THE LAB

News Archive



The hunt for a Ph.D. thesis: Collecting Late Cretaceous plant fossils in New Mexico

May, 2014, by Dori Contreras

Field site on the distant hills (can you see the exposure?), but with modern vegetation of course! Photo by Meriel Melendrez.

Fossil palm frond (with Dori for scale). Photo by Meriel Melendrez.

Meriel and Nick preparing a collecting site. Photo by Dori Contreras.

"It ain't Mexico and it ain't new" [quoted from a postcard in a gift shop]

Armed with hammers, chisels, pry-bars, boxes of newspaper, and sunscreen, two trusty assistants (recent graduate Meriel Melendrez and current undergrad Nicolas Locatelli) and I drove from Berkeley in our 4WD extra-long SUV heading for southern New Mexico. There, we met up with paleobotanist Dr. Gary Upchurch and crew from Texas State University and geologist Dr. Greg Mack from New Mexico State University for two weeks of field work in Late Cretaceous plant localities of the Jose Creek Member. It was a bona fide tri-state expedition working on multiple projects. My interests were to set the foundation for my dissertation work on the ecological diversity of Late Cretaceous forests in warm-wet climates. For this I needed a primary study site to generate new collections and data. The trip wasn’t entirely exploratory — I was familiar with some of the localities from my undergraduate days with Dr. Upchurch, and had collected here previously. Based on this earlier work, we knew that there was an abundance of plant fossils, and preliminary studies have indicated that the fossil assemblages of the Jose Creek Member represent a subtropical-paratropical forest. That’s right, in the present day desert of New Mexico, rich in angiosperms but mixed with conifers and ferns.

Late Cretaceous plant communities often contain interesting combinations of plants that are no longer found living together under the same climatic conditions (for example palms and redwoods). That is because the Late Cretaceous represents an important transitional time, as flowering plants (angiosperms) rapidly diversified and rose to dominance in warmer climates. During this time, the typical early to mid-Mesozoic forests that were dominated by ferns and gymnosperms (conifers and other non-flowering seed plants) transitioned to the modern, angiosperm-dominated forests. This begs several questions: what were the different ecological roles of angiosperms and conifers in these forests, and did conifers and other gymnosperms serve functions that have now been replaced by angiosperms? How has the structure of plant communities in warm-wet climates changed from the Cretaceous to present, and how does this inform our understanding of the evolution of modern tropical forests? These are the questions that fueled my quest into the southwest last summer. The New Mexico sites seemed like an ideal place to start my investigations, and we ambitiously set out to do some major collecting.

In the Jose Creek Member, the best-preserved plant fossils come from beds of recrystallized volcanic ash. My initial goal was to collect quadrats from multiple volcanic ash beds, which would give an indication of the vegetation through time (because beds are not necessarily deposited at the exact same time). But things don’t always work out like you plan, and luckily this was one of those times ….

The first locality we went to had an ash bed that was known for its abundance of plant fossils and beautiful preservation. After setting up the first collecting quadrat with Meriel and Nicolas, Dr. Mack and I headed off to investigate how far we could track the exposed bed, as its lateral extent was hitherto unknown. To our amazement, we were able to track the deposit for ~1.2 km! This was an incredible revelation; here were the remains of a forest preserved in ash for quite an impressive spatial extent, which would enable the reconstruction of a plant community at a single instant in time. This was considerably more attractive for my questions than reconstructing vegetation from multiple beds comprising an unknown amount of geologic time. I adjusted plans and concentrated our efforts on this deposit alone (rather than a compilation of sites) and spent the next nine days collecting small quadrats along the length of the bed. The deposit is so rich that virtually every rock we cracked open had multiple fossil plant specimens! Consequently, almost everything we touched was wrapped in newspaper, hiked out of the field site, and brought back to the UCMP. This was no light task — thank goodness for the incredible Meriel and Nicolas! In total we collected samples from 14 sites along the exposure. These initial collections reveal a rich and laterally diverse flora, and yet are only the tip of the iceberg!

Fossil fern. Photo by Dori Contreras.

Angiosperm leaf with insect feeding damage (holes). Photo by Dori Contreras.

We headed back west with the SUV packed to the brim and riding low from the weight of the fossils; it was the maximum that could possibly be brought back. I should also mention — Cindy Looy and Ivo Duijnstee, along with some of the other Looy Lab members (Jeff, Renske, Robert) — were in New Mexico for a conference and we arranged to meet them. This was particularly fortuitous, not only for good company, but also because they took two large tubs of fossils back with them! Another two tubs went back to Texas, and made it to Berkeley later that summer. All in all, it was enough fossils to fill two double-door cases in the museum!

Of course, the field work is only the beginning and, since then, a lot of work has gone into getting these first collections organized and examined. Currently, two students (James Buckel and Negin Sarrami) and I are describing and photographing leaf morphotypes from the collections to assess the diversity of plants in the flora. A large portion probably represent unknown/undescribed species, so we differentiate ‘species’ as morphotypes based on detailed descriptions of leaf characteristics. The flora includes a diversity of herbaceous and woody ‘dicots’, monocots (e.g., palms and ginger), cycads, ferns, an abundant extinct sequoia-like conifer and several extinct conifers probably related to the Araucariaceae. Overall, it is clear that it will take several more field excursions and countless hours of lab work to understand the taxonomic and structural diversity of this amazing flora. And, of course, I am eagerly looking forward to the return trips and uncovering the treasure trove of fossils still entombed in the rock out in the desert!








