they are rich in history. Not only will these fossils elucidate what the environment and climate of the East Bay was like in the middle Miocene Epoch, 9-16 million years ago, but they also provide clues about what happened to these organisms after they died. It is interesting, for example, that most of the invertebrate fossils are natural molds or ‘impressions’ in pieces of rock, while the vertebrates are preserved mainly as pieces of bones and teeth. Did they live in different habitats? Did they die in different places? How were these fossils preserved? These questions remain to be answered, and we’ll have to wait until further evidence comes in as I unpack and examine more material!

The plant fossils, however, are another story. Their preservation is quite good, and there are many leaves that can be seen very clearly, complete with anatomical details, on small slabs of rock. They are also especially interesting because they are particularly good indicators of the ancient climate of the San Francisco Bay Area, and provide a comparison of current and past geographic ranges of particular species. Watch for more on the Caldecott Tunnel fossils in future blog posts!

UCMP paleontologist Mark Goodwin examines a foot bone of an ancient camel

A drawer full of unpacked Caldecott Tunnel fossils

About once a month, I drive from Berkeley to Walnut Creek to pick up specimens for my thesis (dead birds for a study of the evolution of development in Aves), which necessitates a pass through the Caldecott Tunnel. Each time, I heave a sigh and try to shore up my patience as traffic before the tunnels slows to a stop. However, this bane has recently metamorphosed into an object of great interest, for it has come to my attention that the construction here is also uncovering of one of Earth’s most alluring treasures: fossils!

The construction workers are burrowing through rocks that are 9 to 16 million years old. Here, the hills have yielded thousands of fossils of all types of organisms, from plants, to vertebrates and invertebrates, to microfossils (very tiny plants and animals). They, in turn, provide clues to the past flora, fauna, and paleoenvironment of the Bay Area. Who knew that such a wealth of fossils could be found so nearby?

This semester, I am fortunate enough to be a Graduate Student Researcher (GSR) in the UC Museum of Paleontology (UCMP), a position funded by the California State Department of Transportation (known locally as Caltrans) as a component of a new partnership with the UCMP. The plan, in short, is for Caltrans to deposit the fossils recovered from the 4th bore Caldecott Tunnel construction project in UCMP, and for UCMP to clean, catalogue, and curate them. For further details on the UCMP/Caltrans project, please see Mark Goodwin’s article. As the GSR for this project, it will be my job to prepare the fossils by cleaning the dirt off, gluing together what is broken, and properly curating them in the museum.

Scanning the Prep Lab from left to right. Click on the image to see an enlargement.

When I was a little girl with aspirations to become a scientist and study fossils, I was a volunteer paleontologist at Anza-Borrego Desert State Park in southeastern California. It was here that I first discovered the appeal of fossil preparation, and the wonderful feeling of reward that comes after many hours of meticulous work. Thus, I am quite excited about the work that I will do over the next few months!

I’ve just completed a scrub-down and organization of the UCMP fossil preparation lab in anticipation of this work, and the boxes of fossils will be arriving soon! As I proceed, I will report on the exciting finds that come to light as each box is opened, and the tale these fossils recount about the paleontology and geology of the East Bay hills.