Anatomical drawings, Avizo, and surface scanning – Pre Panama thoughts

I spent a few days getting some anatomical drawings done. They’re not my first. I have a long history in art. I started learning from my first art teacher, my mom, when I was about 5. Growing up, I’d get in trouble in my art classes for doing my own concepts instead of my assigned drawings. In high school, I was accepted to the Cooper Union Saturday art program, an intense all day drawing regiment, open to New York City high school students, which pushed my artwork to new levels and taught me how to systematically improve my artwork. My senior year I won an entrepreneurship contest and was awarded start up money and a space in the high school’s mini mall to start a small custom art business that I’ve maintained in one form or another over the years, teaching myself to use airbrush, Photoshop, and ZBrush along the way. While at the American Museum of Natural History working on a skull of one of my favorite groups of dinosaurs, ankylosaurs, I became obsessed with reconstructing what I envisioned that animal to look like alive. It took a lot of work, but I successfully completed my reconstruction of the Mongolian armored dinosaur, Minotaurasaurus (recently synonymized with Tarchia) which I was happy to include in my SVP presentation on that specimen.

Illustration of turtle skull I am doing research on (Left lateral including actual photograph background, contours (black), sutures with labels (red), and possible reconstruction of missing elements (blue) by author

Illustration of turtle skull I am doing research on (Left lateral including actual photograph background, contours (black), sutures with labels (red), and possible reconstruction of missing elements (blue) by author

So this week, in an effort to solidify my knowledge of turtle anatomy, I decided to draw a series of scientific illustrations of the fossil skull I am working on, with successive layers of added information baked in. One layer that included the contour line drawing of the skull based on a picture, one including a map of the sutures of the skull, another including the labels of all the bones of the skull and another with a reconstruction that included the missing cranial elements as compared to a modern skull.

Camila Gutierrez teaches Andrea DeRenzis how to use the surface scanner during our intro meeting

Camila Gutierrez teaches Andrea DeRenzis how to use the surface scanner during our intro meeting

I also got to put my interest in art and technology to work making 3d images of fossils. We are using 2 very different approaches. One uses CT images of the fossil and the other pictures and lasers to generate 3 dimensional images. CT scanning involves taking serial scans through a subject. These images are then taken and, through a series of steps on the computer, joined slice by slice to reconstitute the image of the original object. Surface scanning involves taking pictures of a rotated object and, using a laser to judge distance, stitching the pictures together to get a 3d representation of the contour of the material. Because of the limits of these techniques there are advantages and disadvantages associated with both. Either way it’s still pretty cool being able to create and manipulate a digital replica of your specimen. Trying to troubleshoot some of our work has led to some really interesting discoveries as to what we are and aren’t able to do with the approaches and I’m very interested in finding possible ways around some of these limitations.

While all that is going on, we prepare for our field trip to Panama. We’re off this weekend and eager to play in the dirt. I’m not looking forward to the heat and humidity we will surely encounter but the prospect of finding some great fossils in such a historic location in another country makes it all worth it. The energy here is excited with everyone anxious for the trip. A full account to be provided when we return. 

Fossil Friday 2/27/15: An echinoid

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UF 240747, the test of Encope sp. (Photo © IVP FLMNH)

For this last Friday of February we have a fossil echinoid, Encope sp. Echinoids (Class Echinoidea) belong to the Phylum Echinodermata, which includes starfish, sand dollars, and sea lilies. Echinoids have a skeleton made up of tightly interlocking plates called a test and fall into two categories: regular and irregular. This echinoid is an irregular echinoid because it is bilaterally symmetrical instead of radially symmetrical. You can tell because you can “fold” one side of the specimen over the other along the axis of symmetry and both sides look identical. Irregular echinoids burrow into the surface of the sediment to collect food.

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A modern Encope perspectiva from Panama. (Photo © Simon Coppard, from Echinoids of Panama)

To read more about echinoid diversity in Panama, click here to download and read a chapter on echinoderm diversity in Panama from the book Echinoderm Research and Diversity in Latin America. To find out more about modern echinoderms from Panama, check out this website: http://echinoderms.lifedesks.org/.

References:

Coppard, S. E. (2010). The Echinoderms of Panama. Accessed online at http://echinoderms.lifedesks.org/ on Feb. 16, 2015.

Waggoner, B. (2001). Introduction to the Echinoidea. Accessed online at http://www.ucmp.berkeley.edu/echinodermata/echinoidea.html on Feb. 16, 2015.