California pollen taphonomy and pollen trap study in Clear Lake, California

May, 2014, Shih-Yi (Winnie) Hsiung

Pollen analysis (or palynology) has been used to study Quaternary changes in vegetation and climate in North America since the nineteenth century. Palynologists generally compare plant assemblages in spatial-time frames instead of focusing on particular plant species. These changes in plant assemblages across landscapes through time are a good indication of vegetation shifts caused by environmental changes. Besides using pollen assemblages to reconstruct parent plant communities in a particular area, certain species, which are sensitive to changes in temperature or precipitation, are of special interest. By comparing assemblages of plant communities and these indicative species through time and space, we can infer how regional flora responded to environmental changes such as changes in climate.

Before comparing these past assemblages of plant communities and inferring environmental changes, palynologists carefully consider the processes leading to pollen accumulation. Do their pollen and spore assemblages accurately reflect local or more regional vegetation? Are certain pollen types over- or underrepresented? Does the assemblage include the majority of taxa present in the local plant communities? Pollen assemblages are incorporated in sediments at the end of a long taphonomic pathway, and are affected by temporal and quantitative aspects of pollen and spore production, differential dispersal characteristics, secondary transport, and other taphonomic processes.

How could we get hints of that process throughout geologic time? Wind-pollinated assemblages are most often transported and they are usually produced in large amounts and have wider dispersal ranges. To study the taphonomic process of pollen and spores, palynologists often use surface samples to research the discrepancy between vegetation composition and pollen assemblages. Such analysis also might help to understand the taphonomic conditions in the sample area and provide a reference point for a regional paleopalynological study.

First version of a modified Olefield pollen trap (Jantz et al. 2013).

For my dissertation research, I am compiling a California pollen reference collection. Focused on the last interglacial period, I plan to reconstruct the vegetation from a relatively warm period during that time interval. My methods involve extracting pollen from core samples from Clear Lake. Clear Lake is the largest lake in California with a sedimentary record going back at least to the last interglacial period (~130 ka). The microscopic pollen grains are expected to yield important clues on the history of vegetation communities and the taphonomic process surrounding Clear Lake; data from pollen traps set in different vegetation areas in the vicinity of the lake — forests up to 2 km from the lake, or small, more distant upstream communities — will enable further analysis of modern vegetation types.

The most common pollen in Clear Lake samples is wind-pollinated, mostly pine and oak pollen. An important question is: does this pollen mainly originate from the northwestern forests, the southwestern forests, or other adjacent places? To solve this question, I started to look for appropriate types of pollen traps to collect surface samples and, with the help of my undergrads, Mary Grace Rodriguez and Rebecca Shirsat, we built some traps to position in the field. After visiting the Clear Lake area a couple of times, I positioned the first 10 pollen traps close to the lake — many thanks to Carolyn Ruttan from Lake County Water Resources who helped me obtain landowners' permits for this.

Left: Preparing to install pollen traps in Clear Lake State Park. Right: Pollen trap in the Lake County Land Trust's Rodman Preserve.

The first time doing field research is often filled with anticipation. On January 20, I left Berkeley in the early morning. I was so excited — not only because I could finally install my pollen traps, but because it would be only my second time driving through winding mountain roads! After meeting Carolyn Ruttan I set off to Clear Lake State Park, our first pollen trap site. I selected a rocky corner of the lake that had a gorgeous view. Securing this first pollen trap to the ground was a challenge, but we stabllized the base with pebbles and used a small iron wire to prevent the trap from blowing over in the wind. The next trap was easier to position, being on soft soil in Anderson Marsh. We only had to avoid picking a spot where weeds might cover the area later in the year. The Lake County Land Trust’s Rodman Preserve is another one of my research sites. The trust was formed as a non-profit organization in 1994 and it works to protect important land resources, wetlands, forests, etc., in Lake County, CA.

The Elem Indian Colony, near Clearlake Oaks on the eastern shore of Clear Lake, is my fourth research site. It is a Native American colony of Pomo, associated with the Sulphur Bank Rancheria. The residents were friendly and curious about our purpose. I am sure they will help prevent tourists from removing the trap that we placed near a power station. We then attached pollen traps to railings and floating platforms at three sites. Installation of the first 10 pollen traps was completed on this first trip; we went back two weeks later to complete the west side of the lake.

Two pollen traps attached to floating platforms.

The most serious threat to my traps is the strong winds around Clear Lake, especially on the northwest side. Strong, seasonal winds can take down deeply-rooted trees and it could damage the pollen traps. Squirrels and birds might also be a problem but hopefully, the iron wires we used will keep them safe from animals. I plan to return to Clear Lake later in the year to replace trap materials and to see what my pollen traps have collected (if the squirrels and birds have not absconded with my trap materials)!







