Set to go live, Wellesley 207x and questions of scale…

In two days, Wellesley 207x – Introduction to Human Evolution, will go live. The course is the culmination of a fairly frenzied amount of work over the past three months, and I am excited to see that work actually reach an audience. With the course on the verge of that threshold though, I find myself thinking all the more about the scale of my audience. The course currently has approximately 18,000 students registered. Is that a big number or a small number?

From the “big” ledger:

  • In my 7+ years of teaching (two at the University of Michigan, five+ here at Wellesley College), I estimate that I have taught approximately 1000 students. So this class, in one semester, gives me a chance to increase my student audience by nearly a factor of 20. That seems big.
  • If I remain at Wellesley College for the remainder of my career (~30 years) and continue to teach a student load roughly equivalent to what I have so far, that would give me access to about 3,500 students. So in one semester, I might teach five times as many students as I will have the opportunity to teach in my entire career here at Wellesley College. Again, that seems big.
  • Wellesley 207x is running in conjunction with my on-campus seminar, Anthropology 207, with the two courses integrated in several ways. The ratio of students in the on-campus seminar to the on-line course is approximately 1:1275. Yet again, that seems huge.

From the “not so big” ledger:

  • I am a rabid baseball fan, with my allegiance falling with Cleveland (having grown up on both the East and West-sides of Cleveland). Cleveland has one of the worst attendance records in the league, averaging a paltry 19,252 paid attendance. In other words, more people pay to see one of the least supported baseball teams in the country, each game (and MLB teams play 81 home games!), than are registered for my course. That makes the enrollment seem small. Ubaldo Jimenez, in his 15 home starts, will have “reached” an audience vastly larger than my course.
  • My graduate alma mater, the University of Michigan, has an undergraduate enrollment of about 25,000 students. So my course will reach fewer people than the number of undergraduate students housed at just one public University in the country. Again, that seems small.
  • A 2005/2006 Pew survey of views on evolution in the United States founds that 42% of Americans think that living things on the planet have always existed in their current form. Assuming the survey is accurate and only adults (age 18+) are considered, this means that approximately 100,000,000 people in this country don’t acknowledge the reality of evolution. That number really makes my course enrollment seem small.

Regardless of whether it is big or small, 18,000 students are 18,000 students. It is a larger classroom to talk about issues of human diversity and evolution than I have ever had before, and hopefully one that will generate rich discussion. If even 1,000 students exit the course with an improved understanding of and greater interest in human evolution, I will consider it a massive success. It is also not too late to sign-up if you want to add to that number.

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Laetoli, Boston-style

How do you film a class segment about the Laetoli footprint trail without going to Tanzania to film? By going to the beach, of course!

Laetoli, if you are not aware, is the ~3.5-3.6 million year old site in Tanzania, where, in 1976, researchers uncovered a series of footprints, including a set made by a few hominins. The site is important in that it provides a flip-side to fossil-based evidence for bipedality in Australopithecines. Whereas fossil evidence (such as A.L. 129-1, or “Lucy” A.L. 288-1) gives us morphology and tasks us with reconstructing function (i.e. movement), the footprints at Laetoli give us evidence of function and task us with reconstructing the morphology necessary to produce such evidence.

So this morning I filmed a few sections for 207x (Introduction to Human Evolution) on Revere Beach in Boston, making footprints and talking about them. As you can see, it was a pretty time and location for some human evolution video production.

Revere1

Revere2

Not from an Australopithecine…

Revere3

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The importance of 300,000 year old cave bear mtDNA

A just released paper in PNAS that reconstructs the mitochondrial DNA of a >300,000 year old cave bear lineage is getting some attention…and for good reason (Dabney, et al., 2013). You might wonder who cares about ancient cave bear lineages outside of ancient cave bear experts. But when those cave bear remains come from the site of Sima De Los Huesos, part of the Atapuerca archaeological complex, and home to the densest concentration of Middle Pleistocene hominin fossil remains anywhere in the world….well, then it gets more interesting.