Fossil Seeds Found At Empire Locality

Empire: a canal locality we had never been to before. Ongoing construction related to the canal expansion has recreated whatever was there before and exposed fresh outcrop, so in a way it was a new locality even for Jorge. We had brought with us two STRI scientist guests, Juan and Florence, who wanted to see our sites, and upon arrival everyone set about scrambling over the rocks, trying to interpret what we saw.

Checking out a well-preserved leaf fossil at the Empire locality.

Checking out a well-preserved leaf fossil at the Empire locality.

Strange concretion pavement we were unable to explain

Strange concretion pavement

There was a pavement of strange concretion-looking things, a bed of mollusks, a leaf imprint in fine dark shale… it was like a paleontologist’s playground. We ran into two other geologists there, a Brazilian and a Panamanian, bringing our count of represented countries to six (Juan is from San Salvador and Florence from France). As we moved closer to the canal the section became even more scrambled, with faults every few meters producing stratigraphic chaos.

Wandering around the mess I noticed a block of light orange sandstone, hard and coarse and truncated at either end so it was only about 2-3 m long. Below it were what looked like logs that had turned to lignite (low-grade coal). Picking them up, however, I found them to be much heavier and less crumbly than lignite we’ve seen elsewhere around here, probably due to permineralization, in which minerals fill in the cavities in an organic form (think petrified wood).

Two fossil seeds discovered in the orange sandstone

Two fossil seeds discovered in the orange sandstone

We followed these stone trunks, branches and stems along the layer and discovered two whole, round, unsquashed seeds approximately 2 cm in diameter encased in the sandstone. Our paleobotanist friends tell us that seeds are particularly useful in identifying fossil plants, so we knew they would be happy to see these. An exciting find!

To finish off our morning in the field we drove up to the top of Cerro Zion and looked down at the ships passing under Centenario Bridge. It’s one of those views that make you feel small, especially when you start to think of the lives that were  poured into building the canal, the slowness with which the isthmus formed, or the incalculable number of fossils still out there waiting for us.

-Sophie

Adam, Florence, Jorge and Juan atop Cerro Zion, overlooking the canal and Centenario Bridge

Adam, Florence, Jorge and Juan atop Cerro Zion, overlooking the canal and Centenario Bridge

Paleobotanist life for me

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These past few days in the prep lab I have been reconstructing the shell of a turtle known as Pleurodira sp. It has been very exciting to see the form of the shell after all the little pieces have been glued back together. I have also been working on my research, sketching the vein characters of my leaves for easy identification. Some of the specimens are so well preserved that it seems as if a modern leaf had been glued to the rock! And the detail of the veins under the microscope leaves me speechless! Every day that passes I become more amazed with my findings.IMG_20150204_164131691

After a week of knowing my project, the paleobotany department was going to renew the student research exhibit, and I was asked to construct a poster on my research. I only had a few days to put my poster together, so I had to work fast, and last Friday it finally became part of the exhibit. In my poster I briefly explain the depositional history of the formation and describe the different morphotypes that were found in the collection (A digital copy of my poster will soon be available at this site www.flmnh.ufl.edu/research/student_poster.htm).

I am also excited for the upcoming trip to Panama, last Monday we had a meeting about the trip and learned that new fossilized leaves were discovered! I can’t wait to see them and compare them to the leaves form Tennessee.

Heavy Lifting and a Productive Week

¡Hola!

This has been an incredibly exciting week for us out here in the field. Yesterday, we went to the Las Cascadas formation to collect sediment for washing and sieving. The quarry had been disappointing us recently, so we were just making a quick stop before we headed on to another locality. As we were showing a guest around the site, I had some free time and I began to poke around in the sediment. Almost immediately, I found a canine. Then another. I called over our supervisor Jorge Moreno so that he could take a look. Over the next few hours, the five of us uncovered more and more – a tooth here, some bone there – and by the time we were done, we had extracted what we believe to be the jaw of a camel! I’m waiting for some photos and conducting some additional research, but I promise I will post more about this soon!

Mystery bone! Just the tip is sticking out... We're in the process of carefully removing the surrounding rock.

Mystery bone! Just the tip is sticking out… We’re in the process of carefully removing the surrounding rock.