Exploring quillwort diversity of the Sierra

April 2014, by Jeff Benca



I am pursuing studies in paleobotany to interpret how plant communities may have responded to major environmental changes in the past. My current work focuses on isoetalean lycophytes, a group of poor competitors that somehow became dominant in the aftermath of Earth’s largest mass extinction, at the end of the Paleozoic Era, 252 million years ago. I am studying what environmental conditions in the present support isoetalean-dominated plant communities. The only living representatives of this group are quillworts (Isoëtes), a genus of small, rush-like plants associated with aquatic and riparian habitats of persistent and seasonal water bodies.

Researchers have extensively studied Isoëtes’ evolutionary history, species concepts, and physiological plasticity. The life history and phytosociology of members of this genus in nature, however, is not well understood. In western North America, and notably California, several counties containing suitable habitats (e.g., highland lakes) have few documented occurrences of Isoëtes. Targeting herbarium sampling efforts in such regions would not only help fill gaps in the genus’ distribution across California, but also may set new maximum elevation limits for some species. For this reason, I went on a prospecting trip to Eldorado National Forest in September with fellow graduate students Seth Kauppinen, Adam Schneider, and colleague Susan Fawcett. During this trip, populations of Isoëtes were discovered in three lakes having no previous herbaria records. Furthermore, two of these three lakes yielded almost pure Isoëtes monocultures. During prior fieldwork in this region, Seth discovered Isoëtes in abundance in many other lakes and small pools—all of which would be new distributional records of the genus for Eldorado County.

With support from the Lawrence R. Heckard Fund, I will begin surveys of Isoëtes diversity in lakes and pools across under-represented counties in the Sierra above 2100m elevation. This summer, survey efforts will concentrate on Eldorado and Lassen Counties, which have eight and two locality records of the genus above 2100m elevation respectively in the Consortium of California Herbaria. From each site, voucher specimens will be collected, pressed, and identified (using mega- and microspore morphology) and spores extracted, preserved, and photographed for the UC and Jepson Herbaria physical and digitized collections. In addition, terrestrial and aquatic habitats will be photographed for herbaria and CalPhotos archives using standard and underwater digital cameras. With both imaged and described habitat data, I will attempt to identify common habitat characteristics of Isoëtestoday to interpret what conditions may have fostered prolonged dominance of isoetalean floras during end-Paleozoic extinction. In addition to surveying Isoëtes biology and phytosociology in the field, I am working on testing and developing repeatable cultivation and propagation techniques for the genus in laboratories, greenhouses, and outdoors. The aim of this work will be to provide a framework for researchers and ex situ conservation programs working with endangered members. I am also building a teaching and research reference collection of living voucher specimens from all localities sampled in California at the Valley Life Sciences Building.




Field notes: A trip to New Mexico

October, 2013, by Renske Kirchholtes

Why New Mexico? Like someone else put it "it ain't new and it sure ain't Mexico!" So why make the trek? To attend the Carboniferous-Permian Transition Meeting! Five members of the Looy Lab piled into a van and drove all the way from Berkeley to Albuquerque. With the enormous number of meetings and conferences being organized, why did we decide to go to this particular one?

I think there is a checklist that most people go over before they decide on which conference to attend. In random order:

Clockwise from top left: The Tehachapi wind farms. The textbook Meteor Crater in Arizona. Most interesting of all: Petrified Forest National Park. The Painted Desert. Photos by Renske Kirchholtes.

These are all things to consider. If the answers to the questions above are 'yes,' or at least positive, then the conference might be worth going to. And that is how we ended up in Albuquerque. Because the conference included two field trips on which we were hoping to collect a lot of fossils, and there were five of us going to the same conference, it made sense to drive. A nice bonus was that we got to see some cool field sites along the way.

After two days of driving we arrived in Albuquerque. The conference was held at the New Mexico Museum of Natural History and Science. The conference room itself was as boring as any other conference room, but during the breaks and the banquet we got to wander around in the museum, which was really nice. It is definitely worth a visit if you're ever in Albuquerque.

The first day of the conference was mostly about stratigraphic issues. Where is the Carboniferous-Permian boundary exactly? Do we base this on findings in Russia, China or perhaps the U.S.? There was definitely quite a bit of disagreement on that particular topic. More applied research was discussed the second day and on the third day, Wednesday, it was our turn. Cindy Looy talked about branch abscission, Robert Stevenson showed us cool movie clips of auto-rotating winged seeds, Jeff Benca discussed patterns of leaf margins and what that does and does not tell us, and I talked about phytoliths. We all got great responses. Sometimes audiences can look like they're about to go into hibernation, but not this time. They were engaged and had good questions and recommendations for all four of us.

Clockwise from top left: The Tehachapi wind farms. The textbook Meteor Crater in Arizona. Most interesting of all: Petrified Forest National Park. The Painted Desert. Photos by Renske Kirchholtes.

We also got to go on two fieldtrips. The first one was to the Kinney Brick Quarry where sediments from the Pennsylvanian, the "younger" half of the Carboniferous, crop out. The locality is considered to be a Lagerstätte, an extremely fossiliferous site with excellent preservation. On another trip, they took us east of Socorro, where the Upper Carboniferous and Lower Permian deposits are exposed along the eastern margin of the Rio Grande rift. This gave us the opportunity to collect a lot of plant fossils. We collected more than six big boxes of material. It will take a while to work our way through all of it, but that won't stop us from collecting more fossils in the meantime. Once paleobotanists are on a roll, nothing will stop them. Not even The Thing, unfortunately.









