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Archive for March 2010

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.

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Highlights from Understanding Evolution


Map and photos: Tom Devitt

Ring species are often touted as examples of speciation in action — and the Ensatina salamander, which forms a ring around California's Central Valley, is a classic example. Biologists discovered this ring species back in the 1950s, and investigations of Ensatina continue today. Learn more about Ensatina in this research profile of biologist Tom Devitt, on the UCMP's Understanding Evolution website. Tom is a graduate student in Integrative Biology here at UC Berkeley. The profile follows him from the field to the lab, from studying the morphology to investigating the molecules. Tom even does some exciting experiments on Ensatina mating behavior — be sure to check out this research profile!

Creatures from the black lagoon

Lake Merritt

Lake Merritt, Oakland, California.

Very little was known about wetland ecology back in 1869, when Samuel Merritt dammed a former tidal slough and began developing its surrounding wetland as his "Jewel of Oakland." By restricting the flow of waters in and out of the newly created tidal lagoon, a.k.a. Lake Merritt, silt and algae were allowed to accumulate and within a few years the lake had become a bit of an environmental disaster. Nevertheless, part of it was designated by Teddy Roosevelt as our nation's first wildlife refuge, protecting more than 90 species of migrating waterfowl. Lake Merritt serves as a drainage basin for the regional flood control system, receiving urban runoff from a 4,650-acre watershed through 60 storm drain outfalls. Four creeks drain into this 145-acre lagoon from the east, while tidegates regulate flow to the south through a narrow channel that connects it with Oakland Inner Harbor and San Francisco Bay. The lagoon is also polluted by illegal dumping of substances such as paints, solvents, and oil, which are highly toxic to marine life. In addition to mechanical harvesting of its widgeon grass, 1,000 to 7,000 pounds of trash are removed from the lagoon every month. Merritt’s short-lived dream as a spectacular swimming hole in downtown Oakland is, in reality, more accurately described as a very large recreational sewer.

Despite all of its tarnish, the Jewel of Oakland has been a haven for some organisms that thrive on an abundant supply of bacteria and algae and tolerate the tidal, seasonal, and anthropogenic changes of this stressed environment. Among them are a few species of microscopic foraminifera (think of sand-sized shelled amoebas) that are being monitored by Ken Finger, Jere Lipps, and Dawn Peterson. Recent studies have shown that foraminifera might be useful environmental indicators of pollution. Lake Merritt presents an opportunity to study how they will respond to the remediation measures planned by the City of Oakland. Currently, only the shoreline of the lake supports living populations of foraminifera, while the deeper lake bottom is a dead zone of black mud stinking of methane. Why is that, you ask? Well, all of the algae, widgeon grass, bird droppings, and other organic waste that escapes harvest sinks to the bottom, and the process of their bacterial decomposition depletes the dissolved oxygen in the stagnant water just above. In contrast, wind-driven circulation keeps the surface waters and shallow margins circulating and aerated, enabling fish, invertebrates, plants, and foraminifera to survive.

But the foraminifera have a higher coincidence of malformed shells in Lake Merritt than in San Francisco Bay, which could be related to their stressed environment, where temperature, salinity, and oxygen levels change regularly. Studies elsewhere suggest that these micro-mutants result from high levels of contaminants, heavy metals, industrial pollution, and domestic sewage. In 2002, Oakland passed a bond measure that will clean up and improve the health of the lake by increasing tidal flow and installing aeration units. With these changes, will the shell deformities become less severe or more infrequent? Will living foraminifera begin to colonize the deeper parts of the lake? We hope to answer these and other intriguing questions as we continue to collect and analyze these minute “creatures from the black lagoon.”

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Fossils found fortuitously

Whale Excavation INot all fossils are discovered by paleontologists combing the earth on special expeditions. Many fossils are found by accident — particularly during construction projects. Impressive fossils, like whales, mammoths, and sloths, have been found while digging foundations for buildings, leveling land for highways, and excavating subway tunnels. This spring, the UCMP blog will take you on a tour of Bay Area construction sites, past and present, to show you some of the fossils underfoot in the region.

This week, Dave Haasl, a former Museum Scientist at the UCMP, tells us about his work with PaleoResource Consultants, a consulting firm that performs what is known as mitigation paleontology. If fossils are found on public lands during construction, the law requires that they be preserved. The fossils need to be excavated quickly, so that construction can carry on. And, the fossils need to be excavated by trained paleontologists, so they are properly preserved for future scientific study. This is a job for mitigation paleontologists! As Dave explains, "we need to mitigate the impact [of construction] to scientifically important resources. This includes fossils, as well as archaeological specimens."

There are two parts to mitigation paleontology. First, the paleontologists do pre-construction field surveys. "We look at the stratigraphy of the area, and plot the potential fossil localities," says Dave. Then, when those areas are dug up, workers know to be on the lookout for fossils. The second part of paleo mitigation is monitoring, which occurs throughout a construction project. Construction workers may not recognize fossils when they come across them, so it's important to have a trained paleontologist on site. If fossils are found, the monitors halt construction and quickly excavate the fossils. They call in a network of paleontologists, and typically they are able to excavate the fossils within a few days.

Recently, two marine mammal skeletons, a whale and a dolphin, were found during the construction of a sea wall along the California coastline. Santa Cruz County is building a sea wall between Santa Cruz and Capitola, to protect the cliffs and buildings from large waves. However, the sea wall will block access to that section of the coastline, preventing any future paleontological exploration of the area. Paleontologists were asked to survey the area before the wall was built, to see if any fossils were present.

An amateur paleontologist had seen vertebrae protruding from the sandstone — these vertebrae belonged to a small whale that lived in the late Miocene, about 5 million years ago. PaleoResource Consultants excavated the specimen, wrapped it in plaster to protect it during transport, and brought it back to their offices in Auburn, California, where it is now being prepared.

A second skeleton, a dolphin, was found by Robert Boessenecker, a graduate student at Montana State University studying marine vertebrate fossils in California. The dolphin, now extinct, is also from the late Miocene, and is related to the Chinese river dolphin. "Marine mammals were much more diverse at that time," says Dave.

While Dave's career path as a paleo mitigation consultant may seem unusual, there is a real need for trained paleontologists in this field. "There is more paleo work in the West than paleontologists who can do it," he says. "Often, archaeologists do the work, because paleontologists are not available." And this work is important. As a result of big construction projects, fossil material is collected that otherwise would still be in the ground. These specimens are then used in scientific research. Says Dave, "This is our historic heritage. If it's destroyed or sealed off, we're losing something of potential scientific value. Yeah, we need roads, we need power plants. But we're going to try to preserve as much of our past as we can."

Learn more about fossils found during construction projects in upcoming blogs!

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