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Class Notes: Bioarchaeology

Wednesday: November 2, 2011

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Week 9: Diet II & Chemistry (Stable Isotopes and Trace Elements)

Tuesday:

Teeth are the only hard tissues in the body that directly interact with the environment. As such, they are of great use for bioarchaeological research. Dental macrowear is scored commonly on Scott’s ordinal scale. Teeth wear over time, and in ancient populations the wear was so great that almost nothing of the tooth would be left, and indeed sometimes the body would purge the tooth altogether. Macrowear studies this pattern, which can have different sequencing depending on diet and subsistence.

Dental topography was developed within the last decade, applying geological mountain mapping software to dental crowns.  This turns what is visually seen in Scott’s scale to quantitative data. [At school, it is part of my job as the research associate to use the 3D plotter machine to profile each tooth from Dr. S’s project to create a virtual catalogue.]

Dental microwear studies a tooth’s microscopic texture, including pitting and scratching. A scanning electron microscope (SEM) is a common method in doing so. Teeth are coated with a very fine layer of metal, then an electron gun shoots the specimen inside a vacuum chamber. The electrons will bounce off the object and the software is able to transform a 3D object into a 2D representation using a horizontal scan. Newer technology does exist to create a 3D model, but this is not yet typical.

A 3D method that is gaining speed, however, is that of the while light confocal microscopy profiler (WLCP). [The major part of my duties in the department.] It is similar to a compound microscope, except a beam of light is shot through the lens and bounces back. This distance is measured to created a vertical scan of the specimen. It uses scale sensitive fractal geometry to calculate variables like complexity of the occlusal surface, anisotropy and heterogeneity of features, and texture fill volume.

As usual, we discussed several case studies to wrap class up.

Thursday:

Class was almost entirely discussion from the texts. I admit that I still need to read these chapters, so this bit may not be the clearest. Stable isotopes and trace elements can provide evidence for the type of diet an individual ate. We discussed measuring carbon, nitrogen, and oxygen with a mass spectrometer. This breaks a sample down to its elemental parts, weighing each element separately. For instance, when measured, the delta of  13C can indicate a marine versus a terrestrial diet. Marine foods will show a delta closer to zero, while terrestrial foods will be closer to -7. Another benefit is that plants discriminate differentially to 13C in their photosynthesis, so C3 plants can be differentiated from C4 plants in the archaeological record. The benefit here is that maize is a C4 plant so the adoption of maize can be noted in archaeological remains. Nitrogen likewise proves a valuable factor of understanding diet, giving a trophic accumulation of 15N. Legumes will provide a base level of 15N, herbivores who eat these legumes will have a slightly higher value, and carnivores who eat the herbivores who eat the legumes will likewise have an even higher value. 15N therefore needs to be understood within the environmental context, because comparisons between environments like coastal versus inland, or arid versus humid will give the incorrect impressions. Oxygen analysis of both bone and teeth (18O), as well as strontium, can show migration patterns because it is linked to the available water source.

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Research Associate

Saturday: September 10, 2011

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I have not truly begun my duties as an RA yet but I have been shown the ropes and began practicing. The process can be simplified as thus:

Researchers from around the globe take molds of molars in their samples and send them to us. I have been given a site from Isreal to work with first, since I am expected to present at the Biological and Forensic Anthropology Association (BARFAA) in October. The first step is to clean the molds with alcohol because sometimes the dirt from a tooth is left in them.

Then, I mix up resin and hardener to cast the teeth. The cast works better to reflect the light from the white light confocal profiler (WLCP) than real teeth, and it standardizes all the teeth samples for comparisons. Not to mention, it also prevents us from having the full responsibility of samples in house and opens up a lot more sites to be studied (some of which may be reburied right away can still have the teeth examined through the casts).

I carefully adjust the tooth on a tray so that Phase II is level. Phase II can be thought of as the part on top of your molar that can be felt with your tongue and hikes up to your cheek (of course, it is much more specific than that). Phase II is useful for dental microwear because it is where food hits the tooth during chewing. Microwear, by the way, refers to the scratches and pits that you (yes you!) have on your teeth that can only be seen via a microscope. Different diets will show different patterns of wear. In older populations, some of the teeth are completely worn down and are flat across the top, even exposing the dentin inside. Although this does not bode well for my particular kind of study, it is a fascinating thing to witness. Teeth were used as major tools back then, but also food processing did little to soften food as we have now. In fact, sometimes stoney grit was added to food as a consequence for grinding it with stone tools. In fact further, some populations today still wear their teeth down!

