monkey's uncle

notes on human ecology, population, and infectious disease

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New Publication, Emerging infectious diseases: the role of social sciences

December 4th, 2012 · No Comments

This past week, The Lancet published a brief commentary I wrote with a group of anthropologist-collaborators. The piece, written with Craig Janes, Kitty Corbett, and Jim Trostle, arose from a workshop I attended in lovely Buenos Aires back in June of 2011. This was a pretty remarkable meeting that was orchestrated by Josh Rosenthal, acting director of the Division of International Training and Research at the Fogarty International Center at NIH, and hosted in grand fashion by Ricardo Gürtler of the University of Buenos Aires.

Our commentary is on a series of papers on zoonoses, a seemingly unlikely topic for about which a collection of anthropologists might have opinions. However, as we note in our paper, social science is essential for understanding emerging zoonoses. First, human social behavior is an essential ingredient in \(R_0\), the basic reproduction number of an infection (The paper uses the term “basic reproductive rate,” which was changed somewhere in production from the several times I changed “rate” to “number”). Second, we suggest that social scientists who participate in primary field data collection (e.g., anthropologists, geographers, sociologists) are in a strong position to understand the complex causal circumstances surrounding novel zoonotic disease spill-overs.

We note that there are some challenges to integrating the social sciences effectively into research on emerging infectious disease. Part of this is simply translational. Social scientists, natural scientists, and medical practitioners need to be able to speak to each other and this kind of transdisciplinary communication takes practice. I’m not at all certain what it takes to make researchers from different traditions mutually comprehensible, but I know that it’s more likely to happen if these people talk more. My hypothesis is that this is best done away from anyone’s office, in the presence of food and drink. Tentative support for this hypothesis is provided by the wide-ranging and fun conversations over lomo y malbec. These conversations have so far yielded at least one paper and laid the foundations for a larger review I am currently writing. I know that various permutations of the people in Buenos Aires for this meeting are still talking and working together, so who knows what may eventually come of it?

→ No CommentsTags: Human Ecology · Infectious Disease

On Anthropological Sciences and the AAA

November 19th, 2012 · No Comments

I guess the time has rolled around again for my annual navel-gaze regarding my discipline, my place within it, and its future. Two strangely interwoven events have conspired to make me particularly philosophical as we enter into the winter holidays. First, I am in the middle of a visit by my friend, colleague, and former student, Charles Roseman, now an associate professor of anthropology at the University of Illinois, Urbana-Champaign. The second is that the American Anthropological Association meetings just went down in San Francisco and this always induces an odd sense of shock and subsequent introspection.

Charles graduated with a Ph.D. from the Department of Anthropological Sciences (once a highly ranked department according the the National Research Council) in 2005. He was awarded tenure at UIUC, a leading department for biological anthropology, this past year and has come back to The Farm to collaborate with me on our top-secret sleeper project of the past seven years. We’ve made some serious progress on this project since he arrived and maybe I’ll be able to write about that soon too.

The annual AAA meeting is one  that I never attended until about four years ago, coinciding with what we sometimes refer to as “the blessed event,” the remarrying of the two Stanford Anthropology departments. It’s actually a bit of coincidence that I started attending AAAs the same year that we merged but it has largely been business of the new Department of Anthropology that has kept me going back – largely to serve on job search committees. This year, I had two responsibilities that drew me to the AAAs. The first was the editorial board meeting for American Anthropologist, the flagship publication of the association.  I joined the editorial board this year and it seemed a good idea to go and get a feel for what is happening with the journal and where it is likely to head over the next couple years.

My other primary responsibility was chairing a session that was organized by two of my Ph.D. students, Yeon Jung Yu and Shannon Randolph. In addition to Yeon and Shannon, my Ph.D. student Alejandro Feged also presented work from his dissertation research.  All three of these students were actually accepted into Anthsci and are part of the last cohort of students to leave Stanford still knowing the two-department system.

It was a great pleasure to sit in the audience and watch Yeon, Shannon, and Alejandro dazzle the audience with their sophisticated methods, beautiful images, and accounts of impressive, extended — and often hardcore — fieldwork. For her dissertation research, Yeon worked for two years with commercial sex workers in southern China, attempting to understand how women get recruited into sex work and how social relations facilitate their ability to survive and even thrive in a world that is quite hostile to them. Her talk was incredibly professional and theoretically sophisticated. For her dissertation research, Shannon worked in the markets of Yaoundé, Cameroon, trying to understand the motivations for consumption of wild bushmeat. Shannon was able to share with the audience her innovative approaches to collecting data (over 4,000 price points, among other things) on a grey-market activity that people are not especially eager to discuss, especially in the market itself. Alejandro did his dissertation research in the Colombian Amazon, where he investigated the human ecology of malaria in this highly endemic region. His talk demonstrated that the conventional wisdom about malaria ecology in this region — namely, that the people most at risk for infection are adult men who spend the most time in the forest — is simply incorrect for some indidenous popualtions and his time-budget analyses made a convincing case for the behavioral basis of this violation of expectations. This was a pretty heterogeneous collection of talks but they shared the commonality of a very strong methodological basis to the research.

