Worst year in review

As we’re wrapping up what may be the worst year in recent global memory, especially geopolitically, let’s take a moment to review some more positive things that came up at Lawnchair in 2016.

Headed home

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Alternate subtitle: Go West
This was a quiet year on the blog, with only 18 posts compared with the roughly thirty per year in 2014-2015. The major reason for the silence was that I moved from Kazakhstan back to the US to join the Anthropology Department at Vassar College in New York. With all the movement there was  less time to blog. Much of the second half of 2016 was spent setting up the Biological Anthropology Lab at Vassar, which will focus on “virtual” anthropology, including 3D surface scanning…

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Cast of early Homo cranium KNM-ER 1470 and 3D surface scan made in the lab using an Artec Spider.

… and 3D printing.

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gibbon endocast, created from a CT scan using Avizo software and printed on a Zortrax M200.

This first semester stateside I reworked my ‘Intro to Bio Anthro’ and ‘Race’ courses, which I think went pretty well being presented to an American audience for the first time. The latter class examines human biological variation, situating empirical observations in modern and historical social contexts. This is an especially important class today as 2016 saw a rise in nationalist and racist movements across the globe. Just yesterday Sarah Zhang published an essay in The Atlantic titled, “Will the Alt-right peddle a new kind of racist genetics?” It’s a great read, and I’m pleased to say that in the Race class this semester, we addressed all of the various social and scientific issues that came up in that piece. Admittedly though, I’m dismayed that this scary question has to be raised at this point in time, but it’s important for scholars to address and publicize given our society’s tragically short and selective memory.

So the first semester went well, and next semester I’ll be teaching a seminar focused on Homo naledi and a mid-level course on the prehistory of Central Asia. The Homo naledi class will be lots of fun, as we’ll used 3D printouts of H. naledi and other hominin species to address questions in human evolution. The Central Asia class will be good prep for when I return to Kazakhstan next summer to continue the hunt for human fossils in the country.

Osteology is still everywhere

A recurring segment over the years has been “Osteology Everywhere,” in which I recount how something I’ve seen out and about reminds me of a certain bone or fossil. Five of the blog 18 posts this year were OAs, and four of these were fossiliferous: I saw …

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Anatomy terminology hidden in 3D block letters,

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Hominin canines in Kazakhstani baursaki cakes,

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The Ardipithecus ramidus ilium in Almaty,

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Homo naledi juvenile femur head in nutmeg,

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And a Homo erectus cranium on a Bangkok sidewalk. As I’m teaching a fossil-focused seminar next semester, OA will probably become increasingly about fossils, and I’ll probably get my students involved in the fun as well.

New discoveries and enduring questions

The most-read post on the blog this year was about the recovery of the oldest human Nuclear DNA, from the 450,000 year old Sima de los Huesos fossils. My 2013 prediction that nuclear DNA would conflict with mtDNA by showing these hominins to be closer to Neandertals than Denisovans was shown to be correct.

giphy

These results are significant in part because they demonstrate one way that new insights can be gained from fossils that have been known for years. But more intriguingly, the ability of researchers to extract DNA from exceedingly old fossils suggests that this is only the tip of the iceberg.

The other major discoveries I covered this year were the capuchin monkeys who made stone tools and the possibility that living humans and extinct Neandertals share a common pattern of brain development.

Pride & Predator

An unrelated image from 2016 that makes me laugh.

The comparison between monkey-made and anthropogenic stone tools drives home the now dated fact that humans aren’t the only rock-modifiers. But the significance for the evolution of human tool use is less clear cut – what are the parallels (if any) in the motivation and modification of rocks between hominins and capuchins, who haven’t shared a common ancestor for tens of millions of years? I’m sure we’ll hear more on that in the coming years.

In the case of whether Neandertal brain development is like that of humans, I pointed out that new study’s results differ from previous research probably because of differences samples and methods. The only way to reconcile this issue is for the two teams of researchers, one based in Zurich and the other in Leipzig, to come together or for a third party to try their hand at the analysis. Maybe we’ll see this in 2017, maybe not.