Today, our good luck followed us to the Centenario locality. Shortly after Jeremy and Sophie set about extracting the turtle carapaces they has discovered earlier this week, Jeremy uncovered a big chunk of shining black bone. We began our speculation… It seemed lodged in, like it continued for a bit into the matrix. Were we seeing an epiphysis (end) of a long bone? Could it be a crocodile quadrate (said Jorge)? We had to see more.

This conglomeratic layer had been good to us recently, so we decided to give it a good cleaning. With our machetes, shovels, hammers, and pickaxes, we chopped through and uprooted elephant grass before digging out sediment and exposing a horizontal bench above our find. “Opening the quarry” allows us to work from the top down, increasing access to this productive layer and making it easier to remove sediment without damaging our fossils. Check out the before and after pictures of our quarry below! Tomorrow, we’ll go back to Centenario and continue excavating the cluster of bone that we uncovered today. More updates to come!

– Adam

Sediment and invasive elephant grass were covering a particularly productive layer.

BEFORE: Sediment and invasive elephant grass were covering a particularly productive layer.

After much digging, shoveling, and sweeping, we now have a clean bench that we can cut down into in our search for fossils.

After much digging, shoveling, and sweeping, we now have a clean bench that we can cut down into in our search for fossils.

3D scanning, Avizo, and more!

Lately Justy and I have been spending a lot of time working with the computer program Avizo in order to process CT scans into 3D images. We recently worked on horse teeth and are now currently working on shark teeth. The process is time consuming, but the results are definitely worth it. We are especially excited because the images will be widely accessible and will be used as learning tools in classrooms for younger students. Below is an example of what Avizo looks like as you are working on an image.

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Last week Justy and I were given a lesson on using a 3D scanner to create 3D images of fossils. The 3D scanner uses lasers, a camera, and a rotating base, in order to create the digital image. This was extremely fun to use and the lesson was really interesting. I am excited because know I will make use of these newly learned skills in graduate school.

I have also continued working in the Fossil Prep Lab. Lately I have been working on a very complete turtle neural (backbone) as well as some other indeterminate material. Working on indeterminate material is fun because once you clean it you may be able to determine what it is. It’s a fun surprise.

The biggest news is that we will be heading to Panama on Saturday! We are going to meet the field interns and participate in fieldwork for a week. I’m incredibly excited for the trip and can’t wait to share our adventures once we return!

Fossil Friday 2/20/15: A bear dog

Cynelos sp.- left mandible

UF 273000, the left mandible of an amphicyonid that includes the canine, fourth premolar and first molar. The first molar (a carnassial) creates a shearing action with the carnassial in the upper jaw to cut the through the flesh of prey. (Photo © VP FLMNH)

For this week’s Fossil Friday, we have a dentary (mandible) of an amphicyonid from the Cucaracha Formation of Panama. This specimen was found near the Centenario Bridge and is Early Miocene in age. Amphicyonids, commonly called bear dogs, were an Old World taxon that migrated from Europe to North America during the Miocene. They are members of the mammalian Order Carnivora along with modern dogs, bears, walruses and raccoons, to name just a few. One of the defining characteristics of carnivorans is their teeth, which include prominent canines and carnassials. The fourth upper molar and first lower molar are termed carnassials and are teeth that are designed to shear meat like scissors.

To find out more about an indeterminate amphicyonid from Panama, read this paper about Miocene mammals of Panama here.

References:

Feldhammer, G. A., Drickamer, L. C., Vessey, S. H., Merritt, J. F., and Krajewski, C. (2007). Mammalogy: Adaptation, Diversity, Ecology. 3rd ed. Baltimore: Johns Hopkins UP. 316. Accessed online at http://books.google.com on Feb. 16, 2015.

A Quick Prep-Me-Up

My name is Will Tifft and I am one of the PIRE interns working in invertebrate paleontology. I graduated from Hamilton College this past May with a Bachelor’s Degree in Geoscience. Before coming to the Florida Museum of Natural History I spent the summer interning at the Paleontological Research Institute (PRI) assisting a PhD student with his work on Eocene posters from the Atlantic Coast. In the future I’m interested in studying brachiopods as well as microfossils. While working on the PIRE project I am mainly interested in getting the most research experience I can.

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Small projects using several prepping techniques.

For the past month I have been working on preparing many of the invertebrate fossils brought back from Panama.  This process includes doing simple things like gluing specimens back together and hardening them all the way to using the rock saws and air abrasive unit. Besides gluing, the first prepping project I worked on used the air scribe, which is a small jackhammer that uses compressed air to remove matrix from around a specimen. This has become the main process by which I prepare specimens. The air abrasive unit uses compressed air to shoot sodium bicarbonate pellets at the specimen to remove smaller amounts of soft matrix. When used correctly it is much less damaging to the specimen than the air scribe.