At at time when many anthropologists express legitimate concerns over their professional prospects, I have enormous confidence in this crop of students, all three of whom are regularly asked to do consulting for government and/or non-govermental organizations because of their subject knowledge and methodological expertise. Anthsci graduates — there weren’t that many of them since the department existed for less than 10 years — have done very well in the profession overall. I will list just a couple here whose work I knew well because I was on their committees or their work was generally in my area

In addition to these grad students, I think that it’s important to note the success of the post-docs who worked either in Anthsci or with former Anthsci faculty on projects that started before the merger. Some of these outstanding people include:

In a discipline that is lukewarm at best on the even very notion of methodology, I suspect that students with strong methodological skills — in addition to the expected theoretical sophistication and critical thinking (note that these skills do not actually trade-off) — enjoy a distinct comparative advantage when entering a less-than-ideal job market. Of course, I don’t mean to imply that Anthsci didn’t have its share of graduates who leave the field out of frustration or lack of opportunity or who get stuck in the vicious cycle of adjunct teaching. But this accounting gives me hope. It gives me hope for my both my current and future students and it gives me hope for the field. Maybe I’ll even go to AAAs again next year…

→ No CommentsTags: Anthropology · Evolution · Human Ecology · science · Teaching

This is Just What Greece Needs

August 23rd, 2012 · No Comments

Greece was officially deemed malaria-free in 1974. Recent reports, however, suggest that there is ongoing autochthonous transmission of of Plasmodium vivax malaria. According to a brief report from the Mediterranean Bureau of the Italian News Agency (ANSAmed), 40 cases of P. vivax malaria have been reported in the first seven months of 2012. Of these 40, six had no history of travel to areas known to be endemic for malaria transmission. The natural inference is thus that they acquired it locally (i.e., “autochthonously”) and that malaria may be back in Greece.

More detail on the malaria cases in Greece can be found on this European Centre for Disease Prevention and Control website. The actual ECDC report on autochthonous malaria transmission in Greece can be found here. A point in that report that is not mentioned in the ANSAmed newswire is that 2012 marks the third consecutive year in which autochthonous transmission has been inferred in Greece. So much for Greece being malaria-free.

→ No CommentsTags: Climate Change · Human Ecology · Infectious Disease

Why the Prediction Market Failed to Predict the Supreme Court

July 8th, 2012 · No Comments

There is a very interesting piece in the New York Times today by David Leonhardt on the apparent backlash against prediction markets such as Intrade and Betfair. In principle, these markets make predictions by aggregating the disparate information of many independent bettors who offer prices for a particular outcome. Prediction markets have enjoyed a fair amount of success in recent elections. The University of Iowa has even set up an influenza prediction market.  But prediction markets are hardly perfect and have had some pretty big recent failures. It turns out that Intrade failed in a pretty spectacular manner to predict the outcome of the recent Supreme Court ruling about the constitutionality of the Affordable Care Act. Leonhardt suggests that some of the failures of online prediction markets is attributable to relatively small number of people who actually trade on the market:

But the crowd was not everywhere wise. For one thing, many of the betting pools on Intrade and Betfair attract relatively few traders, in part because using them legally is cumbersome. (No, I do not know from experience.) The thinness of these markets can cause them to adjust too slowly to new information.

This may have been an issue with the ACA decision but the primary problem with the incorrect prediction is that the crowd doesn’t actually know much about the workings of the very closed social network that is the United States Supreme Court. Writes Leonhardt:

And there is this: If the circle of people who possess information is small enough — as with the selection of a vice president or pope or, arguably, a decision by the Supreme Court — the crowds may not have much wisdom to impart. ‘There is a class of markets that I think are basically pointless,’ says Justin Wolfers, an economist whose research on prediction markets, much of it with Eric Zitzewitz of Dartmouth, has made him mostly a fan of them. ‘There is no widely available public information.’

This point gets at a larger critique of market-based solutions to problems suggested by my Stanford colleague Mark Granovetter over 25 years ago (Granovetter 1985). This is the problem of embeddedness. The idea of embeddedness was anticipated by the work of substantivist economist Karl Polanyi, but Granovetter really laid out the details. Granovetter writes (1985: 487): “A fruitful analysis of human action requires us to avoid the atomization implicit in the theoretical extremes of under- and oversocialized conceptions [of human action]. Actors do not behave or decide as atoms outside a social context, nor do they adhere slavishly to a script written for them by the particular intersection of social categories that they happen to occupy. Their attempts at purposive action are instead embedded in concrete, ongoing systems of social relations.” Atomization is independent bettors making decisions about the price they are willing to pay for a certain outcome.

The argument for embeddedness emerges in Granovetter’s paper from the problem of trust in markets. Where does trust come from in competitive markets? The fundamental problem here regards the micro-foudnations of markets where “the alleged discipline of competitive markets cannot be called on to mitigate deceit, so the classical problem of how it can be that daily economic life is not riddled with mistrust and malfeasance has resurfaced.” (p. 488). The obvious solution to this is that actors choose to deal with alters whom they trust and that the most effect way to develop trust is to have prior dealings with an alter.

