A new year of bioanthro lab activities

September 6, 2015September 6, 2015 / zcofran / 3 Comments

One of my goals in teaching is to introduce students to how we come to know things in biological anthropology, and lab activities give students hands-on experience in using scientific approaches to address research questions. Biological anthropology (really, all biology) is about understanding variation, and I’ve created some labs for students to scrutinize biological variation within the classroom.

In my Introduction class, the first aspect of human uniqueness we will focus on is the brain. To complement readings and lectures, we’ll also investigate variation in brain size among students in class. Of course, measuring their actual brain sizes is impossible without either murdering them (unethical and messy) or subjecting them to CT or MRI scanning (costly and time-consuming). Instead, it’s fast and easy to measure head circumference, so we’ll estimate just how brainy they are in a way that will also introduce them to data collection, measurement error, and the regression analysis.

The lab activity is based on a paper by Bartholomeusz and colleagues (2002), who used CT scanning to measure the external head circumferences and brain volumes of males ranging from 1-40 years. Focusing on the adults of this sample, there are several possible regression equations that students could use to estimate their brain size from their head circumference:

The relationship between head circumference and brain volume in adult humans. Note each regression line is based on different age groups. Data from Bartholomeusz et al. (2002).

Bartholomeusz et al. divided their sample into age groups, and students will learn that the relationship between the two variables differs subtly depending on the age group. Students will therefore have to decide (and justify) which equation they will use – should they pick the one based on their own age group, or the one with the lowest prediction error?

Once students have estimated their brain sizes, I’ll enter the data into R and we’ll look at how (estimated) brain size varies within the classroom, looking also at possible covariates including sex and region of birth. After discussing our data in class, students have to write up a brief report describing our research question and proposing additional hypotheses about brain size variation.

So that’s this week’s lab in Introduction to Biological Anthropology. There will be four more this semester, in three of which students will collect data on themselves, as well as four other labs for my Human Evolution course. In case you’re interested in using this activity for your class, I’m including the lab handout here. I’ll also try to post lab assignments to the blog (as I’ve done here) as the semester progresses.

Activity handout: Lab 1 Instructions and report

Reference

Bartholomeusz, H., Courchesne, E., & Karns, C. (2002). Relationship Between Head Circumference and Brain Volume in Healthy Normal Toddlers, Children, and Adults Neuropediatrics, 33 (5), 239-241 DOI: 10.1055/s-2002-36735

Virtual paleontology activity

April 19, 2015April 19, 2015 / zcofran / Leave a comment

Last week Nazarbayev University hosted an Instructional Technology Showcase, in which professors demonstrated some of the ways we use technology in the classroom. This was the perfect venue to show off the sweet skeletal stuff we study in Biological Anthropology, through the use of pretty “virtual” fossils. In the past year I’ve started using CT and laser scans of skeletal remains to make lab activities in a few classes (I’ve posted two here and here). Such virtual specimens are especially useful since it is hard to get skeletal materials and casts of fossils here in the middle of the Steppe. These scans are pretty accurate, and what’s more, 3D printing technology has advanced such that physical copies of surface scans can be created from these virtual models. So for the Showcase, I had a table where passersby could try their hand at measuring fossils both in hand and in silico.

Lower jaw of an infant Australopithecus boisei (KNM ER 1477). Left is the plastic cast printed from the laser scan on the right.

The Robotics Department over in the School of Science and Technology was kind enough to print out two fossils: KNM ER 1477, an infant Australopithecus boisei mandible, and KNM KP 271 a distal humerus of Australopithecus anamensis. They used a UP Plus 2 printer, a small desktop printer that basically stacks layers of melted plastic to create 3D models; they said it took about 9 hours to print the pair. Before the Showcase, I measured the computer and printed models on my own for comparison with published measurements taken on the original fossils (KP 271 from Patterson and Howells, 1967; ER 1477 from Wood, 1991). The virtual fossils were measured using the free program Meshlab, while basic sliding calipers were used to measure the printed casts.

I was pleasantly surprised at how similar my measurements were to the published values (usually within 0.1 mm), since it means that the free fossil scans provided by the National Museums of Kenya are useful not only for teaching, but potentially also for research.

The Virtual Paleontology Lab. The Kanapoi distal humerus is held in the foreground while the A. bosei jaw rests on the table. Yes, those are real palm trees.

Knowing that these models are pretty true to life (well, true to death, since they’re fossils), I was curious how students, faculty and staff would do. I picked two fairly simple measurements for each fossil. None of the people that came by to participate had any experience with bones or fossils, or measuring these in person or on a computer. Here are their results:

Boxplots showing participants’ data, for two measurements on each of the fossils. The blue stars mark the published values. The red rugs on either side indicate measurements taken on the scans (left side) or printed casts (right).