To step back a bit…we know that DNA tends to preserve better in colder environments, particularly permafrost environments, where the rate of DNA degradation is diminished. Slower degradation means larger fragments of DNA persist for longer periods of time, making it easier to extract and read that DNA. The successful reconstruction of mtDNA from this more than 300,000 year old cave bear specimen at Atapuerca potentially triples the available time frame for looking at ancient human DNA, and was the product not of improved extraction or amplification methods, but instead of better utilization of genomic reference library techniques. Amplifying very small fragments of DNA using PCR requires primers to identify specific fragments, which limits the length at which you can effectively read. The genomic library methods outlined by Dabney, et al. try to circumvent this problem.

the possibility remains that not all sequence information residing in ancient specimens is optimally recovered with these methods. This possibility becomes apparent when inspecting the size distributions of sequences reported from ancient DNA (e.g., refs. 3, 8, and 15), which consistently show a mode of ∼40 bp or larger. It is unclear whether the deficit of shorter molecules is due to poor preservation in ancient biological specimens or their exclusion during sample preparation. This question is of importance because it is expected that the number of DNA fragments in an ancient sample increases exponentially as length decreases and, hence, that most information resides in very short molecules (3, 8). (emphasis added)

If we can properly identify the information available in short sequence reads, we are likely to get access to vastly more ancient genetic information than is currently available.

And obviously if the authors can achieve this with the Sima cave bears, maybe they can do it with the Sima hominins…

mtDNA tree, Figure 3, Krause, et al. (2010) Nature 464, 894-897

mtDNA tree, Figure 3, Krause, et al. (2010) Nature 464, 894-897

Which raises the question of why this is important and what we might expect to find. We already know that mtDNA is only a small part of the evolutionary and biogeographic story of ancient populations, with nuclear DNA presenting a more significant technical challenge to read (because you have vastly more copies of mtDNA than nuclear DNA in your cells, and mtDNA is structurally simpler and much smaller), but also much more valuable information. Current understandings of ancient mtDNA place Neandertals as a side branch relative to contemporary humans, with the mtDNA from Denisova Cave in Sibera a further outgroup (Reich, et al., 2010). Where mtDNA from Sima would fit in (if it is available), particularly relative to the relationship between Neandertals and Denisovans would be a fascinating, if not complete look at the phylogeography of these lineages.

Figure 1, from Reich, et al. (2010) Nature 468, 1053–1060.

autosomal DNA tree, Figure 1, from Reich, et al. (2010) Nature 468, 1053–1060.

John Hawks picks up on a further interesting aspect of the cave bear mtDNA itself:

Personally, I can’t wait until we have a thicker sampling of the Middle Paleolithic time slice for a number of species, because that will enable us to understand the population dynamics in response to at least two and possibly more glacial cycles in Europe.

The more comparative models we have for ancient DNA in other species, the better understanding we can have about how to interpret aDNA in humans from the climatically volatile Late Pleistocene. Indications of widespread regional extinction in other large-bodied mammals, for example, might provide good reason to refine the expectations and thereby test hypotheses about such phenomena in human prehistory. I will add, such data might also allow us to potentially begin to get around issues of equifinality by providing independent lines of evidence. For example, maybe aDNA evidence might support parallel reconstructions of population history in Neandertals and other large-bodied European mammals during the Riss glaciation period (~140-200 kbp), but contrasting models in the Würm period (~20-90 kbp). A differential response between humans and other species during this latter glacial period could allow a more direct test of whether or not archaeological changes in the latter Neandertal record are a result of environmental forcing or biocultural innovation and adaptation.

The greatest obstacle for hypothesis testing in the paleo-record is equifinality. Lots of possible answers seem equally likely (or at least indistinguishably likely) for a given question. Was it environment? Was it culture? Was it demography? Single lines of evidence–archaeological samples, fossil remains, aDNA–are insufficient to get around this problem. But coupling different lines of evidence, particularly when the predictions for such lines of evidence diverge, is, in my view, the most valuable aspect of the continuing emergence of ancient DNA Studies.