Paleobotanical Adventures Down South

Aug 2013, by Stephanie Ranks

Dr. Nadkarni gives the Plenary Address in her awesome sunlit canopy blazer, specially designed in conjunction with fashion industry professionals as a prototype for botany-inspired clothing.

Everyone (finally!) assembled Monday evening for the Paleobotanical Section Banquet. Clockwise from left: Robert Stevenson, Jeff Benca, Dori Contreras, Natalie Nagalingum, Cindy Looy, Meriel Melendrez, Ivo Duijnstee, Stephanie Ranks, and Winnie Hsiung.

Proudly showing off my pieces of flair at the BSA booth, Day 3.

When I stepped through the revolving doors of the Riverside Hilton an icy wave of air washed over me and I thought, finally I can breathe! After wandering the narrow cobbled streets of New Orleans for nearly an hour, with google maps down and no more cash for bus fare, I was completely exhausted. But I had finally arrived. I made it to the Botanical Society of America’s BOTANY 2013 conference. Unfortunately, the rest of the Looy Lab was not so lucky. While I was busy complaining about trekking through the heat and humidity, they were all stuck in Denver, Colorado, having missed their connection to New Orleans – apparently the ground crew of their flight back in San Francisco had thought it a good day to sleep in. So while they jostled for seats on other flights, I was left to explore the conference center solo. Luckily another Cal grad student, Adam Schneider, was also in attendance, so I wasn’t left completely out of my depth.

Together we went to listen to the Plenary Address, given this year by Dr. Nalini Nadkarni of the University of Utah, an expert (some would argue the expert) in tree canopy biology. Her speech reflected on the growing urgency for biologists to better communicate the relevancy of their research to non-scientists, to expand the diversity of approaches we take in order to expand the diversity of our audience. From incorporating plants into fashion and rap, to taking biology lessons into prisons, Dr. Nadkarni had done it all. And she challenged the rest of us to take up the cause, too.

The next day was the first round of presentations. Thankfully, the Looy Lab stragglers didn’t get in too late, and most were able to get some sleep before the morning sessions. All except for Jeff Benca, that is. Unable to get on the same flight as the others, he was left behind in Denver, still trying to find a way to New Orleans. In the meantime, I gave my presentation on the evolution of autorotating winged seeds and their relation to conifer tree height, which was followed up by Robert Stevenson later in the day with an exploration of autorotating seed biomechanics and the appearance of these seed types in the fossil record. Dori Contreras gave a talk on the construction of her new Cupressaceae morphological phylogeny, and how her new fossil redwood fit into it. Since Jeff was otherwise detained, his presentation was given by his former adviser, Dr. Caroline Strömberg of the University of Washington. She explained his work on analyzing the relationship between leaf margins and climate in lycopods and ferns, which garnered a good deal of interest and feedback despite Jeff’s absence. Later in the evening, Ivo Duijnstee and grad student Winnie Hsiung presented posters in the exhibition room on the morphological analyses of fossil conifers found in Texas, and the pollen analysis of sediments from Clear Lake, California, respectively.

Day two saw talks given by Meriel Melendrez and Cindy Looy. Meriel explained the relationship between changes in tree height and cuticle morphology in Sequoia sempervirens and Sequoiadendron giganteum. Cindy presented a new fossil kelp holdfast discovered in Washington, complete with a 3-D reconstruction that displayed the unique ecology of the holdfast, which included several bivalves. Later in the day there was also the Leo J. Hickey symposium on “Themes of land plant evolution,” where his former students gave presentations on the work they did in his lab over the years.

In the end, the Looy Lab managed to take home awards, too. Meriel and Jeff won TRIARCH Botanical Images awards for their beautiful photograph submissions; I won a Vernon I. Cheadle award for travel; Robert received the Maynard Moseley award for the evolutionary implications of his research; and Dori received the Isabel Cookson award for best presentation in the Paleobotanical Section

From exciting lectures and presentations of research by day, to amazing live jazz in the French Quarter by night, this was certainly a conference to remember. In our down time, we explored all the history and culture the city had to offer: grandiose plantation mansions in the Garden District, hauntingly beautiful cemeteries, and more delicious spicy seafood than any one place has the right to lay claim to. New Orleans never had a shortage of places to see or things to entertain us.


Looy Lab shenanigans at the Snug Harbor jazz bar with Dr. Scott Wing and grad Nathan Judd of the Smithsonian Institution. (Clockwise from bottom: Stephanie Ranks, Winnie Hsiung, Robert Stevenson, Meriel Melendrez, Jeff Benca, Nathan Judd, Ivo Duijnstee, and Scott Wing).

Winnie, Meriel, Robert, and Jeff trekking through the crypts of St. Louis Cemetery #1 before hopping on the plane.