For the most part, the inexperienced participants’ measurements are not too far off from the published values. There’s not really an apparent tendency for either cast or computer measurements to be more accurate, although measurements of the Kanapoi humerus are closer than the computer measurements (third and fourth boxes above). In my personal opinion, nothing beats handling fossils (or casts of them) directly, but this little activity suggests students can still make reliable observations using 3D scans on a computer.

Sweet free stuff:
Meshlab software
3D scans of fossils from the National Museums of Kenya

Results of the toe-tally easy lab activity

December 3, 2014 / zcofran / 4 Comments

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. The lower the angle, the more dorsally canted the proximal joint surface. The “Fossil” group includes specimens attributed to Ardipithecus, Australopithecus 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

Lessons from limb lab (activity)

November 16, 2014 / zcofran / 1 Comment

This semester I have added a lab component to my Introduction to Biological Anthropology class. Lab activities and assignments provide students with opportunities to gather data, to think about them in the context of various theories, and to learn about how to analyze them. This past week’s lab looked at limb proportions within our classroom, in the context of “Allen’s rule” – in colder climates, animals tend to have relatively shorter distal limbs (radius+ulna and tibia+fibula). Allen’s rule, along with “Bergmann’s rule,” describe ecogeographic variation in humans and other animals: body size (i.e., mass) and shape (i.e., limb proportions) tend to vary with climate, such that populations living in colder environments tend to have less surface area relative to body mass, as an adapation to retain body heat.

A simple and effective way to quantify the relative lengths of limbs is through ratios: in this case we examined the crural and brachial indices. Here I’ve plotted average human indices against latitude as reported in a recent paper by Helen Kurki and colleagues (2008):

Left: Crural index (tibia length/femur length) related to latitude, as a proxy for climate. Right: Brachial index (radius length/humerus length) plotted against latitude. Data from Kurki et al. (2008). Black=female, red=male. Dashed lines are regression slopes for each sex, and solid lines indicate the 95% confidence limits of the regression lines.

Human limb proportions related to latitude, as a proxy for climate. Left: Crural index (tibia length/femur length). Right: Brachial index (radius length/humerus length). Higher indices mean relatively longer tibia or radius. Data from Kurki et al. (2008). Black=female, red=male. Dashed lines are least squares regression lines for each sex, and solid lines indicate the 95% confidence limits of the regression lines. How well will our class’s data fit these models?…

These plots are consistent with Allen’s rule – the distal limb segments become relatively shorter with increasing latitude. In lab, we test whether our limb proportions reflect this presumably ecogeographic pattern. Here in Astana we are at 51ºN latitude, so these regressions predict that our class should have crural indices between 0.82-0.84, and brachial indices between 0.72-0.79. How well does our class fit these model’s predictions?

…Pretty terribly. Plots are same as above, except with our class’s data added at 51º N latitude (vertical lines). In each, the vertical lines span the class’s 95% range (black=females, red=males), with the dots marking each sex’s average. Kazakhstan is huge, and students could have grown up in latitudes from 42º-55º N, but even assuming students had all come from Shymkent their distal limbs still appear much longer than expected.

These plots show that students in the class have longer distal limbs than expected – both for our latitude, and for humans generally. The poor fit of my students’ limb proportions probably doesn’t mean they’re bad humans. Instead, we probably deviate because we compared apples to oranges: the Kurki data were dry long bones measured on an osteometric board, whereas I had my students do their best to palpate and measure the maximum lengths of their own bones beneath layers of fat, muscle, skin, and clothing. Our high indices probably reflect the underestimation of humerus and femur lengths, whose most proximal points that can be palapated (greater tubercle and trochanter, respectively) lie a bit lower than the respective heads, which would have been included in the Kurki measurements.

It was interesting to review these plots with students. Even though they’re fairly new at reading graphs like these, there was an audible gasp and bewildered muttering when their own data went up on the board. I myself was surprised at these results, but I’m happy with how the exercise went. This particular ‘study’ helps students learn about ecogeography, adaptation and human variation, as well as the importance of homology and comparing like with like.

It’s that time in the semester

April 2, 2014 / zcofran / Leave a comment

When everyone’s losing it.