*****

1. Dabney, et al. (2013) “Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments” PNAS www.pnas.org/cgi/doi/10.1073/pnas.1314445110

2. Krause, et al. (2010) “The complete mitochondrial DNA genome of an unknown hominin from southern Siberia” Nature 464, 894-897. doi:10.1038/nature08976

3. Reich, et al. (2010) “Genetic history of an archaic hominin group from Denisova Cave in Siberia” Nature 468, 1053–1060. doi:10.1038/nature09710

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Six degrees of Earnest Hooton

In my “Race and Human Variation” (Anth 214) I try to use race as a guide to teach some of the history of physical anthropology. One of the lessons I present, using myself as the example, is “six degrees of Earnest Hooton.” Hooton, originally trained as a classicist from Wisconsin, helped train, and thereby populate, much of the first generation of American physical anthropologists. Hooton’s students and their subsequent academic progeny on down the line represent a diverse group–in background, experience, training, and perspective–and yet it is worth considering the impact of this academic founding event.

The Academic Phylogeny of Physical Anthropology project that I linked to last week gives us a tool to look at this in more detail. There are still many additions that could be made to the tree, but at the moment, the tree has nearly 1100 people with no user submissions waiting to be added. Here is a cut-away of Hooton’s section of the overall picture:

HootonTree

As you can see, it is rather large. I admit to having lost count, but it appears to represent ~40% of the total entries into the phylogeny. Hooton’s personal relationship to the field remains remarkably under-studied (Giles, 2012), despite being controversial. Hooton’s legacy, however, largely is American Physical Anthropology, for better and for worse.

One of the other interesting things the above tree clearly demonstrates is the complexity brought about by over-lapping generations. For example, I am an academic “cousin” to one of my undergraduate advisors (George Armelagos), being an equal number of steps removed from Hooton, despite a 38-year gap (1968 vs. 2006) in our Ph.D. dates.

*****

1. Giles, E. (2012) “Two faces of earnest A. Hooton” Yearbook of Physical Anthropology 149(55):105-113. DOI: 10.1002/ajpa.22162

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Forensic osteology resource

The good people at forensicosteology.org have put together a large number of resources related to the field. I see today that they have a wonderful metabase of searchable osteology trauma specimens, including catalog/institution reference information as well as photographic (and in some cases radiographic) images. I can’t wait to pass this along to students when I teach forensic anthropology in the Spring. (h/t Kristina Killgrove @DrKillgrove, University of West Florida).

A “through and through” gunshot wound from the Hamann-Todd collection at the Cleveland Musuem of Natural History, found via the FOROST metabase

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Creating scientific knowledge within an evolutionary framework

In my class today, we are talking about how you create knowledge regarding human evolution. We will discuss, in brief, how we know what we know about the world around us. In that context, we will talk about how scientific knowledge, based on a specific perspective and methodological approach, differs from other kinds of knowledge production. I am not a science purist…I think there are other ways of creating knowledge about the world that have value. But when it comes to understanding the natural world (not necessarily our experience of the natural world, but rather the world itself), science is best.

Applying a scientific perspective to the world of the past, for example the ~5-7 million years of hominin evolution, requires an awareness that we are one or two steps removed from direct observation. Instead of observing how the world works within the controlled setting of a lab, we instead rely on observations of how the natural world has changed throughout time and across space, using our understanding of active forces to infer how such forces operated in the past.

There are pros and cons to such a diachronic perspective. On the positive side, there are no artificial constraints on what has actually happened. The world is what it is, it is not what we have set up on a lab bench (leaving aside the Hitchhiker’s Guide to the Galaxy view…). However, this also means that the observations available to us–fossils, geological formations, traces of past atmospheric conditions, etc…–require their own interpretation. They are not matter of fact things. That they exist is matter of fact, but understanding why they are the way they are and what they mean for the world of the past is a scientific question which demands a scientific answer. That the paleo-sciences require an additional inferential step does not in any way diminish their science bona fides, it just puts them within a particular epistemological framework.

