geometric morphometrics

New decade, new syllabi

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We just kicked off the Spring semester here at Vassar College, and so I’ve got some freshly-updated bio-anthro syllabi hot off the press. This semester, I’m doing my annual introductory class (Anth 120, “Human Origins”), a resurrected seminar (Anth 305: “Human Evo-Devo”), and a second stab at a new methods module (Anth 211: “Virtual Anthropology”).

Anth 120 is similar to previous versions, although this year I’ve taken out a reading/lecture on Paleolithic technology, replaced with articles scrutinizing evolutionary psychology. We’ll see how it goes.

The other two classes are greatly overhauled from previous versions. Anth 211, “Virtual Anthropology,” is my first contribution to a new curricular initiative here at Vassar, which are called “intensives.” Anth 211 is kind of a hybrid between a regular class and an independent study, giving students experience with computer-based, “virtual” methods used in biological anthropology and related fields.  In the first half of the semester, students will get to try out some of these methods and see what kinds of research questions they’re used for. In the 2nd half of the term, students do their own Virtual Anthropology study drawing on the materials in my HEAD Lab, and then present a research poster at the end of the year. I debuted this intensive last Fall, and based on that experience I’m providing a bit more training and have more activities for students this Spring. If last semester’s projects are at all predictive, we should have some fun projects in store this year.

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Anth 305 is a fossil-focused examination of the roles of growth and development in human evolution, and this year’s version is also highly modified from the last time I taught it over two years ago. In that first version, course content was patterned along the skeleton, e.g., one week looked at evolution and development of teeth, next week the spine, etc. Such a bauplan might work for building bodies, but it wasn’t the best for teaching. So this year, we’re spending the first few weeks on the fossil record of human evolution, getting acquainted with the curious characters of our deep past. From there, we go over skeletal / developmental biology, before delving into special evo-devo topics like “morphological integration” and “heterochrony” for the rest of the semester. We’ll also read lots of old, “classic” papers along the way.

Syllabi for these, and other classes, can be found on the teaching page of the site, if you want to learn more.

This just in: Primates have differently shaped skulls

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Sorry for the lag in posting. This semester’s been quite busy and hectic, as I’m trying really now to figure out what I’m doing here in graduate school. But I just had to stop what I’m doing to let everyone know about this ground-breaking discovery.

A study just published in the American Journal of Physical Anthropology has used the powerful shape-analysis technique of geometric morphometrics to discover that primate crania are quite diverse! Sampling one male and one female from a wide variety of primate genera, the researchers determined the shape-differences among these major groups using 3D landmark coordinates and principle components analysis. Wouldn’t you know, that their analysis showed a clear distinction between strepsirhines (lemurs and lorises, the most primitive of all primates) and anthropoids (monkeys and apes, which includes humans). Oh, and humans are markedly different from our ape brethren. So now all those speciesists out there can’t claim that, “all primates look alike.”

Why is this paper interesting? Um…

Reference
Fleagle J, Gilbert C, and Baden A. Primate Cranial Diversity. American Journal of Physical Anthropology, in press.

More LB1 stuffs, but no real news

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New analyses of the Flores “hobbit” material have been published recently, including a geometric morphometric (GM) study of the LB1 cranium (Baab and McNulty, in press). Readers will recall that this particular small-brained specimen has fueled the controversy over whether the Flores material is a unique, small-bodied hominin species, or whether this and other specimens were pathological (humans). At this stage in the game, I still do not know what we can say exactly is going on until we get more fossils. Admittedly, I haven’t yet read the recent analyses of the postcranial material. Maybe they will change my mind. So, I’d like to keep this more descriptive and comparative, than speculative on phylogeny versus pathology. Some neat things from the study:

Coordinates of landmarks were recorded off a “stereolithographic model” of LB1. This is a neat technology in which a plastic 3D model is ‘printed out’ based on data from a CT scan. While this might not give the same resolution as the real thing (or a good cast of the real thing), it’s a great way to make physical models of delicate fossils. Additionally, measuring/collecting landmark data from fossils can always potentially damage specimens, and stereolithography is a way to circumvent this problem. However, I don’t know that it would have been any more difficult to digitize landmarks from the actual CT scan (i.e. with a computer software package), and it almost certainly would have been cheaper. Oh well, smoke them if you’ve got them, right?