Online primate anatomy lab exercise

February 5, 2014February 6, 2014 / zcofran / 3 Comments

I work at a very freshly opened University in Kazakhstan, a school so young that we will not graduate our first class for another year. I came here for the exciting prospects of helping establish an anthropology program, but there are lots of challenges, too. One of the biggest I face as an educator is that infrastructure and other physical materials are still in the process of coming together. Simply put: we don’t got no bones! This is especially troublesome when teaching human evolution, an anatomy-oriented class in which students really can benefit from examining physical bones and casts of fossils first-hand.

So until we get our badass laboratory of anthropological sciences, I’ve put together a lab activity using the Kyoto University Primate Research Institute’s online database of CT scans (blogged about before here and here). The purpose of this activity is to show students ‘virtual’ primate skeletons that they can examine, look inside, and even measure. The KUPRI CT viewers allow students to identify structures, rotate and orient the skeletons, and measure using a handy grid function. While I love this resource, I’ll admit that the program can be a bit unwieldy, and so it takes some time to figure out how to use well.

Measure that gibbon radius!

In this exercise, students will measure cranial width, femur head diameter, and maximum length of the humerus, radius, femur, and tibia. Cranium width is then used to estimate cranial capacity (based on chimps, from Neubauer et al., 2012); femur head diameter allows estimation of body mass (using anthropoid regressions from Ruff, 2003); and the limb dimensions are used to calculate various indices. The class as a whole will look at apes and monkeys, for comparison with published values for other species. Then we’ll gather ’round the campfire to talk about our feelings about it. I’m hoping it will get them familiar with the basic anatomy and names of bones, some experience collecting data, and some understanding of variation between different species.

Best of all, each student will write up their ‘analysis’ on the NU Bioanthro Student blog next week. Stay tuned to see their results!

So, I’m attaching the exercise to this post – feel free to use or modify. If you have any other similar exercises, the rest of the internet and I would be happy to hear about them

Download me: Primate CT lab! [updated 06 Feburary, to fix issues with brain and body size estimation equations in previous version]

A new year of bioanthro student blogging in Kazakhstan

January 9, 2014January 9, 2014 / zcofran / Leave a comment

A new year is upon us, our hair is a bit grayer and our telomeres a touch trimmer. Twenty effing fourteen.

It’s been a bit quiet here at Lawnchair, as I’ve been enjoying the holidays, but also writing a few things up for print. If I weren’t so old and wise, I’d make a New Year’s resolution to add to the blog more frequently. But I have a nascent career to attend to! So in the mean time, with the new year and semester, I’m adding two new courses to the Nazarbayev University bioanthro student blog that can hopefully keep you entertained & edumacated.

The wintry curtain rises for 2014 in Astana.

The first batch of student-written posts for the class “Bones, stones and genomes: Human Evolution” will go up on Monday. There will be a slight lull for a few weeks until this class, as well as “Monkey business: Primate behavior and ecology,” start posting in February. In addition to what’s already been posted by last year’s classes, the human evolution class will be adding posts focused on specific bones and fossils, while the primatology class will be adding article reviews/summaries.

So stay tuned to nazarbioanthro.blogspot.com in the coming months! (I should also have more fun new things to say here at Lawnchair, too)

Calotte or Carapace?

February 27, 2012August 4, 2013 / zcofran / Leave a comment

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…

Look inside bones for free on the interwebs

November 20, 2011August 4, 2013 / zcofran / 2 Comments

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.

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

A poor depiction, indeed

November 10, 2011August 4, 2013 / zcofran / Leave a comment

As I’ve alluded to in some previous posts, in the Spring semester of 2012, I’ll be teaching “Anthrbio 297: Human Evo-devo” at the University of Michigan. It should be a really fun and interesting class, examining the role of development in human evolution.

Ernst Haeckel’s drawing of embryonic stages in some vertebrates. Taken from Richardson et al. 1997

My department recommends I create a flier that can be posted around campus. One of my first ideas was to adapt a Haeckel’s classic illustration of embryos of different animals passing through similar stages in utero (which we know today isn’t exactly correct; Richardson et al. 1997), but spin it to include primates and fossil humans. I started sketching it out (very crudely), but kept getting distracted with my pitiful attempts at multitasking. When I stopped zoning out, I was aghast to find my adaptation had taken a peculiar turn.

I won’t quit my day job.
More about vertebrate embryology
Richardson, M., Hanken, J., Gooneratne, M., Pieau, C., Raynaud, A., Selwood, L., & Wright, G. (1997). There is no highly conserved embryonic stage in the vertebrates: implications for current theories of evolution and development Anatomy and Embryology, 196 (2), 91-106 DOI: 10.1007/s004290050082

Lawn Chair Anthropology

Biological anthropology, paleontology, evolution, and development, by Dr. Zachary Cofran

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