Robert may have worked on that Power Point a little too hard…

And so, in spite of our rocky start, we all had an excellent time in New Orleans, and came away with plenty of memories and accolades to prove it. The Looy Lab definitely showed that Paleobotany is alive and thriving at UC Berkeley. This conference was a great success – and we’re all stoked for the next one. You know, as soon as we all recover from this last adventure.


Where Red Ferns Grow

August 2013, by Jeff Benca

Unfurling frond of Ama'u, Sadleria cyatheoides, found at the world's highest bog (the Alakai Swamp, Kauai).Lacking garish flowers, ferns seldom gain the aesthetic notoriety of flowering plants. However, members of the Hawaiian endemic fern genus Sadleria (Ama'u) may counter this trend. The extreme colors displayed in this 3-foot frond of Sadleria cyatheoides result from the presence of pigments called anthocyanins, which function as a sunblock for the plant, absorbing harmful wavelengths of ultraviolet-B radiation. However, this brilliant show does not last long, limited to the tender stages of cell division as the frond unfurls. In this image, the display draws to a close, as the earliest portions of the frond to unfurl harden and flush chartreuse green. This trait equips Sadleria for colonizing open, UV-stressed environments such as recently hardened lava flows or upland tangle-fern prairies, like this one- fringing the world’s highest bog, the Alakai Swamp of Kauai.



Beautiful Strangler

August 2013, by Meriel Melendrez

A strangler fig wrapping around its host.Even amid the teeming tropical diversity of a Costa Rican cloud forest, the strangler fig (Ficus tuerckheimii) stands out as striking and strange. It has an exclusive partnership with its pollinator, in which a wasp species spends nearly its entire life cycle within the fig. This fruit grows so abundantly it merits the title “keystone species” for all of the animals it feeds. The animals disperse the seeds high in the canopy of another tree, and the strangler fig spends the next several hundred years slowly choking its host to death (as in the picture). The cycle begins again. Bizarre natural history aside, I became interested in where these trees grow. A local observation/legend purported that they tend to grow in clusters, so off I went with GPS and camera in hand. Several weeks and miles of transect later, I compared stranger fig occurrence to a random spatial distribution. The trees did not grow significantly clustered together within the Monteverde valley. However, I observed that they did not grow above 1750m in elevation, where the “Elfin Forest” began. High winds off the mountain crest may prevent germination of the figs, or even the arrival of their tiny pollinators. A different ficus species grew on the other side of the ridge. Furthermore, I noted many strangler figs standing in pastures, spared by the ranchers’ chainsaws for their filigree beauty and function of shading cows. If pastures reverted to secondary forests, as in the 1970s, the mature stranglers would stand out among the saplings and appear “clustered” to the casual observer.



Looylab grads receive Paleontological Society MAPS Awards

May 2013, by UCMPs Lisa White

Dori (left) and Renske (right) busy at UCMP's Cal Day open house.

Renske Kirchholtes and Renske Kirchholtes will each receive awards from The Paleontological Society to support their research. Each year the Society grants Mid-America Paleontology Society (MAPS) Outstanding Research Awards to the top three student proposals received.

Renske Kirchholtes will receive a MAPS Outstanding Student Research Award to support of her research titled: Phytoliths: a novel application to answering ancient questions.

Dori Contreras will receive a MAPS Outstanding Student Research Award to support her research titled: Investigating the evolution of tropical rainforests: A functional analysis of the late Cretaceous Jose Creek Member, McRae Fm.




The Looy Lab paleo detectives: Solving the mysteries of the past and present one rock at a time

February, 2013, by Renske Kirchholtes and Dori Lynne Contreras

Synchotron at LBNL (photo from newscenter.lbl.gov).

East of the Berkeley campus, we see the beautiful, green Berkeley Hills, the golden letter "C" and a somewhat classy-looking, dome-shaped building on the Lawrence Berkeley National Laboratory campus. This houses the ALS, or Advanced Light Source. Personally, I find the name a bit silly because it doesn't seem to capture the awesomeness of this giant machine. It's like calling the Space Shuttle a Progressive Flying Tool.

The ALS is a synchrotron, a particular type of particle accelerator. The particles are sped up by a shifting magnetic field within a closed circuit. The shape of this circuit is an almost circular polygon and since the building was specifically designed for the synchrotron, the building is round. But what happens inside?

Each time when the particle beam is bent at each of the polygon's corners, light is produced — primarily ultraviolet and x-rays. The x-rays are not your ordinary dental office x-rays, but much "harder" x-rays. Unlike the relatively harmless photo at the tooth doctor, this beam would kill you before you could say "¿qué?"

But what can paleontologists and paleobotanists do with this advanced light? Hard x-rays allow us to see fossils while they are still inside the rock. This means that you don't have to crack open the rocks, clear away rock matrix and run the risk of damaging precious fossils. In some cases, the material is simply too fragile to be prepared; it would not hold up. Scanning the rock allows us to make 3D reconstructions of fossils hidden inside the rock without damaging them.

We've been scanning all kinds of really old fossils: horsetails from the Carboniferous (~300 million years ago, or Ma), kelp holdfasts from the Oligocene (~30 Ma), tiny (3 mm or ~1/8 inch) and not so tiny (7 cm or ~2¾ inch) pine cones, early land plants from the Devonian (~390 Ma), and pollen cones of extinct redwoods from the Cretaceous (~70 Ma). The size of the fossils is limited by the size of the protective shielding enclosure that keeps the scientists safe while using these lethal x-rays.