I therefore take the perspective that evolution (and science, in general) is not something that asks for your belief. It only asks for your acknowledgement. And that acknowledgement does not close the door on skepticism. Indeed, the scientific practice is fundamentally based on skepticism, the idea that our current understanding of the observations available to us is subject to revision given new observations.

Applied to paleoanthropology, this provides a valuable perspective for understanding why new fossil discoveries overturn old theories. It is not, as some critics of evolution like to point to, evidence of the failure of our field, but rather evidence of its success. Ideas should change as our observations of the world change.

All of which is a nice excuse for me to link to Holly Dunsworth’s (Anthropology Dept., University of Rhode Island) segment for NPR’s “This I believe” series, titled, “I am evolution.”

Of course I believe evolution.

But that is different from believing in evolution.

To believe in something takes faith, trust, effort, strength. I need none of these things to believe evolution. It just is. My health is better because of medical research based on evolution. My genetic code is practically the same as a chimpanzee’s. My bipedal feet walk on an earth full of fossil missing links. And when my feet tire, those fossils fuel my car.

And to add a little bit at the end, we are also talking this week in my course about how biological anthropology (and paleoanthropology in particular) fit within the broader field of anthropology. I think the same perspective outlined above can be invoked here. Biological anthropology is well-equipped to answer a specific set of questions based on observations of human variability, past and present. Some of these questions overlap with the interests of the other sub-fields of anthropology in dynamic ways, and in some instances, the evolutionary perspective provided by biological anthropology is clearly superior. But not in all cases, and not without leaving the door open for critique and skepticism.

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Paleoanthropology pic(s) of the day

I have not posted a paleoanthropology pic of the day recently, so in honor of a forthcoming JHE paper on a new partial temporal bone from the site of Kromdraai, South Africa (Braga, et al.), here are a few pics of Kromdraai (circa 2005).

Kromdraai entered the paleoanthropological world when fossil hominin teeth from the site were brought to Robert Broom, in 1938. These teeth helped form the holotype of Australopithecus (Paranthropus) robustus. Since that time a variety of research groups have worked at the site, yielding thousands of fossil remains and numerous hominin specimens.

The site itself:

OLYMPUS DIGITAL CAMERA

A close-up of some of the existing breccia:

OLYMPUS DIGITAL CAMERA

The site is located within a region filled with fossil hominin sites, known as the Cradle of Humankind, a designated UNESCO World Heritage Site. Here is the surrounding scenery from a rainy January day:

OLYMPUS DIGITAL CAMERA

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The academic phylogeny of physical anthropology

UPDATE: As a brief update, Andrew is working in equal partnership with Liza Shapiro (Prof. of Anthropology, Univ. of Texas-Austin) and Brett Nachman (Graduate student at UT-Austin) on this project. The project is also going to continue to get updates as the phylogenies expand (currently at 732 people!).

W. Andrew Barr, a doctoral candidate at UT-Austin, appears to be undertaking the project that I think every biological anthropologist I know about has contemplated or fantasized about at some point. The project is an academic phylogeny of physical anthropology. Barr is constructing an interactive tree of who trained whom when it comes to physical anthropology Ph.Ds. This has been going viral on a number of online forums, and the early results look great.

I have always known, for example, that I was part of the large “Earnest Hooton” tree of American physical anthropology (a tree I expect to grow substantially as more users contribute data), having descended academically from Hooton, to William Howells, to Eugene Giles, to my advisor, Milford Wolpoff. It is great to see those interconnections laid out in attractive visual fashion.

Barr’s work on this looks great, but there are a few additional components I would love to see added. First, I would love to be able to add my undergraduate advisor (George Armelagos) in some fashion. Second, I would love to be able to expand the relationships to include doctoral committee members (in my case, that would add paleontologist Phil Gingerich, who is already on the list as part of the big Elwyn Simons tree, archaeologist John Speth, and biomedical engineer Steve Goldstein). Finally, I would love to be able to add dates and institutional affiliations, so that you could cross-reference who was at the same institution at the same time (major field work could be included, too). Adding these latter components would allow for a more thorough interrogation of the basic question, “where did so-and-so’s ideas come from?”