The study used GM to compare the shape of LB1 cranium to the shapes of apes, fossil hominins and modern humans. I like that the study included the analysis in Procrustes shape space (with nuances of location, rotation and scaling omitted) and in form space (omits only location and rotation, leaving size/scaling in the analysis). By examining the specimens in form space, the authors were able to study the relationship between shape and size, i.e. the effects of allometry: what cranial shape would “an LB 1-sized individual” of each taxon have? The results of the form space analyses are kind of neat, although I can’t interpret them too readily since I’m not sure what exactly the first two PC scores indicate, other than size. In a nutshell, though, LB1 appears most similar to what would be expected of a small-bodied fossil Homo individual. Of course, this is nothing new: Gordon et al (2008) came to the same conclusion last year, but using inter-landmark distances as variables (as opposed to landmarks as variables). Additionally, last year we found that the microcephalics in our lab appear more similar in shape to modern than fossil humans (I wonder if we should have tried to publish that…).

The authors also examined asymmetry as a way to address the allegation of pathology in LB1 (left-right asymmetry is believed to be indicative of developmental disruptions arising from environmental or genetic stress). LB 1 is more asymmetrical than the human mean (but within the range of variation), and roughly in the middle of the range of variation for fossil hominins. This suggests to the authors that LB1 is not pathologically asymmetrical, and that asymmetry in the fossil is rather likely due to effects of fossilization. Unfortunately, however, the issue of pathology-related asymmetry is not wholly adequately addressed, so this result must be taken with a grain of salt (fluctuating asymmetry is generally believed to indicate developmental disruptions, and there are two other types of asymmetry that must be factored out…). It is at this point that some GM qualms I have come to the fore. Really there’s one issue specifically: homology and measurement error.

As mentioned above, GM statistically analyzes shapes using landmark coordinates as variables. Of course when comparing things, you want to make sure you’re actually comparing equivalent things (“homologous” structures). So on a cranium there are a few, which Bookstein identified as “Type I,” and are often the intersections of bony sutures, such as the point where your two nasal bones contact your frontal bone. But beyond that, many landmarks are extrema (“Types II-III), i.e. points of widest breadth, which are not necessarily (ever?) homologous structures. The trouble, then, is a large risk of comparing non-homologous structures, which can render biological analyses nearly meaningless. Additionally, many of these such points must be found fairly arbitrarily, which means that even if given landmarks are homologous (i.e. biologically meaningful), there is a good chance of measurement error confounding the study–this is especially true in fluctuating asymmetry studies.

Use of these Type II-III landmarks is not terrible, it’s just a reason to be wary. One must ask, based on how arbitrarily a landmark was found, and the likelihood of measurement error, how meaningful will the results be? One landmark that comes to mind from this study is alare, “the most lateral point on the margin of the nasal aperture.” How significant is ‘lateral-most’ as a criterion–is there something functionally important about this point, and is it very variable within a given taxon (I really do not know, but now I’m interested…)? Moreover, the margins of the nasal aperture (“nose hole”) are not always sharply delineated, but can be rounded, making the margin itself difficult to identify: for example, OH 5 has very rounded margins, but KNM-ER 406 seems to have sharp margins–both specimens are Australopithecus boisei. In this study, alare contributed second most to individual asymmetry in all taxa. Is this because of measurement error, or the fact that this is not a biologically significant point, or both/neither? Other fun landmarks include “malar root origin,” and “Frontomalare temporale… The point where the frontozygomatic suture crosses the temporal line (or outer orbital rim)” (my emphasis). So throughout the study, you took either one intersection or the other?! When did you use which one, and why? Homology FAIL. Maybe I (or someone else) will come up with a new (hopefully better) way to study asymmetry… Now I’ve lost my train of thought.

References
Baab K and McNulty K. Size, shape and asymmetry in fossil hominins: The status of the LB1 cranium based on 3D morphometric analyses. J Hum Evol, in press.

Gordon A, Nevell L, and Wood B. 2008. The Homo floresiensis cranium (LB1): Size, scaling, and early Homo affinities. Proc Nat Acad Sci 105: 4650-4655.

Zacharoo Whereabouts

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As Caroline noted, I have been Missing In Action for a while. So I’m sure the people who read the blog but aren’t in my program (so what, like 1.5 people?) are curious as to where I’ve been and what I’ve been doing.

To begin, I spent the first half of summer here in lovely Ann Arbor, working as a research assistant at UM’s Transportation Research Institute (UMTRI) in the biosciences division. There I basically did the tedious work cleaning up and prepping data so that my boss could analyze them. Mostly I digitized pelves and landmarks from CT scans, which was cool at first but got old pretty fast. Then I had to clean up these laser scans of bodies, which was even more boring than pelvis digitization. Then I left at the beginning of July, and I’ll start working there again today or tomorrow. Though a bit boring, the job provided a good introduction to modern methods, and I got paid a graduate student wage for doing work a competent undergrad could do. So I’m not going to complain too much.