Granovetter’s embeddedness theory is a modest one. He notes that, unlike the alternative models, his “makes no sweeping (and thus unlikely) predictions of universal order or disorder but rather assumes that the details of social structure will determine which is found.” (p. 493)

These ideas about the careful analysis of social structure and networks of interlocking relationships are fundamental for understanding when the crowd will be wise and when it will not. They are also essential for developing effective development interventions and, for that matter, making markets work for the public good in general.  The theory of embeddedness allows for the possibility that markets can work but if we are to understand when they work and when they don’t, we need to think about social structure as more than just a bit of friction in an ideal market and take its measurement more seriously. People are not ideal gases. (Dirty little secret: most gases are not ideal gases). This gets at some problems that I have been thinking about a lot recently relating to the implications of additive, observational noise vs. process noise and its implications for prediction of multi-species epidemics, but that must wait for another post…

 

 

→ No CommentsTags: Social Network Analysis

On Global State Shifts

July 5th, 2012 · No Comments

This is a edited version of a post I sent out to the E-ANTH listserv in response to a debate over a recent paper in Nature and the response to it on the website “Clear Science,” written by Todd Meyers. In this debate, it was suggested that the Barnosky paper is the latest iteration of alarmist environmental narratives in the tradition of the master of that genre, Paul Ehrlich. Piqued by this conversation, I read the Barnosky paper and passed along my reading of it.

The Myers’s piece on the “Clear Science” web site is quite rhetorically clever. Climate-change deniers have a difficult task if they want to convincingly buck the overwhelming majority of reputable scientists on this issue. Myers uses ideas about the progress of science developed by the philosopher Thomas Kuhn in his classic book, The Structure of Scientific Revolutions. By framing the Barnosky et al. as mindlessly toeing the Kuhnian normal-science line, he has come up with a shrewd strategy for dealing with the serious scientific consensus around global climate change. Myers suggests that “Like scientists blindly devoted to a failed paradigm, the Nature piece simply tries to force new data to fit a flawed concept.”

I think that a pretty strong argument can be made that the perspective represented in the Barnosky et al. paper is actually paradigm-breaking. For 200 years the reigning paradigm in the historical sciences has been uniformitarianism. Hutton’s notion — that processes that we observe today have always been working — greatly extended the age of the Earth and allowed Lyell and Darwin to make their remarkable contributions to human understanding. This same principle allows us to make sense of the archaeological record and of ethnographic experience. It is a very useful foil for all manner of exceptionalist explanatory logic and I use it frequently.

However, there are plenty of ways that uniformitarianism fails. If we wanted to follow the Kuhnian narrative, we might say that evidence has mounted that leads to increased contradictions arising from the uniformitarian explanatory paradigm. Rates of change show heterogeneities and when we trying to understand connected systems characterized by extensive feedback, our intuitions based on gradual change can fail, sometimes spectacularly. This is actually a pretty revolutionary idea, apocalyptic popular writings aside, in mainstream science.

Barnosky et al. draw heavily on contemporary work in complex systems. The theoretical paper (Scheffer et al. 2009) upon which the Barnosky paper relies heavily represents a real step forward in the theoretical sophistication of this corpus and does so by making unique and testable predictions about systems approaching critical transitions. I have written about it previously here.

The most difficult part of projecting the future state of complex systems is that human element. This leads too many physical and biological scientists to simply ignore social and behavioral inputs. This said, there are far too few social and behavioral scientists willing to step up and do the hard collaborative work necessary to make progress on this extremely difficult problem. The difficulty of projecting human behavior often leads to projections of the business-as-usual variety and, unfortunately, these are often mischaracterized by the media and other readers. Such projections simply assume no change in behavior and look at the consequences some time down the line. A business-as-usual projection actually provides a lot of information, albeit about a very hypothetical future. What if things stayed the way they are? Yes, behavior changes. People adapt. Agricultural production becomes more efficient. Prices increase, reducing demand and allowing sustainable substitutes. Of course, sometimes things get worse too. Despite tremendous global awareness and lots of calls to reduce greenhouse gas emissions, carbon emissions have continued to rise. So, there is nothing inherently flawed about a business-as-usual projection. We just need to be clear about what it means when we use one.

A criticism that emerged on the list is that Barnosky et al. is essentially “an opinion piece.” However, the great majority of the Barnosky et al. paper is, in fact, simply a review. There are numerous facts to be reviewed: biodiversity has declined, fisheries have crashed, massive amounts of forest have been converted and degraded, the atmosphere has warmed. They are facts. And they are facts in which many vested interests would like to sow artificial uncertainty for political purposes. Positive things have happened too (e.g., malaria eradication in temperate climes, increased food security in some places that used to be highly insecure, increased agricultural productivity — though this may be of dubious sustainability), though these are generally on more local scales and, in some cases, may simply reflect exporting the problems to rich countries to the Global South. The fact that they are not reviewed does not mean that the paper belongs in an hysterical chicken-little genre.

A common critique of the doomsday genre is the certainty with which the horrible outcomes are framed. The Barnosky paper is suffused with uncertainty. In fact, this is the main point I take away from it! The first conclusion of the paper is that “it is essential to improve biological forecasting by anticipating critical transitions that can emerge on a planetary scale and understanding how such global forcings cause local changes.” This suggests to me that the authors are acknowledging massive uncertainty about the future, not saying that we are doomed with certainty. Or how about: “the plausibility of a future planetary state shift seems high, even though considerable uncertainty remains about whether it is inevitable and, if so, how far in the future it may be”?

Myers writes “they base their conclusions on the simplest linear mathematical estimate that assumes nothing will change except population over the next 40 years. They then draw a straight line, literally, from today to the environmental tipping point.” This is a profoundly misleading statement. Barnosky et al. are using the fold catastrophe model discussed in Scheffer et al. (2009). The Scheffer et al. analysis of the fold catastrophe model uses some fairly sophisticated ideas from complex systems theory, but the ideas are relatively simple. The straight line that so offends Myers arises because this is the direction of the basin of attraction. In the figure below, I show the fold-catastrophe model. The abcissa represents the forcing conditions of the system (e.g., population size or greenhouse gas emissions). The ordinate represents the state of the system (e.g., land cover or one of many ecosystem services). The sideways N represents an attractor — a more general notion of an equilibrium. The state of the system tends toward this curve whenever it is perturbed away.