There were other cool things in 2016 that I just didn’t get around to writing about, such as the publication of new Laetoli footprints with accompanying free 3D scans, new papers on Homo naledi that are in press in the Journal of Human Evolution, and new analysis of old Lucy (Australopithecus afarensis) fossils suggesting that she spent a lifetime climbing trees but may have sucked at it. But here’s hoping that 2017 tops 2016, on the blog, in the fossil record, and basically on Earth in general.

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Bioanthro lab activity: Estimating Miocene ape body mass

We’ve arrived at the Planet of the Apes, also known as the Miocene, in my “Bones, Stones and Genomes” course. The living apes are but a small remnant of what was a pretty successful radiation starting around 20 million years ago. There were so many apes that it can be a bit confusing for students, but it’s important for setting up the biological and ecological contexts of hominin origins.

Possible evolutionary relationships of myriad Miocene apes and subsequent hominins. From Harrison (2010)

Possible evolutionary relationships of myriad Miocene apes and subsequent hominins. From Harrison (2010)

This week also marks my students’ first lab assignment, analyzing CT scans of bones. Here, we looked at how we estimate body size in extinct animals, using the KUPRI database and the free CT analysis software InVesalius. Because some of the KUPRI primates have body masses recorded, students can examine the relationship between animals’ weight and skeletal dimensions. The purpose of the assignment is to help familiarize students with skeletal anatomy, CT data and principles of linear regression.

One of the KUPRI specimens, an old female gorilla, with known weight.

One of the KUPRI specimens, an old female gorilla, with known weight.

I selected a few specimens for students to examine. After students download the massive files, they can load them into InVesalius for analysis. This program allows students to easily identify bone versus other tissues, and to create a 3D surface rendering of a highlighted region (tissue) of interest.

A grivet, Chlorocebus aethiops, with bone highlighted in 2D sections and as a 3D model.

A grivet, Chlorocebus aethiops, with bone highlighted in 2D sections and as a 3D model. This little guy weighs only 4 kg!

It’s pretty easy to take simple linear measurements (and angles), assuming students can get oriented within the skeleton and identify the features they need to measure. It can be a little tricky to measure a femur head if it’s still in the acetabulum (below). Luckily, InVesalius lets you take measurements on both 2D slices or the 3D volume.

Let's measure that femur head diameter.

Let’s measure that femur head diameter.

So students do this for a few specimens and enter the data into Excel, which can then easily plot the data and provide a regression equation. They then use this equation to estimate masses of the specimens – if there’s a good relationship between mass and skeletal measures, then the estimates should be close to the observed values. Students use their equation to predict body mass of some Miocene apes based on femur head diameter and femur midshaft diameter, noting how confident they feel in their estimates given how well their regression performed on the training dataset. They also compare their mass estimates to those using another equation generated by Christopher Ruff (2003).

It might be a little intense for students totally unfamiliar with apes, bones and CT scans, but it should be a good way for them to learn lots of concepts we’ll revisit over the semester.

Here’s the lab assignment, in case you want to use it in your own class: Lab 1-Miocene masses

Results of the toe-tally easy lab activity

Alternate title: Dorsal canting in primate PPP4s

Earlier this year I suggested a classroom activity in which students can scrutinize the evidence used to argue that the >5 million year old (mya) Ardipithecus kadabba was bipedal. To recap: Ar. kadabba is represented by some teeth, a broken lower jaw, and some fragmentary postcrania. The main piece of evidence that it is a human ancestor and not just any old ape is from a single toe bone, and the orientation of its proximal joint. In Ar. kadabba and animals that hyperdorxiflex their toes (i.e., humans and other bipeds when walking), this joint faces upward, whereas it points backward or even downward in apes. This “dorsal canting” of the proximal toe joint has also been used as evidence that the 4.4 mya Ardipithecus ramidus and 3.5 mya owner of the mystery foot from Burtele are bipedal hominins. A question remains, though – does this anatomy really distinguish locomotor groups such as bipeds from quadrupeds?

Use ImageJ to measure the canting angle between the proximal joint and plantar surface. Proximal to the right, distal to the left.