It is a cool project though, and if you have data to contribute and have not, you should go ahead and add yourself to the tree.

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Anth 207x – Step 1, integrating the liberal arts classroom and the MOOC environment

Tuesday is the first day of Wellesley classes for the Fall 2013 semester. As such, it also marks the first day in Wellesley’s experiment with online education. That experiment is beginning with my course, Anth 207x (Introduction to Human Evolution). 207x does not go live until September 25th, though, so what happens today?

Tuesday marks the first day of my on-campus seminar, Anth 207 (titled Hominid Evolution to help me keep the two straight). 207x will parallel my on-campus course with about a 3.5 week lag, with that lag gradually shrinking to about one week by the end of the term. The two courses are completely separate, but will be operating off the same EdX platform and utilizing most of the same pedagogical resources. So why teach them both?

When I was selected to be Wellesley’s guinea pig in this endeavor, one of my goals was to find ways to productively integrate. I wanted to take advantage of the properties of a Wellesley College seminar to improve the MOOC, and leverage the MOOC to improve the on-campus course.

So here are the steps I took to try and do that:

1) I am using EdX’s courseware platform to create a far more “flipped” classroom for my on-campus seminar. My Hominid Evolution class is geared towards students with little, or in many cases no, background in biological anthropology. This is a necessity given the small size of our department at Wellesley and the course coverage we can provide. As such, when I have taught this class previously, by necessity I have had to do a lot of in-class talking. It is hard to present the fossil record, in detail, without doing this. In order to avoid this, I have spent considerable time the past two months pre-recording video lecture segments for use in both 207 and 207x. These lecture modules, most 5-20 minutes in length, will present most of the basic lecture content of the course (~1-1.5 hours per week). This will free up a lot of time for the on-campus course.

2) I am also using EdX’s courseware to create virtual lab module. I also do not have the teaching support to run a complete lab for my on-campus course. I do this with my forensic anthropology (Anth 209) course, running an osteology lab, but cannot also do it in Anth 207. Access to the EdX platform and the teaching support to get this course ready have given me the opportunity to put together a set of virtual lab modules, adding what I hope will be a very valuable component to my on-campus course.

3. I will, at various points, be capturing in-class activities to create video content for 207x. At the moment, there is almost exactly a 1000:1 ratio between students in 207x and students in my seminar. The smaller environment, the ability to assign and guide students through more complex assignments, and the extended interaction time, all allow for the generation of potentially rich dialogue and engagement between students. I want to capture some of this and use it to seed certain discussions within 207x.

4. I want to leverage the large size of 207x to create teaching content for the seminar course. A classroom with 20 Wellesley College undergraduates can be surprisingly diverse. But that diversity is obviously (size) and structurally (gender, age) limited. One of the great challenges in teaching about the fossil record is getting students to maintain a population variation focus while examining individual fossil specimens scattered in time and space. I am planning on vastly expanding my ability to bring a perspective on what real patterns of biological variation look like in living humans by using the 207x class as a generator of pedagogical materials.

5. Creating a unique forum for alumnae interaction. I have been told Wellesley will be marketing my class with its alumnae network and I hope to enroll a large number of alumnae in 207x. In the long run, I think this is potentially one of the most productive outgrowths of a liberal arts College like Wellesley entering into this realm of educational outreach. Open, online courses become not only a way for alumnae to re-engage with the campus they once occupied, but also share directly in learning experiences with current Wellesley students.

This is a first iteration of this experiment, and I imagine it will require considerable future tweeking, if not substantial rehauls, before it airs for a second time. But for now, I am excited about seeing the first step go forward.

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Planning ahead: Wellesley, online education, and 207x

With 207x (Introduction to Human Evolution) about a month away preparations have entered a frenzy mode. As it turns out, right after the class goes live, I will be speaking at Wellesley “Family and Friends” weekend about the intersection between online education, the liberal arts college experience, and human evolution. I will be sure to share more of my specific thoughts as the event gets closer.

WellesleyXLecture

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