The region in the interior of the fold (indicated by the dashed line) is unstable while the upper and lower tails (indicated by solid lines) are stable and tend to draw perturbations from the attractor toward them. The grey arrows indicate the basin of attraction. When the system is perturbed off of the attractor by some random shock, the state tends to move in the direction indicated by the arrow. When the state is forced all the way down the top arc of the fold, it enters a region where a relatively small shock can send the state into a qualitatively different regime of rapid degradation. This is illustrated by the black arrow (a shock) pushing the state away from point F2. The state will settle again on the attractor, but a second shock will send the state rapidly down toward the bottom arm of the fold (point F1). Note that this region of the attractor is stable so it would take a lot of work to get it back up again (e.g., reduce population or drastically reduced total greenhouse gasses). This is what people mean when they colloquially refer to a “global tipping point.”

This is the model. It may not be right, but thanks to Scheffer et al. (2009), it makes testable predictions. By framing global change in terms of this model, Barnosky et al. are making a case for empirical investigation of the types of data that can falsify the model. Maybe because of the restrictions placed on them by Nature (and these are severe!), maybe because of some poor choices of their own, they include an insufficiently explained, fundamentally complex figure that a critic with clear interests in muddying the scientific consensus can sieze on to dismiss the whole paper as just more Ehrlich-style hysteria.

For me — as I suspect for the authors of the Barnosky et al. paper — massive, structural uncertainty about the state of our planet, coupled with a number of increasingly well-supported models of the behavior or nonlinear systems (i.e., not simply normal science) strongly suggests a precautionary principle. This is something that the economist Marty Weitzman suggested in his (highly technical and therefore not widely read) paper in 2009 and that I have written about before here and here. This is not inflammatory fear-mongering, nor is it grubbing for grant money (I wish it were that easy!). It is responsible scientists doing their best to communicate the state of the science within the constraints of society and the primary mode of scientific communication. Let’s not be taken in by writers pretending to present “just the facts” in a cool, detached manner but who actually have every reason to try to foment unnecessary uncertainty about the state of our world and impugn the integrity of people doing their level best to understand a rapidly changing planet.

References

Kuhn, T. 1962. The Structure of Scientific Revolutions. Chicago: University of Chicago Press.

Scheffer, M., J. Bascompte, W. A. Brock, V. Brovkin, S. R. Carpenter, V. Dakos, H. Held, E. H. van Nes, M. Rietkerk, and G. Sugihara. 2009. Early-Warning Signals for Critical Transitions. Nature. 461 (7260):53-59.

Weitzman, M. L. 2009. On Modeling and Interpreting the Economics of Catastrophic Climate Change. The Review of Economics and Statistics. XCI (1):1-19.

 

→ No CommentsTags: Climate Change · Human Ecology

AAPA 2012 Run-Down

April 16th, 2012 · 2 Comments

I am done with this year’s American Association of Physical Anthropologists annual meeting in Portland. Alas, I am not yet home as I had a scheduling snafu with Alaska Airlines yesterday and there was literally not a single seat on a flight to any airport in the Bay Area. So, I hung out in PDX for the night, where my sister-in-law is finishing up her MD/MPH at OHSU. Staying an extra night allowed me to have dinner at what is probably my favorite pizzaria on the West Coast, Bella Faccia on Alberta Ave in Northheast (Howie’s in Palo Alto is a close second). I also had a lovely breakfast of rissotto cakes and poached eggs at Petite Provance, also on Alberta. All in all, a fantastic couple days’ worth of food.
It was great to get a chance to catch up with old friends and colleagues and meet new ones. This is really what professional meetings are about. I had a chance to spend time with Charles Roseman, Rick Bribiescas, Josh Snodgrass, Nelson Ting, and Frances White. I also had very nice, if too brief, chats with Connie Mulligan, Lorena Madrigal, Larry Sugiyama, Greg Blomquist, Zarin Machanda, Melissa Emery Thompson, Cheryl Knott, and Chris Kuzawa.
I only go to the AAPAs every couple of years. Given the interdisciplinarity of my work and interests, I struggle to find a “home” professional meeting. Sometimes I feel like it’s PAA; sometimes Sunbelt; sometimes AAPA/HBA.  One thing I can say for certain is that it is not AAA, my semi-annual experience in ethnographic surreality. Such a peculiar discipline anthropology is. Part of the reason I don’t go to AAPAs all that often is that I rarely find all that much interesting there. There are a few really fantastic people working in the field but most of the talks I find stupifyingly boring. I’m just not that interested in teeth. I suppose this is true for any professional meeting, so I shouldn’t be too hard on AAPA — I’m also not that interested in contraceptive uptake, social media/online networks, or governmentality, apparently the modal topics in my competing meetings. In fact, I was pleasantly surprised by the diversity and quality of talks I saw at AAPA this year.
In my session alone, I saw really terrific and interesting talks by Steve Leigh and Connie Milligan. Steve spoke on the comparative gut microbiomes of primates and Connie presented early results on the modification of gene expression through methylation of infants born to women who experienced extreme psychosocial and physical trauma in eastern Congo. Really important stuff. It also struck me that you’d probably only see these types of talks at the AAPAs.
There were a lot of young people at this meeting — a greater fraction than I remember from past meetings.  Maybe it was the draw of hipster Portland with its great beer, great food, and general atmosphere of grooviness. Maybe there really are lots and lots of young physical anthropologists being trained these days. I must admit that I had mixed feelings about this thought as I looked out over the vast ocean of twenty-something faces in the hotel bar Saturday night. On the one hand, it’s great that people are being trained to do good work in physical anthropology. On the other hand, I worry about the ability of our discipline, which shows no signs of stopping with the charade that somehow anthropology is really akin to literary criticism, to absorb this many new Ph.D.s from (one of) the scientific wings of modern anthropology.
Two of the talks immediately before me in my session were, in fact, by young scientists and they were great. Andrew Paquette, from Northern Arizona University, gave a talk on the evolutionary history of Southeast Asian Ovalocytosis (SAO), a twenty-seven base pair deletion in the eleventh exon of the SLC4A1 gene that confers strong protection against infection with Plasmodium falciparum, the most dangerous form of malaria. Turns out this mutation, which has its geographic epicenter in Nusa Tenggara in Indonesia, is surprisingly ancient. Lots more to come from this, I’m sure. Margaux Keller, from Temple, gave a fantastic talk on finding some of the missing heritability in Parkinson’s disease. Missing heritability of complex disease phenotypes is a major topic in genetic epidemiology and Margaux and her colleagues applied Genome-Wide Complex Trait Analysis to eight cohorts of case-control studies of PD. Their results substantially increase (i.e., by a factor of 10!) the fraction of total phenotypic variance in PD explained by straight-up genome-wide association studies (GWAS). In addition to the excellent scientific content of her presentation, I was struck by the very nice and original visual aesthetic of her slides.
I spoke on my recent work on the quantiative genetics of life-history traits.  With Statistics grad student Philip Labo, I’ve been doing some pretty serious number-crunching to examine the heritabilities of and (more interestingly) genetic correlations between human life-history characters. Good results that should be seeing some more light soon (including at PAA next month!).