Next, I use the microscope to find a representational place on Phase II and then use the software that came with the WLCP to profile the texture of the tooth. The light shines down and bounces back to the lens and this is calculated so that it can be represented through computer output, rendered in several ways. First, it shows as a gradient of elevation. I then show it as a true image which can give the appearance of an Scanning Electron Microscope image (SEM). This is important because our technology is new and therefore we need to make sure that our results are comparable to SEM results for a control factor, but also because SEM images are what everyone is already familiar with.

Here, I will inspect the image for evidence of dirt. At this point, it will be microscopic dirt, and likely part of the cast so instead of removing it in real life which is likely impossible, I can edit the images so the program understands that it should not be included in the calculations.

Amidst all the linear scratches or circular pitting, you may wonder how I can identify dirt, but the trick is that dirt generally looks like tiny little balls, unlike anything else on the tooth surface so really it is not that difficult to determine. I use the program to erase little spots and then tell it to finish with the calculations.

There is more after this step, but at this point, I am just focusing on finding Phase II (it is not that easy for a newb like me since I am still learning simply how to identify which tooth is which) I also poke around learning the program (and earned the title Rebecca the Grey which quickly transformed into Rebecca the White and even sometimes all the way elevated to Gandolf since I happen to have magic computer powers). I should start on the real thing in the coming week and my next post about it hopefully will include some sort of visual reference for you.

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checking out campus

Sunday: August 28, 2011

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Thursday night, Boy and I stayed in Indy with his mom so that I could move some of my stuff to her guest room. On Friday, we wandered around campus to get my parking permit, find the different offices that may come in handy, locate the cafeteria and bookstore, find my class rooms, and so on. Dr. S had also invited me to attend a MS thesis defense by Lindsy Frazer, titled “Dental Microwear Texture Analysis of Early/Middle Woodland and Mississippian Populations from Indiana.”

This was the first defense I had attended, and it was much more relaxed than I had expected. I followed her presentation pretty well, though she said afterward part of her committee had a question or two they felt were unanswered. Her thesis hits on a difference between the SEM technology and the new 3D technology that she utilized at UIndy (I will explain in another post). Defending a thesis sounds really horrible, but watching her public presentation lightened my anxiety somewhat. Of course, I was not there during the private committee part and I am sure that will be much more difficult.

During her private defense, Boy and I met my cohort – there are three of us on the bioarchaeology track. We also hung out with a third year student, Laura, who showed us the white light confocal microscope (which I will reference from now on as the WLCP, and when I learn more about it I will explain that that means to you, but this is the new 3D technology I mentioned). I only got to hang out with one of my cohorts because the other had to leave campus right away, but I feel I will have a good time there.

Afterward, I met with Dr. S to discuss a funding opportunity that equated to roughly half the tuition cost for the entire time I am at UIndy. It is a research associate position, which can basically be thought of as a research assistantship (RA). I will be in charge of making sure all the incoming molds of teeth from around the world are getting examined with the WLCP, and that any student needing to use it will get an appropriate time on it. This is great for me, because I wanted to be a part of this new technology, but I am not sure I wanted to base my thesis with it, since I very much like macroscopic research (things you can see with your own eyes without technology). Having this position will also give me something to do on my off time down there on campus, and of course the funding aspect is wicked cool. He is going to train me on it this week, so I should be able to post more details.

Boy was impressed that the whole campus uses Lenovo instead of the “crappier Dells and other garbage” you see at other universities. He also enjoyed Dr. S’s sense of humor. A lot.

I am looking forward to class starting tomorrow. I am enrolled in geoarchaeology, human osteology, and bioarchaeology. I’ve had two weeks off of work now and my brain is fully recharged and itching to go. I do feel a bit of anomie going into this new situation without really being able to understand the changes my life will take until it happens. In addition, a lot of stuff started to go wrong right when I was leaving my job (my car stopped shifting, my glasses broke, and some other snafus popped up). I suppose a pessimistic person would have told themselves that it was Fate trying to tell them something. I looked at it differently. In the face of all these unexpected expenses, I asked myself, “How sure are you that this is the best decision to make?”

Absolutely sure.

Undaunted and uprooted, I will be a Master of the Universe! Science! :)

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