Osteology everywhere: Pelvis has left the building

The vernal awakening has brought rain to Ann Arbor, and right on here on main campus I spotted the rain-splotched silhouette of an articulated human pelvis (left).

Check out those short and flaring iliac blades, and the shortness of the ischium. These features are associated with repositioning key muscles for walking and running on two feet, and are very unlike what is seen in the four-legged, suspensory climbing apes.

But just how 'human' are these features? The crushed pelvis of Oreopithecus bambolii, a ~8 million year old fossil ape from Italy, has somewhat human-like short ilia (left). This pelvis also has weak anterior inferior iliac spines (Rook et al. 1999), which anchor the hip/trunk flexor muscle rectus femoris, and are allegedly a developmental novelty seen only in hominids (Lovejoy et al. 2009). These traits have led some to claim that Oreopithecus was a hominid, or at least bipedal. Without getting into that debate, I'll just say that seeing these 'bipedal' features in this late Miocene ape's pelvis weakens the case that their presence in Ardipithecus ramidus indicates a unique connection between Ardi and later, true hominids like australopiths.


UPDATE: Check the comments for notes on the Ardi and Oreo fossils from someone who's actually studied them (I myself have only seen pictures and read about them).

References
Lovejoy, C., Suwa, G., Spurlock, L., Asfaw, B., & White, T. (2009). The Pelvis and Femur of Ardipithecus ramidus: The Emergence of Upright Walking Science, 326 (5949), 71-71 DOI: 10.1126/science.1175831

Rook, L. (1999). Oreopithecus was a bipedal ape after all: Evidence from the iliac cancellous architecture Proceedings of the National Academy of Sciences, 96 (15), 8795-8799 DOI: 10.1073/pnas.96.15.8795

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 - africanfossils.org. 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...

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.)

Anyone 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

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 the ASK-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.

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

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.

Those 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

Taking back Epigenetics

If I'm good at anything, it's looking into one topic and then getting distracted by something else during my search. In a recent case, I was scouring the literature on growth and life history. One ribald thing led to another, and next thing I know I've stumbled upon Gunter Wagner's recent review of the book Epigenetics: Linking Genotype and Phenotype in Development and Evolution. WTF is epigenetics, you ask? That's actually a pretty good question (see here). In the past several years, the term has most often been associated with the causes/effects of structural modifications to chromatin (the DNA-containing stuff that makes up chromosomes). For sure, coincident with Wagner's review, a paper in last week's Nature Reviews Genetics defines epigenetics as "the study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence." (Feil and Fraga 2012).

This is an extremely narrow focus for a term that was originally meant to be about basically everything besides genes that contribute to an organism's phenotype (this idea was developed by the great, rather underrated, 20th century biologist Conrad Waddington). Lotsa epigenetics research by the narrow definition (i.e. modifications to histones and chromatin) focuses on how cells - not organisms - retain their identity/function (or, phenotype). Epigenetics in the narrow sense are important determinants of an organism's phenotype, but these alone are insufficient to understand how and why organisms' become the way they are. Yes, the narrow definition leaves room for environmental influences on gene expression (though "environment" could refer to the state of affairs within a cell or an organism, in addition to the outside world). But it nevertheless imparts agency solely to genes in affecting an organism becomes.

And this is what the aforesaid book and review are about. Wagner asks, "what would be lost if the original perspective of epigentics [as defined by Waddington] was lost to science?" This is important because an organism is not simply a robotic readout of its genes, but people cannot seem to shake this centuries-old biological determinism.

Is that a homunculus
in your [sperm's]
pocket?

In the early days of 'modern' (or let's say 'recent') biology, there was a popular idea of "Preformationism," that animals grew from these pre-formed miniature versions of themselves (homunculi) in germ cells. It did not take long for this idea to be quashed, but the underlying idea persisted. Wagner recounts, "With the rise of genetics during the 20th century, however, a new form of quasi-preformism arose, basically replacing the old homunculus with the genome, whereas the developmental process creating the phenotype was put in a black box" (emphasis mine). [See Gilbert et al. (1996) for a nice historical overview describing how the rise of population genetics in the early 20th century left embryology and developmental biology by the wayside of the Modern Evolutionary Synthesis]

This latent desire to essentialize biology to some singular determinant (be it an homunculus or a gene) is something people just can't get away from. Srsly, there's a persistent sentiment in biology that Real Science is only the high-profile, lab-coated work in genetics. Along these lines, even I adopted the recently popular narrow view of "epigenetics" a while back when I dated a woman who worked at an epigenetics lab, in hindsight probably so I would sound more like a capital-S Scientist (below).

Hipster scientist. H3S10 phosphorylation correlates with 

decreased levels of heterochromatin, possibly regulating

chromosome condensation (Chenet al 2008). Image: bit.ly/zEfPaq

Of course, genes code for how a cell should behave, but we have this tendency to want to extrapolate from the cell to the organism, and this is where developmental biology becomes a critical link. And this is what the new Epigenetics book is about (so far as I can tell, I haven't yet had a chance to read it all).

It's abundantly clear that phenotypes arise out of an inextricably complex series of interactions - between genes, proteins, cells, tissues, environments, etc. These interactions do not occur solely at the genetic (or narrow-sense epigenetic) level. Developmental biology helps 'connect the dots' between genes and morphology, but cannot do so by focusing solely on genes and chromatin.

References
Chen, E., Zhang, K., Nicolas, E., Cam, H., Zofall, M., & Grewal, S. (2008). Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature, 451 (7179), 734-737 DOI: 10.1038/nature06561


Feil, R., & Fraga, M. (2012). Epigenetics and the environment: emerging patterns and implications. Nature Reviews Genetics DOI: 10.1038/nrg3142

Gilbert, S. (1996). Resynthesizing Evolutionary and Developmental Biology. Developmental Biology, 173 (2), 357-372 DOI: 10.1006/dbio.1996.0032

Hallgrímsson B and Hall BK, eds. 2011. Epigenetics: Linking Genotype and Phenotype in Development and Evolution. Berkeley: University of California Press.

Wagner, G. (2011). Epigenetics in all its beauty Trends in Ecology & Evolution DOI: 10.1016/j.tree.2011.09.003

A little reassurance

I was putting together a lab lesson for this week, focusing on the skeletal differences between living apes and Old World monkeys, when I'd noticed the distal humerus of this gorilla (Gorilla gorilla, not the most "scientific-sounding Latin names," right?). Looks kinda like a thumbs-up, I thought. It seemed to say, "Keep up the good work, kid!" And that's when I knew it was time to get some sleep.