I am done with this year’s American Association of Physical Anthropologists annual meeting in Portland. Alas, I am not yet home as I had a scheduling snafu with Alaska Airlines yesterday and there was literally not a single seat on a flight to any airport in the Bay Area. So, I hung out in PDX for the night, where my sister-in-law is finishing up her MD/MPH at OHSU. Staying an extra night allowed me to have dinner at what is probably my favorite pizzeria on the West Coast, Bella Faccia on Alberta Ave in Northeast (Howie’s in Palo Alto is a close second). I also had a lovely breakfast of risotto cakes and poached eggs at La Petite Provence, also on Alberta. All in all, a fantastic couple days’ worth of food.

It was great to get a chance to catch up with old friends and colleagues and meet new ones. This is really what professional meetings are about. I had a chance to spend time with Charles Roseman, Rick Bribiescas, Josh Snodgrass, my EID buddy Nelson Ting, Kirstin Sterner, and Frances White. I also had very nice, if too brief, chats with Connie Mulligan, Lorena Madrigal, Larry Sugiyama, Greg Blomquist, Zarin Machanda, Melissa Emery Thompson, Cheryl Knott, Andy Marshall, and Chris Kuzawa.

I only go to the AAPAs every couple of years. Given the interdisciplinarity of my work and interests, I struggle to find a “home” professional meeting. Sometimes I feel like it’s PAA; sometimes Sunbelt; sometimes AAPA/HBA.  One thing I can say for certain is that it is not AAA, my semi-annual experience in ethnographic surreality. Such a peculiar discipline anthropology is. Part of the reason I don’t go to AAPAs all that often is that I rarely find all that much interesting there. There are a few really fantastic people working in the field, but most of the talks I find stupifyingly boring. I’m just not that interested in teeth. I suppose this is true for any professional meeting, so I shouldn’t be too hard on AAPA — I’m also not especially interested in contraceptive uptake, social media/online networks, or governmentality, apparently the modal topics in my competing meetings. In fact, I was pleasantly surprised by the diversity and quality of talks I saw at AAPA this year.

In my session alone, I saw really terrific and interesting talks by Steve Leigh and Connie Mulligan. Steve spoke on the comparative gut microbiomes of primates and Connie presented early results on the modification of gene expression through methylation of infants born to women who experienced extreme psychosocial and physical trauma in eastern Congo. Really important stuff. It also struck me that you’d probably only see these types of talks at the AAPAs.

There were a lot of young people at this meeting — a greater fraction than I remember from past meetings.  Maybe it was the draw of hipster Portland with its great beer, great food, and general atmosphere of grooviness. Maybe there really are lots and lots of young physical anthropologists being trained these days. I must admit that I had mixed feelings about this thought as I looked out over the vast river of twenty-something faces pouring into the hotel bar Saturday night. On the one hand, it’s great that people are being trained to do good work in physical anthropology. On the other hand, I worry about the ability of our discipline, which shows no signs of stopping with the charade that somehow anthropology is really akin to literary criticism, to absorb this many new Ph.D.s from (one of) the scientific wings of modern anthropology.