STUDENT SCIENTISTS TO THE RESCUE! Use ImageJ to measure the canting angle between the proximal joint and plantar surface, as I’ve done on this Japanese macaque monkey (they are not bipedal). Proximal to the right, distal to the left Note I changed the measured angle from the March post.

I sicked my students in Ant 364 (Human Evolutionary Developmental Biology) here at NU on this task. I had students look at only 11 modern primates from the awesome KUPRI database. Most groups are only represented by 1 (Homo sapiens, Hylobates lar and Macaca fuscata) or two (Pongo species and Gorilla gorilla) specimens, all adults. For chimpanzees (Pan troglodytes) there is one infant and four adults. The database has more individuals, and it would be better to include more specimens to get better ideas of species’ ranges of variation, but this is a good training sample for a class assignment. The fossil group includes one Ardipithecus ramidus, one Ar. kadabba, one Australopithecus afarensis, and the PPP4 of the mystery foot from Burtele. The human and all fossils except Ar. kadabba are based off of lateral photographs and not CT scans like for the living primates, meaning there may be some error in their measurements, but we’ll assume for the assignment this is not a problem. Here are their results:

Dorsal canting angle of the fourth proximal pedal phalanx in primates.

Dorsal canting angle of the fourth proximal pedal phalanx in primates. The lower the angle, the more dorsally canted the proximal joint surface. The “Fossil” group includes specimens attributed to ArdipithecusAustralopithecus and something unknown.

Great apes have fairly high angles, meaning generally not dorsally canted proximal joint surfaces. The two gorillas fall right in the adult chimpanzee (adult) range of variation, while chimp infant and orangutans have much higher angles (≥90º means they’re actually angled downward or plantarly). The gibbon (Hylobates) is slightly lower than the chimpanzee range. The macaque has an even more dorsally canted joint, and the human even more so. The fossils, except the measurement for Ar. ramidus (see note above), have lower angles than living apes, but higher than the human and the monkey. If dorsal canting really is really a bony adaptation to forces experienced during life, then the fossil angles suggest these animals’ toes were dorsiflexed more so than living great apes (but not as much as the single monkey and human).

This lab helps students become familiar with CT data, the fossil record, taking measurements (students also measure maximum length of the toe bones and look at the relationship between length and canting), analyzing data, and hypothesis testing. You can also have fun exploring inter-observer error by comparing students’ measurements.

Here’s the full lab handout if you want to use or modify it for your own class: Lab 5-Toe instructions and report

Online skeletal and dental datasets (links links links!)

The TM 1517a fossil, from here

Jean Jacques Hublin has a commentary [1] in the current issue of Nature, about making fossils available for scanning, digital replication, and ultimately hopefully open dissemination. As Hublin points out, it’s a bit ridiculous that a fossil is a rare enough thing as it is, but even after their discovery, fossils “can become unreachable relics once they are in storage.” Fortunately, Hublin goes on to point to online collections that are available to anyone interested. Somewhat ironically, the article about free-ish data is behind a paywall, so here are the resources Hublin describes:

  • The Ditsong CT Archive, created by the collaboration of Hublin’s group at Max Planck and the Ditsong (formerly Transvaal) Museum in South Africa, which contains digitized hominin fossils from the site of Kromdraai (see also [ref 2]). Check out the type specimen of Paranthropus robustus, from this site, above!
  • You can download CT scans of the Skhul V early human fossil, thanks to the Harvard Peabody Museum.
  • Wanna see the the oldest possible animal embryos, early humans, insects, and other crazy fossils? Check out the European Synchrotron Radiation Facility’s microCT database.
  • Get free CT scans of 2 human skulls, thanks to the Virtual Anthropology program at the University of Vienna.
  • Finally, the NESPOS initiative is a large repository of Pleistocene hominin fossil scans, which I somehow don’t know enough about.

In addition to these sources, here are 2 other datasets that are pretty badass:

ResearchBlogging.orgI haven’t had much opportunity to look into these datasets Hublin pointed out, but they look promising. If you know of other good resources, please do share!