Because the cyclotron basically runs 24/7, the scanning time slots are generally 24 hours long and scanning rocks can take a while. Here's the general process that we go through for each scan:



Left: First, we select a fossil. Right: Then we mount it on a stand (improvising a la MacGyver). These and the rest of the photos are by Cindy Looy and Dori Lynne Contreras. Orienting a fossil on the stand


Next we orient the fossil on the stand just right to get the best quality scan of the target specimen (which surprisingly takes a bit of work and "expert guess-timation").


Once ready, the mount and fossil are placed in a "hutch" made of radiation shielding. Left: This is the hutch, a big container that protects everyone around from the harmful x-rays. Right: Inside the hutch there is a normal optical camera (at ~9 o'clock), the stand on which the fossil is mounted, and the x-ray detector (the big black box at the right).


To start the scanning process a number of safety procedures have to be followed, otherwise the beamline will not open. Left: The doors of the hutch have to be closed, and while an ominous alarm sounds, you have to press certain buttons to actually allow the x-ray to come into the hutch. Once it does, a red rotating emergency light comes on and the doors cannot be opened. Right: Once the sample is in the hutch we use the normal camera to focus in on the sample.


Left: As each fossil sample is different, adjustments to the settings are needed. For instance, thicker rocks generally need a higher dose of x-rays than thin ones. Right: And we are good to go! It's scanning time!


Left: Actually, there is not a whole lot of sitting about going on, because the data that the x-ray collector gathers has to be analyzed. This takes up quite a bit of time (note the ridiculous amount of caffeine) and a LOT of computing power. Luckily, the computers at Lawrence Berkeley National Lab are up to the task! Right: Then we celebrate our success!


Clear Lake Drilling Project

May 14th, 2012, by Robert Stevenson

On April 26th-May 6th, Cindy Looy lead a team of researchers on a project to core Clear Lake, CA to better understand biological adaptation to climate change as a part . You can read about the project at:









Hannah Bonner Visits the Looy Lab

Feb 11th, 2012, by UCMP

On Jan 11th, writer and illustrator Hannah Bonner visited the lab to discuss the scientific and creative processes behind her series of paleontology books for children. Read about it over at the UCMP











Devonian Liverworts and Permian Conifers

May 5, 2011, 12:07pm by Cynthia Looy

On a cold Berkeley morning late in March paleobotanist Cindy Looy and grad student Susan Tremblay hopped on a plane to Washington DC. Their goal was not to enjoy the gorgeous spring weather and peaking cherry blossoms, but instead to search for clues to the early evolution of plants in the collections of the National Museum of Natural History (NMNH). Devonian liverworts and Permian conifers were on the menu.

Pallaviciniites devonicus, described by Francis Hueber in 1961, is one of the oldest known fossil liverworts. The shale from which the fossils originated, a locality in Eastern New York, has been completely quarried and used for road repairs. Until recently the taxon was thought to exist only in the form of six type slides. However, on a previous visit to the NMNH, Devonian specialist Carol Hotton pointed Cindy to several cabinets with the original shales collected by Hueber. One of our goals was to re-examine the material.

At first glance the shales don’t seem to contain any fossils at all. But when looked at with a stereo microscope using polarized light a variety of plant fossils, including liverwort thalli, become clearly visible. A selection of this material was shipped to the UCMP, where preparations are being made to free the fossils by dissolving the matrix. P. devonicus and other Paleozoic liverwort taxa have dark cells scattered across their surfaces. These are hypothesized to be homologous to the scattered, oil body containing-cells of some extant liverworts. Susan will use morphometrics and biogeochemical information to test possible homology. This might elucidate the evolution and possible function of these mysterious organelles found only in liverworts, the sister group to the rest of the land plants.

Cin’s quest to reconstruct the early history of the Paleozoic conifers also continued. The earliest conifers are small trees with a growth habit similar to that of extant Norfolk Island Pine. They played a prominent role in the composition of plant communities in the equatorial Euramerican floral realm during the Late Carboniferous and Early Permian. Conifers generally fossilize as leaves or isolated shoots, or fragments thereof. The specimens studied were collected by Cindy and NMNH colleagues and originate from an Early Permian seed-plant-dominated flora from Texas. The presence of complete branch systems provides valuable information about the life history of the plants that produced them. New finds from New Mexico were loaned for further study at the Looylab.



On Sequoia and Metasequoia

May 2011. by Diane Erwin

What do California and China have in common? Answer: redwoods. Although the modern Dawn Redwood, Metasequoia glyptostroboides, is native to a remote region of central China, fossil species were growing in California 40 million years ago. California's State trees, the redwoods, Sequoia sempervirens and Sequoiadendron giganteum, are the tallest and most massive conifers on Earth reaching heights of 85–115 m (279–380 ft.). The Dawn Redwood is relatively smaller in stature and deciduous. Extant redwoods are "relicts" of ancestral populations that grew throughout the Northern Hemisphere since the Cretaceous. As the Cenozoic climate became cooler and drier, redwood environments changed, causing them to die out. Coast redwoods survive in California thanks in part to coastal fog. A large part of Sequoia's water uptake comes from fog drip, leaving one to wonder about the future of these trees if summer fog continues to decrease. Giant Redwoods are restricted to small groves at mid-elevations in the Sierra Nevada and grow nowhere else in the world as native populations.