Two of the talks immediately before me in my session were, in fact, by young scientists and they were great. Andrew Paquette, from Northern Arizona University, gave a talk on the evolutionary history of Southeast Asian Ovalocytosis (SAO), a twenty-seven base pair deletion in the eleventh exon of the SLC4A1 gene that confers strong protection against infection with Plasmodium falciparum, the most dangerous form of malaria. Turns out this mutation, which has its geographic epicenter in Nusa Tenggara in Indonesia, is surprisingly ancient. Lots more to come from this, I’m sure. Margaux Keller, from Temple, gave a fantastic talk on finding some of the missing heritability in Parkinson’s disease. Missing heritability of complex disease phenotypes is a major topic in genetic epidemiology and Margaux and her colleagues applied Genome-Wide Complex Trait Analysis to eight cohorts of case-control studies of PD. Their results substantially increase (i.e., by a factor of 10!) the fraction of total phenotypic variance in PD explained compared to straight-up genome-wide association studies (GWAS). In addition to the excellent scientific content of her presentation, I was struck by the very nice and original visual aesthetic of her slides.

I spoke on my recent work on the quantitative genetics of life-history traits.  With Statistics grad student Philip Labo, I’ve been doing some pretty serious number-crunching to examine the heritabilities of and (more interestingly) genetic correlations between human life-history characters. Good results that should be seeing some more light soon (including at PAA next month!).

→ 2 CommentsTags: Anthropology · science

(Text Processing) Paradigms Lost

April 11th, 2012 · 2 Comments

Tom Scocca has wrote a brilliant essay in Slate today on the absurdities of Microsoft Word being the standard text processing tool in the age of digital publishing. I struggle to get students doing statistical and demographic analysis in R to not use Word because of all the unwanted junk it brings to the most trivial text-processing task. Using the word2cleanhtml website, Scocca shows how a two-word text chunk written in Word contains the equivalent of eight pages of unnecessary hidden text!

I encounter all the nonsense associated with the annoying default “annoying typographical flourishes” that Scocca discusses in my role as associate editor of a couple of journals and a regular reviewer for NSF. Both of these roles make extensive use of web-based platforms for managing workflows associated with writing-intensive tasks (ScholarOne for editing and Fastlane for NSF) and both snarf on the typographical annoyances Scocca enumerates (“smart” quotes, automatic em-dashes, etc.). When you do an NSF panel, you receive a briefing explaining that if you are going to write your panel summaries in Word, you need to turn off smart quotes and avoid other things that will lead to nonsense in the plain-text formatted fields of Fastlane. Of course, no one does this.

Don’t get me started on track changes…

I do the great majority of my own writing in a plain text-processor. My personal favorite is Aquamacs, a Mac-native variation on GNU Emacs. Emacs is definitely not for everyone, but there are lots of other possibilities. Scocca writes that he has turned to TextEdit, which is another Mac-native, but there are plenty of other options that run on different systems. Here is a list of possibilities.

It will be interesting to see how online collaborative tools such as Google Docs change the way people do text processing.  I find that more of my students do their work in Google Docs. It’s certainly not a majority yet but the fraction is growing rapidly each year. As Scocca notes, Google Docs provides a much more sane alternative to track changes, among other things.

Microsoft clearly needs to get serious and do a bit of innovation here if they want to stay in this particular game. I, for one, will not miss MS Word if it should go the way of WordStar.

→ 2 CommentsTags: Uncategorized

Wealth and Cheating

March 20th, 2012 · 1 Comment

I recently read a story in the Los Angeles Times about a team of psychologists at UC Berkeley who showed, in a series of experimental and naturalistic studies, that wealthy individuals are more likely to cheat or violate social norms about fairness. The Story in the Times referred to the paper by Piff et al. in the 27 February edition of PNAS.  Here is the abstract of this paper:

Seven studies using experimental and naturalistic methods reveal that upper-class individuals behave more unethically than lower-class individuals. In studies 1 and 2, upper-class individuals were more likely to break the law while driving, relative to lower-class individuals. In follow-up laboratory studies, upper-class individuals were more likely to exhibit unethical decision-making tendencies (study 3), take valued goods from others (study 4), lie in a negotiation (study 5), cheat to increase their chances of winning a prize (study 6), and endorse unethical behavior at work (study 7) than were lower-class individuals. Mediator and moderator data demonstrated that upper-class individuals’ unethical tendencies are accounted for, in part, by their more favorable attitudes toward greed.

This study was apparently motivated by observations that people in expensive luxury cars are more likely to bolt ahead of their turn at four-way stop intersections in the San Francisco Bay Area, a daily experience for anyone driving in Palo Alto! It’s terrific that these authors actually took the trouble to systematize their casual observations of driving behavior and make an interesting and compelling scientific statement.

On Friday, I made my own observations about class, cheating, and the violation of norms as I flew down to LAX to attend Sunbelt XXXII (the annual conference for the International Network for Social Network Analysis). Of late, I’ve racked up a lot of miles on United and, as a result, occasionally get upgraded to first class or business class seating. My trip Friday was one of those occasions. As I sat in the (relatively) comfy leather seat of the first-class cabin reading Jeremy Boissevain’s rather appropriate (1974) book Friends of Friends: Networks, Manipulators, and Coalitions, I noticed that nearly everyone around me was busily chatting away or otherwise fiddling around with their smart phones. When the cabin door finally closed and the announcement was made requesting that phones be switched off, none of the people in my neighborhood did so. They put their phones down or in their shirt pockets and watched the flight attendants.  When the flight attendants passed through the cabin and were occupied with other business, out came the smart phones again. The one gentleman across the aisle from me looked like a school kid writing a note in class or something. He kept a wary half-eye out for the flight attendants and looked extremely guilty about his actions, but he nonetheless kept doing his, no doubt, extremely important business.  The man on the phone in the row ahead of me was a little more shameless. He seemed completely unconcerned that he might get busted. The woman in the row ahead of me and across the aisle moved her phone so that it was partially hidden by the arm-rest of her seat as she continued to scroll through her very, very important email. Of the six people I could easily see in my neighborhood, fully half of them continued to use their phones right into taxi and take-off.  Based on their attempts at concealment, at least two of them knew what they were doing was wrong. Now, any regular traveler has seen people using their phones on the plane after they are supposed to. However, I had never seen this sort of density of norm violation on a single flight before.