References
[1] Hublin, J. (2013). Palaeontology: Free digital scans of human fossils Nature, 497 (7448), 183-183 DOI: 10.1038/497183a

[2] Skinner MM, Kivell TL, Potze S, & Hublin JJ (2013). Microtomographic archive of fossil hominin specimens from Kromdraai B, South Africa. Journal of human evolution, 64 (5), 434-47 PMID: 23541384

An end to Ediacaran embryology?

The things people can do these days. Therese Huldtgren and colleagues reported in last week’s Science that they identified nucleus-like structures in 570 million year old fossilized cells from China. These date to the Ediacaran period, before the “Cambrian explosion” of animal life forms. Superficially, these fossilized balls of cells rather resemble the early stages of animal embryos (see A in the figure below), in which cells are dividing and increasing in number but the overall embryo size stays the same. To get the “inside story” (…sorry), Huldtgren and team used very fancy “synchrotron x-ray computed tomography” to look at the insides of these fossilized cells. The resulting images have micrometer resolution – that’s one thousandth* of a millimeter. The things people can do these days.

Fig. 2 from Huldtgren et al. 2011

And lo! each of these fossilized cells contains a small, globular structure that looks like a nucleus (left; if you cross your eyes you can merge the 2 halves of fig. C to make it look even more 3D).

Could these really be the earliest animal embryos? Probably not – some of these balls-of-cells had what resemble budding spores, unlike animals but similar to “nonmetazoan [non-animal] holozoans.” In other words, something neat and old, but not one of our earliest ancestors.

I’m really impressed with the biological applications of computed tomography (CT). Recall that a while ago, I posted about the potential to use synchrotron tomography to examine the small-scale, internal structure of bone (e.g. Cooper et al. 2011). Such non-destructive, high-resolution imaging techniques could be used to compare near-cellular-level growth in living and fossil animals. This is really significant because it adds a completely new kind of information we can get from fossils, which before now could only be studied well at the gross, macroscopic level (though scanning electron microscopy of teeth has been very informative about diet; see for example Ungar and Sponheimer 2011). Indeed, one of the most common applications of CT imaging in anthropology is making 3D computer models of body parts for morphometric (shape) analysis.

But high-resolution, synchrotron CT imaging opens up a whole new world of paleontology, new questions that can be asked. For example, many researchers have examined the microscopic appearance of bone surfaces to determine whether bone was being added or removed during growth, and comparing different species (Bromage 1989, O’Higgins et al. 2001, McCollum 2008, Martinez-Mata et al. 2010). These have been very informative studies, but it is not totally clear how growth at the cellular level relates to growth at visible level. Moreover, fossil surfaces are often abraded, obfuscating surface details. So, I can envision using synchrotron microscopy similar to Cooper et al. (2011) and Huldtgren et al. (2011), to examine bone growth in fossil hominids, at and beneath the surface. This can help us understand how facial growth was modified over the course of human evolution, from the snouty visage of Australopithecus afarensis to the tiny, starry-eyed faces we have today. People could also examine how activities like chewing, running or even talking affect (and effect) bone growth. There is much work to be done.

ResearchBlogging.orgNeat as these projects would be, it’s pretty humbling to consider that we have the technology to analyze microscopic fossils hundreds of millions of years old, and shed light on the developmental processes in our earliest ancestors.

Read those things I’d mentioned

BROMAGE, T. (1989). Ontogeny of the early hominid face Journal of Human Evolution, 18 (8), 751-773 DOI: 10.1016/0047-2484(89)90088-2

Cooper, D., Erickson, B., Peele, A., Hannah, K., Thomas, C., & Clement, J. (2011). Visualization of 3D osteon morphology by synchrotron radiation micro-CT Journal of Anatomy, 219 (4), 481-489 DOI: 10.1111/j.1469-7580.2011.01398.x

Huldtgren, T., Cunningham, J., Yin, C., Stampanoni, M., Marone, F., Donoghue, P., & Bengtson, S. (2011). Fossilized Nuclei and Germination Structures Identify Ediacaran “Animal Embryos” as Encysting Protists Science, 334 (6063), 1696-1699 DOI: 10.1126/science.1209537

Martinez-Maza, C., Rosas, A., & Nieto-Diaz, M. (2010). Brief communication: Identification of bone formation and resorption surfaces by reflected light microscopy American Journal of Physical Anthropology, 143 (2), 313-320 DOI: 10.1002/ajpa.21352

