The waves of the beach pound against the sand...
posted August 08, 2014
The waves of the beach pound against the sand, and me and my fellow interns hug the walls of the cliff to avoid getting wet. As the waves come perilously close to my feet, I look at the rocks below me, and they are chock full of fossils: bivalves, molluscs, and other shelled marine organisms. It's a jumble of shells and every single one is incredibly detailed and rich.
The face of the cliff is also covered in similar fossils, and mossy green algae drips over the sides of the cliff as we walk along the sides. It's really quite a sight to behold (and I'm miffed that I didn't get a picture of it). Afterward, we also collected samples of water and sand from the sea to catch some small crabs and invertebrates to look at in the sand.Back at the lab, we dissected them and looked at many of the small organisms in the microscope as well.
The field trip doesn't end there, of course. After the visit to the San Gregorio Beach, we headed over to Bean Hollow, where we went tidepooling. At tidepooling, we saw all sorts of limpets, kelp, and hermit crabs. The tide was so low, and it was enjoyable to watch the water slowly rise through the surge channels. There were also lots of cute arthropods to be seen at the beach as well!
The beginning of the end of the internship began with the trip to the beach, the last field trip that we would have. The last few weeks have been a fitting end to the overall experience. It was absolutely one of the most unique summers I have had. By the end, we stopped measuring ostracod books to work feverishly on our projects, hoping to finish them early to avoid a last minute crunch. Figures were made in R over and over, and red text appeared over and over on our screens to show our errors.
My research project, that I did while working with Sean, involved using stochastic models and probability distributions to model ostracod size evolution. The complex diversity in size of all living organisms is astonishing, ranging from a basketball to the size of Pluto, according to metaphor by Professor John Payne. In ostracods, we found that it has ranged a similarly huge magnitude, almost 6-7 orders of magnitude.
In the end, our project was very interesting and took hundreds of lines of coding in R, which seems to have been a consistent struggle throughout our internship. Our final graph is below. We made two models to graph our data, an average unbiased model and a biased model to simulate to test our hypothesis on ostracod evolution.
We were able to model the size decrease accurately There is a more rapid decrease starting in the very beginning, signalling a more complex trend than what we attempted to model and definitely indicates a more complex trend, which could be a great start for our next research projects.
All of the other research projects at our poster session and in the presentations were all great, each having very detailed and careful hypotheses and observations. I could tell that all of my fellow interns had worked hard throughout the summer working on their projects, and also presenting it at the end. I am proud that I was able to work wih such bright students and I am already looking forward to a reunion at AGU. Until next time then...
I walk into the front of the University of California Museum of Paleontology...
posted July 22, 2014
I walk into the front of the University of California Museum of Paleontology at Berkeley, and I'm met with an enormous Tyrannosaur standing in the lobby, cute stubby arms and all. Overhead, a pterodactyl hangs form the third floor. As the director of the museum, Dr. White, comes out to greet us, all of the interns are too grabbing pictures with the T. rex, getting into every possible permutation for a photo. But the dinosaurs are just the lookers; and I was soon to learn that the real juicy fossils are much smaller, and hidden away in dusty collections. As Dr. White gives us a private tour UC Berkeley's extensive collection, one that boasts millions and millions of fossils, I'm shocked at the incredible size of the place. All of the shelves are huge, reaching to the ceiling and are on giant wheels to save space. What's inside is even more amazing.
Many more fossils are to be found: giant sabertooth cats from the La Brea tarpits, huge alligators, but the hallways are so packed with people it's hard to get a good picture.
All in all, our last two weeks have been hectic and fierce, with presentations and field trips back to back. There's no time for rest in the work of a paleobiologists. When I thought that my life would be in the lab, working with heaps and heaps of ostracods, I didn't know how wrong I was.
After the trip to the museum, we head to the football stadium at Cal. The mission? To discover evidence of the Hayward Fault, not to watch a game. To imagine that a fault runs right under the noses of thousands of spectators is quite awe-inspriing. The stadium is large and majestic, like many other stadiums, but something's different on the southwest end of the elliptical stadium: a large crack in the stone masonry. When I look below at the rows of seats below me, I can see they've been displaced by a slight amount. The stadium was built in 1923, and from the cracks, it has been displaced by maybe about 3 or 4 inches in that time. In a couple hundred more years, if football is still around to be played, the oval of the stadium will have been bisected by almost a foot on either side.
Afterwards we take a short trip to see a riverbed that has been intersected by the fault. The creek has run dry, a sad example of California's drought, but at least we don't get our feet wet. The river runs in one direction, then abruptly makes a 90 degree turn for about 5 feet, before turning again back in its original direction: a clear-cut case of a fault.
After the field trip, things get interesting back at the lab as well. We did research and gave presentations on many important marine organisms that were preserved in the fossil record, from brachiopods to bivalves. Our group the inarticulate brachiopods; brachiopods with a large fleshy hinge and tail, with a complex muscle system. The articulate ones instead have a simple toothed higne and look more like clams. The most famous inarticulate brachiopod is Lingula, a very cute brachiopod with a long pedicle that is used to burrow into the sand, still alive today.
Noel even taught us a cool way to distinguish bivalves nad brachiopods, sometimes easily confused at first sight. Brachiopods have their bilateral symmetry running left to right, like humans, where our left and right halves are mirror images of each other. Bivalves, like clams on the other hand, have a symmetry that does up and down, that is, each shell half is exactly the same as the other. If your waist was the plane of symmetry, that would be like you had a torso and another head on the bottom instead of a pair of legs. Very fun to conceptualize, I think.