So I left in July to attend a geometric morphometrics (GMM) summer school (that was 4 days long) hosted by the University of Vienna and the European Virtual Anthropology Network (EVAN). Geometric morphometrics is basically just a fancy way of saying ‘quantification and statistical study of shapes.’ Though the field has been developing since the 1970s with the work of Kendall on the distribution of archaeological sites, this methodology has become quite refined and very popular in recent years among biologists. Using the coordinates of landmarks (the most popular of which tend to be intersections of bony sutures on a cranium, for example) as individual variables, shapes (again, often of crania) can be summarized by numbers and subject to statistical analyses. A lot of interesting biological information can be discovered from shapes (say, of crania and their parts, of bee wings, etc.), and GMM preserves all shape data, much of which is can be less well preserved from more traditional morphometric methods (like using just distance ratios and angles).

I was sent there to work on a reconstruction project (of a famous fossil), which I have alluded to in previous posts. After I finished molding and casting the various bones of the cranium I was intending to reconstruct, I started looking into GMM as a means of reconstructing the cranium, using a fairly complete specimen of the same species as a reference. My advisor contacted the Viennese and EVAN for advice, and they ended up bringing me to Vienna to learn some methods and discuss collaborating on the reconstruction. But here’s the rub: my advisor did not tell them which fossil we intended to reconstruct, for fear that they might simply take the idea and do it more quickly than I could. So once I was out there I had to talk to their people about the logistics of the project, and which specimen we would reconstruct would, of course, be revealed. At lunch I went over the basic idea—what specimen we’d be reconstructing, which one we’d use as the reference, etc—and there was a brief silence. Their guy was smiling and kind of chuckled and said (paraphrase), “Well, that sounds like a good project. But we have a conflict of interest, because we’re already planning on reconstructing that specimen to do some biomechanical study. We are already working with one group in America and have a grant for it. We’ve been planning this for a few years.” I definitely was not expecting this.

At which point I maintained a cool façade, but was in fact so freaked out that I was crapping not just my own pants, but everyone’s pants in the whole restaurant. EVAN has paid for me to fly out to them, for my accommodations and course fees, and even for me to attend their other activities, under the condition that we collaborate on this project that I can’t do with them anymore. But their guy (let’s call him GW) is very nice about it. He is smiling and tells me we’ll have to come up with a new project on which to collaborate. He even paid for lunch, even though I had wanted to take him to lunch. For about a day and half after this conversation I was freaking out pretty badly, scrambling to come up with a new, interesting research question that could be addressed with GMM, so that their bringing me to Vienna was not a complete waste of a lot of money. Then I came up with an idea that I thought was pretty interesting, GW said it was interesting when I presented it to him, and so I think things might work out. Now I need to start talking to my advisor about the new project and get in contact with GW and EVAN so that we can start collaborating. Hopefully everything will work out this time.

I learned some very important lessons from this whole experience, starting with the reconstruction. I initially began this project last January, beginning with the molding and casting and not worrying about the actual analytical methods involved in the reconstruction. It was hard to work the molding and casting at the museum into my busy schedule, so of course I wasn’t done with the project by the end of the semester, when I’d intended to be done. So that’s the first lesson, as Milford put it (paraphrase), “Almost everything takes longer than you initially plan.” Lesson number two comes from the fact that the fabric of my plan completely unraveled basically at the very beginning, when all I did was tell GW my basic plan. Things fall apart, as Chinua Achebe wrote. Also, both Milford and GW have emphasized to me the paramount importance of having a good research question, and not simply to base your questions off of a method. But when I had to come up with a new project idea, I basically had to look for a question that could be answered with a specific method. But that’s not always a bad thing. When you’re fresh and green like I am, sometimes learning a method opens your eyes to the types of questions you can ask, and that’s what happened to me at the summer school (nevertheless, ideally the question should come first). Finally, the people from Vienna and EVAN were very nice, laid-back and intelligent, and I am really grateful to them for all I learned from them, about GMM and about life in general.

And after that hyper-intense week in the capital of the Eastern Empire, I spent the rest of the month in Croatia visiting my friend and peer Seki, examining some Bronze Age crania from Bosnia, trying to learn Croatian, and being awesome.

P.S. once I develop my new research idea and make sure it won’t blow up in my face like the last one I’ll post more about it.