Category Archives: Animals

Mapping the Pratt Mammoth excavation using GPS and basic surveying technology

The discovery of a partial mammoth skeleton in 1999, and its subsequent excavation in 2000, provided an opportunity to implement several innovations in the on-site mapping of the excavation and relating the excavation to real-world coordinate systems. What follows is a basic primer on what we did.

The mammoth specimen was found during the excavation of a waste-water lagoon on property owned by the City of Pratt, Kansas being leased to Pratt Feeders. While digging the lagoon the heavy equipment operator encountered a hard lens of sediment. Upon digging into it, several large bones were found. News of the discovery found its way to a reporter at the Pratt newspaper, who subsequently contacted me, then at the Sternberg Museum of Natural History. A small group from the museum traveled to Pratt for an initial investigation of the site. After an afternoon of excavating around the exposed bones it became clear that the site was more extensive and a longer excavation was needed. We planned to return to the site several weeks later.

A four-day excavation was planned with numerous volunteers and we returned to the site in November, 1999. After this exploration it again was clear that a longer period of time was needed to fully investigate the site, as we kept finding more and more fossil bone. We re-covered the site once again, and planned to return in the summer of 2000.

A volunteer excavates around a mammoth vertebra at the Pratt Mammoth site.

A volunteer excavates around a mammoth vertebra at the Pratt Mammoth site.

Because we had time to plan a larger excavation for the summer, and it was clear that there were many bone elements preserved, I wanted to be sure to map the site in detail, both for its paleontological resources, but also for other physical characteristics. So, I arranged to have a surveying total station on hand for the dig. We also lined up numerous volunteers, arranged a university class to be taught using the site as a learning tool, and obtained numerous donations from the generous community of Pratt. The entire community got behind the excitement of the dig, and because the site was easily accessible being at the airport, we hosted numerous visitors.

Establishment of points within the site

During the November, 1999 dig, I had established three control monuments at the site. The monuments were a hub (2 inch x 2 inch stake) and tack (a special surveying nail) driven into the ground away from the areas we were going to be disturbing in our excavations. This insured that we could re-find the control monuments and they would be used to relate all the points of the excavation to each other within the dig area.

Using the control monuments, we established an arbitrarily-oriented meter grid system. I was not concerned with the cardinal orientation of the grid so much as wanting the grid to be useful for in-site control of the dig. One of the principle uses of the grid was to demarcate 2 x 2 meter spaces to assign to volunteers to control their digging efforts. Having the grid on the ground helped to keep their efforts orderly, as they could be assigned to “dig here” and not be on top of each other. The use of the surveying total station allowed for accurate layout of the grid system across the entire site, and allowed for unlimited expansion of the system as needed.
 
The reason that the grid was redundant for the within-site location of bones is that all bones were located with the total station using standard radial surveying techniques. Every element removed from the site was given a field number, and the location of the element was documented in three-dimensions. Initially, the grid system was assigned assumed x and y coordinates in meters, and an assumed elevation was assigned to the control monuments so that the z dimension could be calculated relative to other points in the site.

The total station is set up over a point and aliened with another control point to get a starting line. The instrument can accurately measure distances by shooting a laser to a reflecting prism and measuring the time it takes to return to the instrument. It also accurately measures horizontal and vertical angles. With the vertical angle and the distance, it can calculate the difference in height (z) between the reflector and the instrument. So, with relatively simple calculations the x, y, and z coordinates of any point within the site can be determined. The instrument is highly accurate (within 1/1000’s of a meter in distance) so within-site accuracy is estimated to be high, likely within a centimeter or two given the reliability of using inexperienced volunteers to help with the surveying.

Teaching a young volunteer to use the total station surveying instrument.

Teaching a young volunteer to use the total station surveying instrument.

Most of the elements removed from the site were located with a minimum of two points. The smallest bone fragments were located with point locations of a single measurement. If they bone had any linearity to it, it was located as two points (end and end) giving both the approximate length of the bone and its linear orientation. Several of the larger bones were located with three or more points.

All of the points located at the site are described as their three dimensional coordinates, and therefore can be plotted for visualization.

Point cloud from the Pratt Mammoth site shown in map view with the meter grid.

Point cloud from the Pratt Mammoth site shown in map view with the meter grid.

View the point cloud in a short animation.