Museum Nomads

September 9, 2010, 5:06 PM by Cynthia Looy and Ivo Duijnstee

For many paleobiologists summer is that part of the year during which data is gathered in its purest form: fossils. Such summers may take you in diametrically opposite directions, though. Some bring broadly boasted outdoor adventures of fieldwork. Others, however, take you deeper and deeper into the collection labyrinths in the dark bowls of natural history museums around the globe. Despite what others may let you believe - and don’t tell anyone we told you - fieldwork is often boring, tedious work, the outcome of which - if any - is generally unknown. Sometimes long after you have made it back to the lab - as is the case for most palynological expeditions - you still have no clue if the trip was successful or not.

Digging deep in museum collections, on the other hand, can be surprisingly exciting. It is like treasure hunting with the guarantee of success. Now when you tour the big museums in the world, you’re bound to run into fellow hunters. Wherever you may go, you always run in to other members of our tiny community. They are like snowbirds that tour the same limited number of Arizonian RV parks in winter. This year we realized: we’ve joined this small herd of museum nomads. Our trip this summer to the Museum für Naturkunde in former East Berlin was no exception. On the first day of our visit Harvard’s Andy Knoll gave a talk, and we saw Scotsman and paleontologist Allistair McG striding the hallways, a sight we had seen before during our stay at the Smithsonian’s NMNH.

The species that brought us to Berlin is Pleuromeia sternbergii - a 250 million year old quillwort. P. sternbergii is one of the few plant species that actually thrived during the aftermath of the end-Permian crisis, the largest mass extinction ever recorded. From the moment we heard of the plant, we were intrigued by the incredible success of this paleobotanical oddball. Word has it that the first Pleuromeia was discovered in the 1830s when - during a repair - a sandstone block fell from the Cathedral of Magdeburg and broke into pieces on the pavement (Mägdefrau, 1968). The accident revealed a piece of fossil Pleuromeia stem; nine years later first described by count Georg zu Münster as a Sigillaria species. Fortunately for us, the quarry that produced the stones that built the cathedral was known to be close to the nearby town of Bernburg. Many more important specimens have been found in the same quarry since, and that’s exactly what we were after in Berlin.

Typical Pleuromeia fossils look like a small baseball bat, often with a spirally arranged pattern of dimples on it. These are almost always sandstone casts (infillings) of decayed Pleuromeia stems. Since the decay of these lycopsid stems occurs in distinct phases - starting from the inside-outward, depending on the resilience of concentric tissue layers – virtually all remains are casts of inner stem tissues layers. Now among the many published papers on Pleuromeia sternbergii - the first ones starting in the late 1800s - there was one of by Mägdefrau (1931) that figured a rare feature: the detailed leaf scars on the outside of a Pleuromeia stem. This is crucial information for a new reconstruction we plan to make of P. sternbergii. However, for most of the 20th century this important specimen was considered lost, until someone recently rediscovered it in Berlin. So we had to see it.

While walking through the hallways of the 121 year old museum building, we stared in the face of a Brachiosaurus brancai, the largest mounted dinosaur skeleton (really, it's in the Guinness book of records), walked past a wooden closet decorated with Paleozoic sea lilies and fossil horsetails in wood carvings, and saw many nice old paleo reconstructions. A stone staircase led the way to the attic of the museum; that’s where the Mesozoic paleobotany collections are housed. The collections space is not air conditioned, and it was around 100 degrees Fahrenheit outside. Up on the attic it was quite a bit warmer, so we had to take care not to spill little streams of sweat on the fossils. Luckily, a small table fan was already performing its duty. We sat down and started browsing though three cabinets with Buntsandstein collections.

Mesozoic plant curator Barbara Mohr very modestly apologized that the collection was not very extensive, but we couldn’t believe our eyes. They turned out to have a huge number of specimens, most of which were collected in the 19th century. Many of the specimens showed important features that have never been published on. Beside the unique specimen with detailed features of the outside of the stem, we found three more specimens. There was a lot of reproductive material in the collection as well - terminal cones, isolated sporophyls and dime to quarter-sized sporangia. Moreover, a short stack of drawers contained hundreds leaf fragments. Now leaves have hardly been figured in Pleuromeia publications, so that was something we knew very little about. For two days, we felt like two little kids in a candy store, photographing as much as possible.