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Shell being glued with Elmer’s glue and supported by sand.

While I was working on projects with the air scribe and abrasive unit, I was also working on several shells and other specimens that had to be glued back together. For most of these Elmer’s glue is sufficient enough to hold them together. In order to hold the specimen in the correct position while it is drying, a sandbox is used. The sand gives more support to the pieces while they dry than placing it on the table or even trying to hold it in place. It also allows the person preparing it to work on other projects while it dries. When this isn’t strong enough, Butvar or Epoxy is used, though it is  more damaging to the specimen if it gets on the shell or exposed surface. Often times specimen that are still contained with a partial matrix are brittle and will fall apart when exposed. In order to prevent the specimen from falling apart B-72 is applied to the surface. This soaks into the shell and gives it some extra strength.

3D Horse Teeth!!!

I’m super excited to be rolling up my sleeves and finally getting some 3D imaging experience. My big passions being fossils and art, I found preparation to be a happy medium between the two. I learned how to do fossil prep at Stony Brook University under Joe Groenke after a semester of undergraduate research that led to my first presentation at the annual meeting of the Society of Vertebrate Paleontology. After graduating and spending the summer doing field work and prep at the Grand Staircase in Utah, I accepted a Preparator position at the American Museum of Natural History in New York, where I worked for 5 years. Now I am gearing up for grad school in the fall. I think 3D work will be the same happy medium between research and digital art.

We are learning to use Avizo 8.1 to post process CT scans of horse and shark teeth into manipulatable 3D images. The process looks way more overwhelming than it’s actually been. There are just many little steps to remember, but I’m sure with a few run-throughs, and our trusty protocol by our side, we’ll be cranking them out in no time.

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PCP-PIRE Intern Justy Alicea learning how to use the Avizo 3D imaging software

I am very interested in seeing how far we can push this technology and what novel applications Avizo can be used for that may have been overlooked. For now, though, we are just happy learning the basics. These 3D images will not only be used for research and visualizing the intricacies of tooth morphology, but I’m proud to say they will also be hosted online as part of the MorphoSource digital science library and downloaded by classes all over the world for use in research, teaching science and fossil outreach initiatives. It’s very exciting.

Outside of learning Avizo, we have spent much of the beginning of the program doing fossil prep and organizing the Panama collections. We’ve spent a good amount of time getting up close and personal with the collection as we decide what our research projects will be for the duration of the internship. I’m eyeing a fossil trionychid turtle skull that I would learn to do a morphometric analysis on, and a fossil carnivore tooth which may be the earliest record of these guys in Central America. I’m eager to get to work on these projects and accomplish great things.

Fossil Friday 2/13/15: Fossil Wood

Fossil Wood

Three sections through a specimen of Guazumaoxylon. The vessels transported water throughout the tree and the rays transported waste products from the outer, living part of the tree to the inner, dead part. The rays are made up of small dark-colored cells and large light-colored cells, which is characteristic of members of Malvaceae. (Photo © Paleobotany FLMNH)

This Fossil Friday we are lucky to be showcasing an Early Miocene fossil wood specimen from the Lirio East locality, Cucaracha Formation. To identify the wood, different cuts (sections) were made. Paleobotany Intern Chris Nelson explains, “You need to cut the wood at three different angles: cross section, radial section, and tangential section. The cross section is the one people are most used to seeing (a cut perpendicular to the height of the tree, often showing growth rings if they are present). The radial section is perpendicular to the cross section (parallel to the height of the tree) and ideally goes through the center of the tree’s trunk (i.e. it is a diameter or radius). The tangential section is similar to the radial section but does not go through the center, so it catches the anatomical features at a third angle (a cut that is tangent to a growth ring). After you have those three views, you can examine the anatomy.”

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Guazuma ulmifolia, the West Indian Elm. Photo © J. M. Garg, via Wikimedia.

The tree from which this wood came likely belongs to the genus Guazumaoxylon of the family Malvaceae, which includes okra and cotton. A modern relative of this tree, Guazuma, is found throughout the Neotropics. Members of this genus are pioneering tree species, meaning that they are one of the first species to colonize a disturbed area.

To read more about similar fossil wood from the Hodges Hill locality, check out the paper here.