Translation and rotation to real-world coordinate systems

During the excavation we used assumed coordinates and elevations. However, it is desirable to be able to locate the site, and all the points located within the site, in a real-world coordinate system so that it can be related to other localities anywhere in the world. We did not have high-precision global positioning system (GPS) equipment available, although such equipment does exist. However, using the following method we were able to get very effective results using a basic Garmin handheld GPS unit.

The accuracy of the handheld unit varies with availability of satellites, access to the open sky, variations in atmospheric conditions, basic limitations of the unit itself, and other variables. However, it is possible to locate a point on the globe to within approximately 15 feet or so. I used the GPS to record the location of two of my control monuments. I used the coordinates of the GPS reading to calculate the azimuth between the control monuments, and assumed that was the true azimuth. I knew the distance between the monuments based upon my field survey of measuring between them. I assumed the GPS reading on one of the control monuments to be true and “held” its coordinates to that reading. Using the azimuth to the other monument from the GPS reading, and the distance measured in the field, I then calculated the new coordinates for the second control monument.

With the assumption of the coordinates of the first monument, the accurate real-world azimuth, and the measured distance to the second control monument providing its coordinates, it was possible to recalculate the coordinates of every point within the dig site. It is a basic mathematic routine to translate (move points horizontally in space) and rotate (turn the points on an axis in space) all the points located at the dig site to a very close approximation of their real-world coordinates. Since we measured all the points in meters I used the Universe Transverse Mercator (UTM) coordinate system. I estimate that the accuracy of these coordinates should be within about 15 feet (the error of the reading on the handheld GPS). This is not as accurate as you could get with high-precision equipment, but it is accurate enough for almost all purposes, and can be achieved with inexpensive equipment that is readily available.

I have modified the system somewhat, but I have since used this basic system at other excavation sites with very good results. The real-world coordinates of every point from the site allows very accurate plotting of fossil sites, and even individual bone elements, in relation to other sites. It also allows for the application of geographic information systems (GIS) technology on the sites.

Bones drawn using the points located at the Pratt Mammoth site.

Bones drawn using the points located at the Pratt Mammoth site.

Feathered dinosaurs may have changed coats

Some of the most exciting finds of the last couple of decades were the discovery of feathered dinosaurs. These fossils mostly have come from fine-grained formations of the Cretaceous Period in China, where feather impressions were preserved along with the bones. Each of these fossils gives us a snapshot image of the body covering sported by that species. Other recent finds have even given us clues to the coloration of the feathers in a few species.

In yet another new find, announced in the April 29 issue of Nature, we learn that the feathery covering may have fundimentally changed over the lifetime of individuals of at least one species. Two small oviraptors in the genus Similicaudipteryx were preserved at different stages of their life history, each showing the pattern of feathers covering the body at different life stages.

Artist reconstruction of a juvenile and adult Similicaudipteryx

Artist reconstruction of a juvenile and adult Similicaudipteryx. Artwork by Xing Lida and Song Qijin

The smaller, juvenile individual had short flight feathers with a “ribbon-like” stem on its forearms, much long feathers on the tail, and a downy covering over the rest of its body. The larger, young adult individual showed a different pattern, with much longer, and more developed flight feathers with a strong central shaft on the forearm. Thus, the flight feathers of the forearm show two very different morphologies at the two life stages. This does not happen in modern birds, where the flight feathers that emerge on the juveniles are the same, only smaller versions of the adult feathers.

There is some debate that this interpretation of the fossils is correct. It could be, argue some paleontologists, that the smaller individual was preserved during a molting phase, with the new feathers only partially emerged from the tube-like sheath that feathers form in. In other words, they suggest that the different morphology is only temporary and an artifact of preservation. The authors of the original paper maintain it is not an artifact based upon the proportions of the feathers. So, we need to keep digging.

It is now accepted that the ancestors of birds were the theropod (meat-eating) dinosaurs. It is clear from these fossils, and many similar ones, that birds inherited their feathers from dinosaurs, and we have greatly expanded our knowledge of feather evolution with the last few years.

Other dinosaur related posts can be found here. Just search or select the category.

Denning behavior in the Giant Short-faced Bear

One of the most exciting things in paleontology to me is when we can begin to tease apart how extinct animals, animals that humans often never set eyes upon, lived their everyday lives. I am often amazed at how my colleagues can drill deep into questions that at first seem unanswerable; using creative ways to get answers from all the evidence that has survived, the bones, teeth, and sometimes trace fossils.