Overseeing this enormous collection, we realized how far off we were with our earlier whole-plant reconstruction of Pleuromeia (see fig.). Now we need to get started on a new one a.s.a.p. Of course, each illustrated reconstruction of an extinct organism or landscape is a hypothesis, and should be treated as such. However, such graphic hypotheses seem almost immune to the natural selection of other memes such as more conceptual, verbal hypotheses. That is because most ‘users’ are not so much interested in the intellectual merit of the hypothesis, but are looking for a pretty picture of an old dead thing. Therefore, falsified but pretty reconstructions have a very slow decay rate, or may even grow in importance. Thus, falsifiability - the one thing that sets scientific claims apart from most non-scientific ones - is continuously threatened by esthetics... The fact that in most reconstructions it is impossible to see the degree of accuracy of the various depicted components adds to the problem. In an ideal world all reconstructions come with an integrated disclaimer or are all just really ugly. Until then, we’d better make sure that each new reconstruction looks better than the predecessor it replaces.

Karl Mägdefrau 1934. Zur Morphologie und phylogenetischen Bedeutung der fossilen Pflanzengattung Pleuromeia. Beih. Bot. Centralbl. 48: 119-140.
Karl Mägdefrau 1968. Paläobiologie der Pflanzen. 4th edition, Fischer, Stuttgart, 549 pp.




The game of prehistoric life

April 23, 2010, 1:23 PM by Jennifer Skene

Evolve or Perish is a new board game – not from the makers of Monopoly, but from ETE, the Evolution of the Terrestrial Ecosystems Program, at the Smithsonian National Museum of Natural History. UCMP Faculty Curators Cindy Looy and Ivo Duijnstee designed the game in collaboration with illustrator Hannah Bonner. Hannah is well-known for her cartoon paleobooks "When Bugs Were Big" and "When Fish Got Feet". The three enjoy collaborating -- Hannah created the logo for Cindy's lab's web site, and she is currently consulting with her on a regular basis for her next book.

Evolve or Perish is similar to Chutes and Ladders. It begins 635 million years ago, with the first multi-celled organisms. Each square on the board represents 10 million years. On the path to the present, numerous fates await you: slip on an early animal and go back one square; land on the Cambrian Explosion and jump ahead; land on the largest extinction event the world has ever known and go back nine spaces. The game is populated by cute animals (the first four-legged animal wears a party hat!) and strange-looking plants (like Lycopods from the coal swamps of the Carboniferous). All of the beautifully drawn creatures represent real plants and animals, known from the fossil record; a taxa list helps you learn your Oxynoticeras from your Omeisaurus. As you move your game piece from the past to the present, Earth's major milestones appear along the way – you'll pass meteors, millipedes, and the rise of giant mammals. The first player to make it to the present day wins the game – but experiences a gross revelation about how some of Earth's first inhabitants inhabit us humans, too.

The game can be downloaded for free here

 



Field notes: Hunting for Paleozoic biogenic silica

March 2010 by Cindy Looy and Renske Kirchholtes

At the crack of dawn on March 5, UCMP paleobotanist Cindy Looy and prospective grad student Renske Kirchholtes hopped on the plane to Dallas. There they were met by Neil Tabor, a professor in the Department of Earth Sciences at Southern Methodist University, Tabor's van, and his post-doc Scott Myers.

Looy and Tabor are part of a research team studying the terrestrial paleoenvironmental record crossing the Permian-Triassic transition of Texas and New Mexico. Their roadtrip led them to several sections in northern Texas, including the stunningly beautiful Caprock Canyon State Park. Caprock Canyon's rust-colored sediments were deposited during the Permian and Triassic under hot climatic and oxidizing conditions. These "red-beds" are often barren of organic microfossils such as pollen and spores, but might still contain biogenic silica particles, e.g., phytoliths, that were formed in Permian and Triassic plants. The earliest results look promising, and Looy and Kirchholtes hope to describe biotic changes during this time interval using these minute plant-based silica bodies as an alternative to conventional organic plant fossils.

 

The Origin and Evolution of Conifers

Workshop at The Jepson Herbarium and University of California, Berkeley (co-sponsored by University of California Museum of Paleontology)

February 6, 2010 by Diane Erwin, Cindy Looy, and Lenny Kouwenberg

Conifers represent one of the four major groups of gymnosperms that contribute to today's vegetation and flora, and California alone is home to about 10% of all conifer taxa in the world. Our State natives include the world's tallest (Coast Redwood), most massive (Giant Sequoia), and longest-lived (Bristlecone Pine) conifer trees. Studies using molecular analyses have added significantly to understanding the evolution and phylogeny of this group. However, only from the fossil record can we gain a fuller understanding of the conifers' origins, deeper evolutionary history, and the morphological and ecological diversification that members of this group have undergone over hundreds of millions of years. Conifers and their gymnosperm relatives started their rise during the late Paleozoic more than 300 million years ago and were a major component of the vegetation during the Mesozoic (252-66 mya). Some gymnosperms have remained virtually unchanged since this time and are considered living fossils: Ginkgo, Dawn Redwood (Metasequoia), and Wollemi Pine (Wollemia nobilis).

In this workshop, we will trace the origin, evolution, and diversification of conifers through geologic time addressing such questions as: What does the fossil record tell us about the origin of the earliest gymnosperms and conifer-like trees? When and where do we see the appearance of modern conifer families? What do comparative studies of fossil and modern conifer ecology and physiology tell us about the presence and distribution of conifers in the past and the present? In addition to lectures and discussion, lab set-ups with fossil and modern conifer representatives will help participants gain a better appreciation of this fascinating group of plants.