Of course, this is an anecdote but the study by Piff et al. (2012) shows how anecdotes about social behavior can go on to be systematized into interesting scientific studies.

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Get Off the Sexual Network

March 10th, 2012 · No Comments

When I was in Uganda last month, I was talking with collaborators, field assistants, villagers, taxi drivers, bartenders – pretty much anyone who would listen – about social networks, I was struck by what a sophisticated understanding of social networks my average interlocutor had.  As part of our project examining the risk of zoonotic disease spillover in rural Uganda, we are gathering data on individual people’s personal networks. We are interested in contact networks, for sure, but we are also examining people’s social capital – the resources to which an individual has access for instrumental action that are embedded in his or her social network. There are generally two classes of definitions of social capital used in the literature. The first, made famous by Robert Putnam‘s book, Bowling Alone, is really a measure of community solidarity. How cohesive are communities and how does this contribute to individuals’ and communities’ welfare?  The definition I typically employ is attributable to Bourdieau and a host of other scholars, especially Nan Lin. This definition emphasizes both the networked nature of social capital and the instrumentality of it.

The reasoning behind doing a social capital inventory in conjunction with our study of zoonotic disease spillover risk is to have a thorough description of the “state” of individuals. Social surveys typically measure income, household wealth, land holdings, etc. One measures such things in a social survey because one is interested in the economic state of the individual or household in which she is embedded. Social capital is a measure of economic – and social – well-being for people where many of the resources that they need to succeed, or even just get by, are not specifically located in the household or with the individual. We suspect that people in rural Uganda will vary in the amount of social capital they have and that this may be a major axess of vulnerability.

So, there I am, talking to anyone who would listen about the best way to gather information on personal social networks and it turns out that everyone I spoke with was amazingly familiar with the whole concept of social networks. The catch is, the networks with which they are familiar are a special type of networks – sexual networks. When I asked how everyone seemed to know so much about sexual networks, they pointed me to a public-service advertising campaign for which the tag line is “get off the sexual network.” Despite the Central African origin of HIV-1, Uganda was an early center for the epidemic. However, as noted by Stoneburner and Lowbeer, in their important 2004 paper, Uganda experienced substantial – and early – decline in HIV-1 incidence because of health communication through social networks. They write:

The response in Uganda appears to be distinctively associated with communication about acquired immunodeficiency syndrome (AIDS) through social networks. Despite substantial condom use and promotion of biomedical approaches, other African countries have shown neither similar behavioral responses nor HIV prevalence declines of the same scale. The Ugandan success is equivalent to a vaccine of 80% effectiveness. (Stoneburner & Lowbeer 2004)

I definitely need to check out the current state of the art to see if other countries in Sub-Saharan Africa have now experienced similar public health gains as a result of network-oriented interventions.

Based on my rather unsystematic sample, I’d say that this campaign has really worked raise people’s understanding of relational interconnectedness.  I was not able to get a picture of the huge billboards on the Kampala-Entebbe Highway (because it was always dark when I drove by them) but the TV ad is available on youtube. On the one hand, this is really great (both for the obvious public health reasons and because people seem to have a good understanding of webs of social relations). On the other hand, it will probably mean we will need to work hard to clarify what types of networks we mean when we gather our network data.

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Three Questions About Norms

March 3rd, 2012 · 1 Comment

Well, it certainly has been a while since I’ve written anything here. Life has gotten busy with new projects, new responsibilities, etc. Yesterday, I participated in a workshop on campus sponsored by the Woods Institute for the Environment, the Young Environmental Scholars Conference. I was asked to stand-in for a faculty member who had to cancel at the last minute. I threw together some rather hastily-written notes and figured I’d share them here (especially since I spoke quite a bit of the importance for public communication!).

The theme of the conference was “Environmental Policy, Behavior, and Norms” and we were asked to answer three questions: (1) What does doing normative research mean to you? (2) How do your own norms and values influence your research? (3) What room and role do you see for normative research in your field? So, in order, here are my answers.

What does doing normative research mean to you?

I actually don’t particularly like the term “normative research” because it sounds a little too much like imposing one’s values on other people. I am skeptical of the imposition of norms that have more to do with (often unrecognized) ideology and less about empirical truth – an idea that was later reinforced by a terrific concluding talk by Debra Satz. If I can define “normative” to mean with the intent to improve people’s lives, then OK.  Otherwise, I prefer to do “positive” research.