There are many examples of using the clues provided in the fossil record to come to better understand beasts from the past. In an earlier story, we looked at a disease process in Tyrannosaurus, and glimpsed how the mighty tyrant king could be brought down by a lowly protozoan. Here, we will explore some evidence for denning in the Giant Short-faced Bear (GSFB).

In a paper from several years ago Schubert and Kaufmann (2003) discussed the discovery of a GSFB in an Ozark cave. While incomplete, it is still one of the most complete specimens of the bear ever found. In addition to bones in partial articulation, they also found a thin layer of clay and minerals underneath the skeleton that preserves the remains of hair. Unfortunately, the hair is too deteriorated to tell us what color it was or exactly what its texture might have been, but its discovery is tantalizing.

This Ozark specimen is small compared to others of its species. There is a lot of evidence that there was a significant difference in size between male and female GSFBs. For example, at Rancho La Brea in southern California, both smaller and larger individuals have been found in contemporaneous deposits. It is easy to tell if the individuals are adult, so seeing large and small forms suggests two options: either there are two species, or there is one species with large and small individuals. It later is most likely. This is not surprising as all modern bears are sexually dimorphic.

Schubert and Kaufmann noted that over 1/3 of the known specimens of the GSFB come from caves, and that those specimens are smaller in general than the specimens found in open environments. (See the story about the type specimen, also found in a cave in northern California). It is logical to reason that the smaller individuals using the caves are predominately female.

Modern female bears are much more prone than males to den during periods of unfavorable conditions. And male bears are more likely to remain active throughout the year. It seems as if the GSFB followed a similar pattern—the females were using caves as denning sites, and were denning when they perished. In Cope’s original paper (1879), he called this new animal the cave bear of California—seems he was right.

From the accumulation of small bits of information we continuously piece together the lives of prehistoric beasts, slowly bringing them into sharper focus. That is the thrill of paleontology.

Cope, E. D. 1879. The cave bear of California. American Naturalist 13:791.
Schubert, B. W., and J. E. Kaufmann. 2003. A partial short-faced bear skeleton from an Ozark cave with comments on the paleobiology of the species. Journal of Cave and Karst Studies 65(2):101-110.

There are many other interesting facts here at Boneblogger. Just look around and enjoy.

Saving Boo boo the chicken

And now, for something completely different.

This video went around on the web a few years ago, and in honor of my friend who is starting to raise chickens, I present it here for you. Enjoy.

Yogurt with probiotics

There is no question that yogurt is good for you. However, you should know what is in this dairy product that you consume. This nutritious treat that dates back to centuries ago is rich in potassium and calcium, low in sugar and fat and contains natural microorganisms that are beneficial to the digestive system. Known as probiotics, these live active cultures are simply good bacteria.

Dannon, the Paris-based food company behind Activia®, one of the familiar names in yogurt, notes in its official website that probiotics, as defined by the World Health Organization is “a living microorganism that, when administered in adequate amounts, confers a health benefit on its host”.

Sounds good, right? But before anything else though, let me ask you these two questions: what is considered an “adequate amount” of probiotics? And, what are the benefits of yogurt with probiotics?

Activia® is a yummy low-fat yogurt that contains friendly bacteria. The key ingredient is DN-173010 which has been claimed with a trademark status by Dannon, being indicated in its US labels as Bifidus regularis. As part of a healthy lifestyle, the same site recommends consumption of 4 oz Activia® daily for a couple of weeks, the adequate amount and period in order to start experiencing its positive effects on the digestive system. These benefits include regular bowel movement and the relief of constipation and diarrhea, among others. Apart from this, additional benefits are ridding the body of toxins and maintaining good health.

So what is this Bifidus regularis exactly? This name is coined by Dannon and it varies in the different countries where the product is available. More important to note, however, is that this bacterial strain is a sub-species of Bifidobacterium animalis which is found in the large intestines of mammals, including humans. It is considered an effective probiotic since it is able to withstand the gastric juices in the digestive tract from the stomach down to the small intestines, until it reaches the large intestines where it works its magic.

On an interestingly related note, in his March 2008 article on individual probiotic bacteria, Matthew Hogg discussed a study conducted at Finland’s National Public Health Institute. In this research it indicated that probiotic bacteria, when used singly are more effective in boosting the immune system as opposed to when several strains are used in combination.

So the next time you grab a yogurt, enjoy but do read the label. Make sure that it is one which contains high-quality probiotic to make it a tasty yet nutritious respite.