McCollum, M. (2008). Nasomaxillary remodeling and facial form in robust Australopithecus: a reassessment Journal of Human Evolution, 54 (1), 2-14 DOI: 10.1016/j.jhevol.2007.05.013

O’Higgins, P., Chadfield, P., & Jones, N. (2001). Facial growth and the ontogeny of morphological variation within and between the primates Cebus apella and Cercocebus torquatus Journal of Zoology, 254 (3), 337-357 DOI: 10.1017/S095283690100084X

Ungar, P., & Sponheimer, M. (2011). The Diets of Early Hominins Science, 334 (6053), 190-193 DOI: 10.1126/science.1207701

Look inside bones for free on the interwebs

I forget how I stumbled upon this badass resource, but Kyoto University’s Primate Research Institute made a “Digital Morphology Museum: an awesome online database of CT scans of sundry primate skeletal parts. Ever wonder what an articulated siamang skeleton looks like? Or whether the flaring bony snout of a mandrill is hollow or filled with bone (below)? If you’re a normal person, probably not. But either way, this website provides easy access to the internal views of all sorts of body parts.

Coronal slice through a male mandrill face.  You can see a bone-filled lower jaw,  internal views of some teeth, the nasal cavity. The pics above and on the right give an idea of where in the skull we are. Note the fat flanks above the nasal cavity are filled with bone (they hollow out as you move further into the face).

What’s cool is you can view and manipulate 3D views of these things on the website, or you can register with KUPRI to download the raw CT data. Really a great resource.

A few weeks ago, a paper came out wherein researchers used CT scans to compare the the sides of the nasal opening in skulls of Australopithecus species (Villmoare and Kimbel 2011). They found that although the external nose of the South African Australopithecus africanus and A. robustus appear similar in looking like rounded “pillars,” on the inside these pillars differed between the two species. A. africanus‘s (and the earlier, east African A. afarensis‘s) nasal pillar was hollow, while A. robustus‘s was filled with “spongy” bone, like the contemporaneous A. boisei in East Africa. So the early (and “gracile”) australopiths had hollow pillars while the later (and “robust”) ones had a bony pillar, hmm… It’d be neat to try to see how such bone-filled or hollow pillars develop (i.e. are they hollow in babies but then fill with trabecular bone during growth in the “robust” group? Does this difference arise for functional (e.g. chewing) reasons, or could it be a developmental ‘byproduct’ of the tall robust australopithecine face [cf. McCollum 1999]).

It’s a neat study, and they include lots of great CT images of the hominid sample. But another question arises – what is the inside of the bony nose like in modern primates, and how much variation is there within a species? (NB Villmoare and Kimbel found pretty much no variation within each fossil species, save for two curious examples, but which were based on casts). If I had the time (i.e. weren’t dissertation-ating) I’d love to peruse the KUPRI files to see what “pillar” variation is like in, say, chimps (paleoanthropologists’ go-to referent species). Cursorily looking at just one (female chimpanzee, left), it looks like the sides of the nose are empty higher up, but then fill with bone to form the tooth socket surrounding the canine root. I’ll leave it to someone else to see what the rest look like.

But just lookit what other fun stuff you can see! At the top (anatomically toward the back) are the bone-filled mandibular condyles, beneath (anatomically a bit more toward the front) and between them are the pterygoid plates, and beneath them is a big gross maxillary sinus. Man, if only I had the time, I’d make an anatomy scavenger hunt on this site, and it’d be pretty epic.
ResearchBlogging.org


Those papers I mentioned
McCollum, M. (1999). The Robust Australopithecine Face: A Morphogenetic Perspective Science, 284 (5412), 301-305 DOI: 10.1126/science.284.5412.301

Villmoare, B., & Kimbel, W. (2011). CT-based study of internal structure of the anterior pillar in extinct hominins and its implications for the phylogeny of robust Australopithecus Proceedings of the National Academy of Sciences, 108 (39), 16200-16205 DOI: 10.1073/pnas.1105844108

Pictures worth thousands of words and dollars

ResearchBlogging.orgLooking into subdural empyema, which is a meningeal infection you don’t want, I stumbled upon a study from the roaring 1970s – the glorious Nixon-Ford-Carter years – using computerized axial tomography (hence, CAT scan) to visualize lesions within the skull (Claveria et al. 1976). Nowadays people refer to various similar scanning techniques simply as “CT” (for computed tomography, though this is not exactly the same as magnetic resonance imaging, MRI).