Not long after, we embarked on our camping trip to the Pinnacles. The ride there was a non-eventful three hour drive, punctuated by card games, radio pop songs, and conversations. I remember sitting in family cars and being incredibly bored, but somehow this one was different. When I got to the field, the skies overhead were cloudy, a great relief. Supposedly, the temperatures were to range up to the high nineties on a regular day out here in the Salinas, but it looks as if we had lucked out.We first began on our geology hike, grabbing a look at the beautiful volcanic formations of the park. The Pinnacles park was created by volcanoes from the past. Below is a banded rhyolite from the slopes of the trail as we were descending.
After the five mile hike, we settled down for a nice dinner of fajitas and spaghetti, even with some pre-baked smores courtesy of Noel. Fires are banned in the Pinnacles due to extreme fire risk, so we couldn't make our own.The next day, after a good sleep with the crickets chirping loudly, we awoke to leave early to make it over to find some good quality fossils. We headed for the Monterey formation, to find some bivalve and mollusc fossils along with some fabled crab fossils! We headed off of a dusty country road to find many bivalves on an outcrop near a winery.
The fossils were amazing, the outcrop was very steep and I remember people clamoring with rock hammers to beat the fossils out of the rock. I stayed down there in the float to grab all the fossils that my more intrepid interns missed, and I wasn't disappointed. Aside from the ocasional rockslide from feet above, we managed to abscond with a whole box of bivalves!Next were the crabs which took ages to find. We paced back and forth along the road trying to match up the picture given to us. I remember navigating with three bumpy hills in the distance and a hill on the left side. The walkie-talkies were abuzz with chatter, and we spent almost 30 minutes doubling back and forth. We eventually found the outcrop though, and the crabs were amazing:
With fossils safely in hand, we traveled back to base to identify with our hand lenses and a couple of databases. It was extremely fun, comparing the symmetry and morphologies of our clams. While some groups lucked out and only had one species of crab to identify, our bivalves had about 4 different species. But in the end, we got to enter our fossils into Stanford's collection! The thought that our hard work will be seen by future students is a really interesting thought.
After a long series of trips, we all breathed a sigh of exhaustion. In all of our times off, we had also been measuring ostracods nonstop and even coming up with our own project proposals. The remainder of our week was spent quietly, with Excel, R, and statistics. The dichotomy of quiet work in an air conditioned room, and the punishing heat of the Central Valley lets one really appreciate the diversity of California weather. Hours spent in front of a command-line terminal had never been so fun and relaxing until after days of long field trips.
posted July 01, 2014
Flying over San Francisco from a bird's eye view, everything looks normal, with the Golden Gate and tall skyscrapers standing out the in skyline. With a click of a button, suddenly entire swaths of neighborhoods have been reclaimed by the San Francisco Bay. Suddenly, with the click of a button, the sea dramatically rises and entire neighborhoods are swept under the San Francisco Bay. In some places, all that remains are the roofs of buildings and a couple of treetops. As Google Earth takes us through an aerial tour from Pier 39 to the Golden Gate Bridge, everything seems devastated.
Fortunately, it was just a simulation. Using GIS software like Google Earth, me and my fellow interns were able simulate sea level rise due to global, without all the catastrophic circumstances of course. We also used the mapping software to draw landmarks and polygons on the surface of the earth and also created our own elevation profiles. I had many amazing discoveries about technologies and things that were all around me that I had never realized before. I saw the earth and geography in a whole new way. Our experiences with GIS were eye-opening and uniquely different from our high school science curriculum.
Of course, this was just one event in our great experiences in the paleobiology lab here at Stanford. Currently, our main project in our lab is to explore the evolutionary relationships between animal body size throughout time in marine ostracods. We spend at most maybe two hours a day collecting data, which sounds tedious at first but quickly becomes enjoyable as we talk and pass the hours away. Most of our time is actually spent on fascinating lessons and hands-on tutorials in a variety of subjects from learning about R, a programming language for high level statistics, to actually handling a whole range of fossilized marine invertebrates different from the ones we have been measuring in the lab. R can produce very powerful plots and graphs with such extremely simple commands, and with a very intuitive interface, I was able to make beautiful histograms and plots within just half an hour of starting.
In addition, I have explored many different kinds of unique fossils, ranging from trilobites to bryozoans and even some cool brachiopods. I'm always amazed at the rich detail of some of the fossils, and I almost everyday I find myself a pleasant surprise:
Next to a brilliantly fossilized trilobite is a plant-like fossil, with a beautiful imprint seemingly imprinted on the rock. Noel, our supervisor, with a wry smile on his face announced that it actually was not a fossil! Instead the marks were from mineral rich water, likely with iron percolating through the rock and leaving the indentation. The beautiful pattern resembled a plant so much that it was difficult to believe. Questions flurried through my mind: could it be that plants grow in a similar way to water seeping through a rock? Having my mind on so many statistical regressions done throughout the week, I began to wonder in my mind if the complicated mechanics of plant growth could be related to a such a simple model. Even things that aren't fossils are still fascinating as well, what a shocker! :)
So far, we're only about a week and a half into the internship. With over a month left, I can't wait to see how the rest of this evolves. So far, we've made and presented presentations in front of the entire lab and also had various hands on activities and meetings with other postdocs and grad students working in the lab for the summer. The downtime and perks are really worth it as well; we even got to watch the Germany v. US World Cup game displayed on the huge projector, which definitely puts any home television to shame. There's never any monotony in our schedule, and we're always doing something new that provides plenty of opportunities to be immersed and absorbed. Tomorrow is the day of our first field trip to UC Berkeley and the Hayward fault, and I am so excited to finally be exploring real geology out in the field. I can't wait to tell you guys all about it later!!