Ant 179

A new year of bioanthro lab activities

/ 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.

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

ResearchBlogging.orgReference

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

The "human" genome?

/ zcofran / Leave a comment

The topic this week in my Intro to Bioanthro course is genetics, with the subtheme being the mechanisms getting us from a genotype to “the” human phenotype (next week is variation and population genetics). Of course we talked about things like DNA, simple Mendelian inheritance (even though many traits/diseases probably aren’t really Mendelian), and even epigenetics and genomic imprinting. But I also wanted to point out the many ways that our very existence relies on life extrinsic to that encoded by our personal genomes (this was inspired by the intriguingly titled, “A symbiotic view of life: We have never been individuals,” [Gilbert et al., 2012; free pdf]).

Mitochondria are classic examples. These “powerhouses of the cell” or “cellular powerplants” (thanks, Wikipedia!) seem to have once been, at least a billion years ago, their own unicellular organisms that somehow came under the employ of early enterprising eukaryotes. These little organelles are indispensable players in cell metabolism, implicated also in ageing and certain diseases.

In addition, there’s been a lot of research lately on the human ‘microbiome‘ – the specific set of bacteria living in and on our bodies, which aren’t incorporated into our individual cells like mitochondria, but are nevertheless requisite for us to thrive. Analyses of poop, of all things (a scatological lecture is always a good one), have revealed that the bacterial composition of human digestive tracts varies between geographical regions, but also that age-related changes in the microbiome are similar between regions (Yatsunenko et al., 2012; see the review by Ed Yong). These bacteria are crucial to our ability to digest certain foods, and some variation in gut flora probably underlies some diseases (Smith et al., 2013); this is why you may have read about a rise in poop transplants lately (van Nood et al., 2013).

Finally, and I think perhaps most intriguingly, there is evidence that our own genes may be commandeered by the the RNA produced by the things we eat. Now, the regulation of gene expression is bewilderingly complex, and one important player in this are various types of non-coding RNA, including micro RNA (miRNA), piwi-interacting RNA, etc. (I grew up under the paradigm ‘a gene codes for a protein and our genomes contain all this “junk” DNA,’ so RNA-interference and the like blow my mind). Recently, Lin Zhang and colleagues (2012) have found that some miRNA produced by plants can not only survive cooking and digestion, but that these miRNAs can actually interact with, and alter the expression of, at least one human gene (involved in removing bad cholesterol in this case). WHAT?!

ResearchBlogging.orgOne of the most exciting areas of modern biology is the discovery of the various genetic and developmental mechanisms and processes that literally make us human. Of course the genetics of human uniqueness and variation are, to use a phrase I hate, ‘much more complex than previously thought’ (such a pervasive mantra in any field of research…). Not only that, but being human, arguably the most successful complex organism in recent history, is something we cannot even do on our own.

References
Gilbert, S., Sapp, J., & Tauber, A. (2012). A Symbiotic View of Life: We Have Never Been Individuals The Quarterly Review of Biology, 87 (4), 325-341 DOI: 10.1086/668166

Smith MI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R, Cheng J, Kau AL, Rich SS, Concannon P, Mychaleckyj JC, Liu J, Houpt E, Li JV, Holmes E, Nicholson J, Knights D, Ursell LK, Knight R, & Gordon JI (2013). Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor. Science PMID: 23363771

van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, Visser CE, Kuijper EJ, Bartelsman JF, Tijssen JG, Speelman P, Dijkgraaf MG, & Keller JJ (2013). Duodenal infusion of donor feces for recurrent Clostridium difficile. The New England Journal of Medicine, 368 (5), 407-15 PMID: 23323867

Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, & Gordon JI (2012). Human gut microbiome viewed across age and geography. Nature, 486 (7402), 222-7 PMID: 22699611

Zhang L, Hou D, Chen X, Li D, Zhu L, Zhang Y, Li J, Bian Z, Liang X, Cai X, Yin Y, Wang C, Zhang T, Zhu D, Zhang D, Xu J, Chen Q, Ba Y, Liu J, Wang Q, Chen J, Wang J, Wang M, Zhang Q, Zhang J, Zen K, & Zhang CY (2012). Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Research, 22 (1), 107-26 PMID: 21931358

Introducing a biological anthropology student blog in Kazakhstan

/ zcofran / Leave a comment

I’m excited to announce a new blog authored by students in my Introduction to Biological Anthropology course here at Nazarbayev University in Astana, Kazakhstan. The goals of this project are manifold, namely: [1] to familiarize students with the blogosphere, and open their eyes to the vast amounts of academic material available – much of it good but lots of it junk – through this and other social media; [2] to help them develop skills in scientific/academic literacy, and more importantly writing and communication; and [3] to show off to the rest of the internet how talented our students are here at NU.

The site is called “Biological Anthropology @ NU.edu.kz,” and can be found at nazarbioanthro.blogspot.com. You can follow the class on Twitter, too (@BioAnthNUeduKZ) to stay up to date on students’ posts. Assuming this pilot semester goes well, I hope to continue the blog and twitter feed for future semesters of this, and other, bio anthro courses at NU.

The first set of posts are going up as we speak: students’ first impressions and expectations for the course, sort of a literary ‘before’ half of a ‘before-and-after’ segment. This semester-long series will culminate in a set of abstracts for mini-grant proposals for research projects that students will devise and write themselves. So stay tuned over the next four months, as these incipient anthropologists post their thoughts, reactions and research on a wide range of topics in this highly interdisciplinary field!

I’m planning on doing a similar blogging project with another course this term, too (Critical Issues in the Humanities and Social Sciences). Details to follow…