Monday, February 27, 2012

Calotte or Carapace?

Is this the top of a hominid skull, replete with sagittal crest running down the middle, or is it the top of a tortoise shell?

This image comes from great resource I just found (thanks to Louise Leakey on Twitter) for paleoanthropology students - I won't answer here whether this is hominid or turtle, you'll have to find it at the African Fossils site.

The site has 3D, manipulable images of fossil hominids and other animals from Kenya and Tanzania. The Smithsonian Museum of Natural History also has a very nice 3D collection, similarly manipulable. Resolution isn't always what you might want it to be (for instance, you won't be able to tell if the basi-occipital suture is fused in the Homo erectus cranium KNM-ER 42700), but you still get good overall view of some neat and bizarre animals. Like this robust australopithecus! (KNM-ER 406) Hey, its brain case does look kinda like the pic above...

Friday, February 24, 2012

You may have my statistical codes

As I've been working on my dissertation, I've had to come up with some new ways to compare (cross-sectional) growth in crappy fossil samples with a larger reference population. I've coded a procedure in the R statistical program that uses resampling to test whether two groups differ in the amount of size change experienced between various different ages (i.e. growth). This code is now available on my website.**

And how timely - a commentary in this week's issue of Nature demands that researchers publish the codes used in their analyses (Ince et al. 2012). After all, what good is Science if it's not reproducible? (Admittedly, the commentary is geared toward more intense, data-generating programs than anything I've written, which is mathematically very simple and generally comprises less than 100 lines of code. Nevertheless.)

ResearchBlogging.orgAnyone is free to use or adapt the code, with the caveat that one must have at least a little experience using R. In many ways the procedure is similar to a method called Euclidean Distance Matrix Analysis (EDMA; Lele and Richtsmeier 1991), although unlike EDMA my program centers around the problem of making comparisons in the face of lots of missing data. And lots of fun!

**  Oh crap! I just remembered I also posted a simple resampling procedure here on Lawnchair two and a half years ago. Where does the time go...

Some inspiration
Ince, D., Hatton, L., & Graham-Cumming, J. (2012). The case for open computer programs Nature, 482 (7386), 485-488 DOI: 10.1038/nature10836

Lele, S., & Richtsmeier, J. (1991). Euclidean distance matrix analysis: A coordinate-free approach for comparing biological shapes using landmark data American Journal of Physical Anthropology, 86 (3), 415-427 DOI: 10.1002/ajpa.1330860307

Wednesday, February 22, 2012

Osteology Everywhere

I saw a humerus bone sticking out of the ground on my walk home today.

Just kidding. It was just a stupid tree (left). But it does look a lot like a reversed back-side view of thASK-VP-3/78 distal humerus of Ardipithecus kadabba (right-most of the right pic; Haile-Selassie 2001). It's like someone blew up and unacceptably interred it, exposing only the top of the olecranon fossa (the big pit in the pic on the right, where the roots bifurcate on the tree at left). "ARE YOU A HOMINID OR NOT?" I almost yelled at the tree.

When you spend so much of your time working with bones, well you start seeing bones everywhere. And you'd be surprised how often you'll find something when you're looking for it, even inadvertently.

ResearchBlogging.orgWhat nature reminded me of: Haile-Selassie Y (2001). Late Miocene hominids from the Middle Awash, Ethiopia. Nature, 412 (6843), 178-81 PMID: 11449272

Friday, February 3, 2012

Ameloblast from the past

I've posted a couple times about the prospects of using high-resolution computed tomography imaging to assess cellular-level processes of growth and development. Today, Paul Tafforeau and colleagues present a synchrotron-based visualization of the adventurous paths that individual enamel-forming cells'(ameloblasts) take to form tooth crowns. I've been focusing more on using these techniques for studying bone growth, but I got the idea of that from previous studies of teeth (see Macchiarelli et al. 2006 and Smith et al. 2010).

Tafforeau et al 2012, Fig 3. Scale bar = 0.25 mm
Time was, the internal microstructure and growth of enamel could only be examined using sectioned (either cut or naturally fractured) tooth crowns. Synchrotron imaging of teeth allowed Tafforeau and colleagues to get at this internal information in complete teeth whose insides are unexposed.

To the left is a "virtual" section of a molar tooth, the 'base' of the enamel (at the enamal-dentine junction) is at the bottom right, and the external surface of the tooth is at the top left. The lines radiating from the EDJ to the crown surface are enamel prisms, the mineralized paths of cells called "ameloblasts" that form tooth crowns. This is the cellular process by enamel is deposited to form a rock-hard tooth.

Note that the prisms start off packed closely together as they start their journey from the EDJ, but slowly diverge along roughly-parallel paths to be a bit further apart from one another (cross-sections in the cubes). The prisms' shadow on projected onto the exposed crown shows how non-linearly ameloblasts course to their final destination in some dimensions - I for one don't know why the path contains these kinks.

As with any awesome method, there are nevertheless limitations. Tafforeau and team say that enamel closer to the inside of the tooth is somewhat muddled, due to differences in the extent to which prisms had mineralized. And I don't know any numbers, but I'd guess that scanning a lot of teeth would get pretty expensive. But ultimately is a pretty badass research tool. This fine-scale internal view of tooth microstructure can allow researchers to reconstruct how a tooth grew, and from there to examine the cellular growth processes involved in certain crown shapes, mechanical properties of teeth, and how enamel hypoplasias (markers of health stress) are created by affecting the behavior of cells. Very cool stuff.

ResearchBlogging.orgThose papers
Macchiarelli, R., Bondioli, L., Debénath, A., Mazurier, A., Tournepiche, J., Birch, W., & Dean, M. (2006). How Neanderthal molar teeth grew Nature, 444 (7120), 748-751 DOI: 10.1038/nature05314

Smith, T., Tafforeau, P., Reid, D., Pouech, J., Lazzari, V., Zermeno, J., Guatelli-Steinberg, D., Olejniczak, A., Hoffman, A., Radovcic, J., Makaremi, M., Toussaint, M., Stringer, C., & Hublin, J. (2010). Dental evidence for ontogenetic differences between modern humans and Neanderthals Proceedings of the National Academy of Sciences, 107 (49), 20923-20928 DOI: 10.1073/pnas.1010906107

Tafforeau, P., Zermeno, J., & Smith, T. (2012). Tracking cellular-level enamel growth and structure in 4D with synchrotron imaging Journal of Human Evolution DOI: 10.1016/j.jhevol.2012.01.001