It’s pretty amazing how medical imaging has advanced in the 35 years since this study. For example, to the right is a CAT scan from Claveria et al. (1976, Fig. 4). These are transverse images (“slices”) through the brain case, the top of the images corresponding to the front of the face. You can discern the low-density (darker) brain from the higher density (lighter) bone – the sphenoid lesser wings and dorsum sellae, and petrous pyramids of the temporal bones are especially prominent in the top left image. In the bottom two images you can see a large, round abscess in the middle cranial fossa. Whoa.

What makes this medical imaging technique so great is that it allows a view inside of things without having to dissect into them. Of course, the downside is that it relies on radiation, so ethically you can’t be so cavalier as to CT scan just any living thing. If I’d been alive in 1976, CAT scanning would’ve blown my mind. Still, the image quality isn’t super great here, there’s not good resolution between materials of different densities, hence the grainy images.

But since then, some really smart people have been hard at work to come up with new ways to get better resolution from computerized tomography scans, and the results are pretty amazing. To the left is a slice from a synchrotron CT scan of the MH1 Australopithecus sediba skull (Carlson et al. 2011, Supporting on line material, Fig. S10). You’re basically seeing the fossil face-to-face … if someone had cut of the first few centimeters of the fossil’s face. Just like the movie Face Off.

Quite a difference from the image above. Here, we can distinguish fossilized bone from the rocky matrix filling in the orbit, brain case and sinuses. Synchrotron even distinguishes molar tooth enamel from the underlying dentin (see the square). The post-mortem distortion to the (camera right) orbit is clear. It also looks as though the hard palate is thick and filled with trabecular bone, as is characteristic of robust Australopithecus (McCollum 1999). Interesting…

Even more remarkable, the actual histological structure of bone can be imaged with synchrotron imaging. Mature cortical bone is comprised of these small osteons (or Haversian systems), that house bone cells and transmit blood vessels to help keep bone alive and healthy. Osteons are very tiny, submillimetric. To the right is a 3D reconstruction of an osteon and blood vessels, from synchrotron images (Cooper et al. 2011). The scale bar in the bottom right is 250 micrometers. MICROmeters! Note the scan can distinguish the Haversian canal (red part in B-C) from vessels (white part in B). Insane!

Not only has image quality improved over the past few decades, but CT scanning is being applied outside the field of medicine for which it was developed; it’s becoming quite popular in anthropology. What I’d like to do, personally, with such imaging is see if it can be used to study bone morphogenesis – if it can be used to distinguish bone deposition vs. resorption, and to see how these growth fields are distributed across a bone during ontogeny. This could allow the study the proximate, cellular causes of skeletal form, how this form arises through growth and development. If it could be applied to fossils, then we could potentially even see how these growth fields are altered over the course of evolution: how form evolves.

References
Carlson KJ, Stout D, Jashashvili T, de Ruiter DJ, Tafforeau P, Carlson K, & Berger LR (2011). The endocast of MH1, Australopithecus sediba. Science (New York, N.Y.), 333 (6048), 1402-7 PMID: 21903804

Claveria, L., Boulay, G., & Moseley, I. (1976). Intracranial infections: Investigation by computerized axial tomography Neuroradiology, 12 (2), 59-71 DOI: 10.1007/BF00333121

Cooper, D., Erickson, B., Peele, A., Hannah, K., Thomas, C., & Clement, J. (2011). Visualization of 3D osteon morphology by synchrotron radiation micro-CT Journal of Anatomy, 219 (4), 481-489 DOI: 10.1111/j.1469-7580.2011.01398.x

McCollum, M. (1999). The Robust Australopithecine Face: A Morphogenetic Perspective Science, 284 (5412), 301-305 DOI: 10.1126/science.284.5412.301