A Guide to Digital Paleontology


Museum intern Justy Alicea (left) and SMIF technician Jimmy Thostenson set up the CT scanner using a live X-ray image of teeth inside the scanner. (Photo courtesy of Andrea De Renzis)

[This is the unabridged version of museum interns Andrea De Renzis and Justy Alicea’s April 2015 eNewsletter article.]

Traditional specimen-based research in paleontology sometimes requires destructive sampling in order to obtain measurements of features to identify specimens or understand ancient environments. Micro-CT scanning uses x-rays to create high-resolution virtual slices that, when layered together, form a three dimensional model that can be manipulated and measured. These digital models can also be shared with other researchers, educators, and the public, giving more people access to fragile, rare, or scientifically valuable fossils. Continue reading


Fossil Friday 4/24/15: A kinosternid turtle


UF 242076, a peripheral element of the plastron of Staurotypus moschus. (Photo © VP FLMNH)

This Fossil Friday we have a peripheral element of the plastron (ventral surface of the shell) of a kinosternid turtle called Staurotypus moschus. This fossil, which is early Miocene in age, was collected by Michael Kirby under the Centenario Bridge from sediments of the Cucaracha Formation. The specific name for Staurotypus moschus was chosen due to the turtle’s relatively deep anterior musk duct groove. In life, the musk duct groove would have held a gland that contained foul-smelling musk that the animal release when disturbed.

To read more about this specimen, read the publication on it here.


A photo of a modern Staurotypus salvinii, the Chiapas Giant Musk Turtle. The publication describing S. moschus claims that the fossil turtle has its closest affinities with S. salvinii. (Photo © L. A. Dawson)

Thomas Farm Trip and Earth Day Festivities

Last week myself and the other interns took a field trip for two days to dig at the fossil site Thomas Farm, about an hour away from the museum here in Gainesville. The Thomas Farm site is from a comparable time frame (early Miocene) to our localities in Panama, and similarities in the fauna we find at each site show a biogeographic connection. Some examples of taxa that are in common are Parahippus, Floridatragulus, and Petauristodon.

Once at the site, we were given an introduction by Dr. Richard Hulbert. He told us that it used to be a large sinkhole, with some limestone caves. We talked about the sediment we would encounter and the types of fossils we would be finding. At Thomas Farm, they dig in 10 cm intervals, using a grid system to denote different squares. This is similar to how archaeological digs are done. Much of my fieldwork training comes from archaeological work, so I was very familiar with this and felt very comfortable digging this way. Various fossils were uncovered, and I even got to make my first jacket, which was for a mandible belonging to the camel Nothokemas.

The Nothokemas mandible in it's jacket, after it had been cleaned by a volunteer.

The Nothokemas mandible in it’s jacket, after it had been cleaned by a volunteer.

Scapulae found at Thomas Farm.

Scapulae found at Thomas Farm.

Continue reading

Fossil Friday 4/17/15: Fossil Plants preservation and Identification

We all must have had in a point of our life heard about how extinct organisms remains become fossilized, either by books, movies or even in the Discovery or History channel. There are many different types of fossilization processes including Permineralization, Cast and Molds, Replacements and Crystalization,  and Carbonization, We often encounter these in the context of animal shells or bones, but what we hardly ever hear about is the preservation plant fossils. Plants, just as the megafauna, can be preserved in the rocks. Typical plant fossils are wood, seeds, roots, flowers, pollen, and leaves which are by far the most commonly preserved macroscopic plant part. Continue reading

Update on BioMuseo Adventures


The fruits of Jorge Moreno Bernal‘s labor at Lake Alajuela. Two crocodile teeth, a ray tooth (both bottom-right), and a possible mammalian pelvis or shoulder plate.

In a previous post, Jeremy told us of some of the many exciting things that have been happening in the field as of late.  Lake Alajuela is proven to be not only a very beautiful field site, but fruitful as well; we hope to continue prospecting and discovering there!  In this post, however, I want to talk a little bit more about our work outside the field.

We only have about three weeks left in Panama, and there are many things that we still want to get done.  Creating a narrative for the BioMuseo is one of our main priorities, and there is still much to do.  As promised, today I will give an update on how things are going with our work with the BioMuseo. Continue reading

Smithsonian’s Panama Debate Fueled by Zircon Dating | Newsdesk

Ocean currents before the formation of the Isthmus of Panama. Photo Smithsonian Tropical Research Institute

Ocean currents before the formation of the Isthmus of Panama. (Photo © Smithsonian Tropical Research Institute)

Camilo Montes and colleagues have made exciting discoveries about the dating of the rise of the Isthmus of Panama using detrital zircons! Visit the following link to the Smithsonian’s website to read the press release! Smithsonian’s Panama Debate Fueled by Zircon Dating | Newsdesk.

Duke Trip

Last week Justy, Nathan and myself headed to Duke to microCT scan fossils from the Panama Canal. Our main goal was to scan 71 fossil teeth belonging to various rodents, but we brought various other fossils along as well in case we had extra time. Overall we ended up scanning all 71 rodent teeth, 6 crab fossils, and various plants all from the canal sites. We even scanned some fossils for our personal research projects including a turtle skull and some sciurid postcrania.

When we arrived at Duke we met with Jimmy Thostenson, the engineer/technician in charge of running the scanner. Jimmy taught us how to position our fossils in the scanner, and then he set up the scanner and explained to us how it worked along the way. We queued up our specimens that would be scanned that day, and then left to explore campus. We returned later when they were finished scanning and checked the images to make sure they were looking good. At one point the center of rotation of our scans were off, so Jimmy taught us how to fix that. We then opened up each scan in Avizo and made a rough 3D image to make sure all was well. All of our scans ended up great!


Jimmy teaching us how to set up the scanner as Nathan and Justy look on.


The inside of the microCT scanner.

A Sciurid humerus from the Thomas Farm site in Florida, as it was being scanned.

A Sciurid humerus from the Thomas Farm site in Florida, as it was being scanned.

While our specimens were scanning, we were able to explore Durham. Continue reading

Full Plaster Jacket

Today was yet another beautiful day at Lago Alajuela, where we have spent the last two days searching for fossils from the relatively unexplored Alajuela Formation. This site hosts an amazing array of marine fossils ranging from mollusks and sharks to turtles and crocodiles, as well as the occasional terrestrial vertebrate. We were fortunate to have this opportunity, as water levels are usually too high to expose a decent amount of the outcrops due to either excessive rainfall or water not being released from the dam which is used to fill the canal. The hunt was on!

An amazing find. The large bone plate was found relatively compete in situ. This specimen was collected from the relatively weathered sandstone horizon on the southern shore of the lake.

An amazing find. The large bone plate was found relatively compete in situ. This specimen was collected from the relatively weathered sandstone horizon on the southern shore of the lake.

From the beginning the findings were good. Continue reading