For me, normative research is about doing good science. As a biosocial scientist with broad interests, I wear a lot of hats. I have always been interested in questions about the natural world, and (deep) human history in particular. However, I find that the types of questions that really hold my interest these days are more and more engaged in the substantial challenges we face in the world with inequality and sustainability. In keeping with my deep pragmatist sympathies, I increasingly identify with Charles Sanders Pierce‘s idea that given the “great ocean of truth” that can potentially be uncovered by science, there is a moral burden to do things that have social value. (As an aside, I think that there is social value in understanding the natural world, so I don’t mean to imply a crude instrumentalism here.) In effect, there is a lot of cool science to be done; one may as well do something of relevance.  I personally have little patience for people who pursue racist or otherwise socially divisive agendas and cloak their work in a veil of  free scientific inquiry.  This said, I worry when advocacy interferes with intellectual fairness or an unwillingness to accept that one’s position is not actually true.

I think that we are fooling ourselves if we believe that our norms somehow don’t have an effect on our research.  Recognizing what these norms that shape your research – whether implicitly or explicitly – helps you manage your bias. Yes, I said manage. I’m not sure we can ever completely eliminate it. I see this as more of a management of a necessary trade-off, drawing an analogy between the practice of science and a classic problem in statistics, between bias and variance. The more biased one is, the less variance there is in the outcome of one’s investigation. The less bias, the greater the likelihood that results will differ from one’s expectations (or wishes). Recognizing how norms shape our research also deals with that murky area of pre-science: where do our ideas for what to study come from?

How do your own norms and values influence your research?

Some of the the norms that shape my own research and teaching include:

transparency: science works best when it is open. This places a premium on sharing data, methods, and communicating results in a manner that maximizes access to information. As a simple example, this norm shapes my belief that we should not train students from poor countries in the use of proprietary software (and other technologies) that they won’t be able to afford when they return to their home countries when there are free or otherwise open-source alternatives.

fairness: this naturally includes a sense of social justice or people playing on an equal playing field, but it also includes fairness to different ideas, alternative hypotheses, the possibility that one is wrong. This type of fairness is essential for one’s credibility as a public intellectual in science (particularly supporting policy), as noted eloquently in this interview with Dick Lewontin.

respect for people’s ultimate rationality: Trying to understand the social, ecological, and economic context of people’s decision-making, even if it violates our own normative – particularly market-based economic – expectations.

flexibility: solving real problems means that we need to be flexible in our approach, willing to go where the solutions lead us, learning new tools and collaborating. Flexibility also means a willingness to give up on a research program that is doing harm.

good-faith communication: I believe that there is no room for obscurantism in the academy of the 21st century. This includes public communication. There are, of course, complexities here with regard to the professional development of young scholars.  One of the key trade-offs for young scholars is the need for professional advancement (which comes from academic production) and activism, policy, and public communication. Within the elite universities, the reality is that neither public communication nor activism count much for tenure. However, as Jon Krosnick noted, tenure is a remarkable privilege and, while it may seem impossibly far away for a student just finishing a Ph.D., it’s not really. Once you prove that you have the requisite disciplinary chops, you have plenty of time to to use tenure for what it is designed for (i.e., protecting intellectual freedom) and engaging in critical public debate and communication.

humility: solving problems (in science and society) means caring more about the answer to a problem than one’s own pet theory. Humility is intimately related to respect for others’ rationality.  It also means recognizing the inherently collaborative nature of contemporary science: giving credit where it is due, seeking help when one is in over one’s head, etc. John DeGioia, President of Georgetown University, quoted St. Augustine in his letter of support for Georgetown Law Student, Sandra Fluke against the crude attacks by radio personality Rush Limbaugh and I think those words are quite applicable here as well.  Augustine implored his interlocutors to “lay aside arrogance” and to “let neither of us assert that he has found the truth; let us seek it as if it were unknown to both.” This is not a bad description of the way that science really should work.

What room and role do you see for normative research in your field?

I believe that there is actually an enormous amount of room for normative research, if by “normative research,” we mean research that has the potential to have a positive effect on people’s lives. If instead we mean imposing values on people, then I am less sure of its role.

Anthropology is often criticized from outside the field, and to a lesser extent, from within it for being overly politicized. You can see this in Nicholas Wade’s critical pieces in the New York Times Science Times section following the American Anthropological Association’s executive committee excising of the word “science” from the field’s long-range planning document. Wade writes,

The decision [to remove the word 'science' from the long-range planning document] has reopened a long-simmering tension between researchers in science-based anthropological disciplines — including archaeologists, physical anthropologists and some cultural anthropologists — and members of the profession who study race, ethnicity and gender and see themselves as advocates for native peoples or human rights.

This is a common sentiment. And it is a complete misunderstanding. It suggests that scientists can’t be advocates for native peoples or human rights.  It also suggests that one can’t study race, ethnicity, or gender from a scientific perspective.  Both these ideas are complete nonsense.  For all the leftist rhetoric, I am not impressed with the actual political practice of what I see in contemporary anthropology. There is plenty of posturing about power asymmetries and identity politics but it is always done in such a mind-numbingly opaque language and with no apparent practical tie-in to policies that make people’s lives better. And, of course, there is the outright disdain for “applied” work one sees in elite anthropology departments.

Writing specifically about Foucault, Chomsky captured my take on this whole mode of intellectual production:

The only way to understand [the mode of scholarship] is if you are a graduate student or you are attending a university and have been trained in this particular style of discourse. That’s a way of guaranteeing…that intellectuals will have power, prestige and influence. If something can be said simply, say it simply, so that the carpenter next door can understand you. Anything that is at all well understood about human affairs is pretty simple.

Ultimately, the simple truths about human affairs that I find anyone can relate to are subsistence, health, and the well-being of one’s children. These are the themes at the core of my own research and I hope that the work I do ultimately can effect some good in these areas.

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