Monthly Archives: April 2012

Anthropology, science

AAPA 2012 Run-Down

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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!).

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(Text Processing) Paradigms Lost

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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.